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  • Correction to: Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity
    Clin. Epigenet. (IF 5.496) Pub Date : 2020-01-27
    Maria Desemparats Saenz-de-Juano; Elena Ivanova; Katy Billooye; Anamaria-Cristina Herta; Johan Smitz; Gavin Kelsey; Ellen Anckaert

    After publication of the original article [1], we were notified that.

    更新日期:2020-01-27
  • Knowledge and attitudes on pharmacogenetics among pediatricians
    J. Hum. Genet. (IF 3.545) Pub Date : 2020-01-27
    Shahad Rahawi; Hetanshi Naik; Kathryn V. Blake; Aniwaa Owusu Obeng; Rachel M. Wasserman; Yoshinori Seki; Vicky L. Funanage; Kimihiko Oishi; Stuart A. Scott
    更新日期:2020-01-27
  • The identity and methylation status of the first transcribed nucleotide in eukaryotic mRNA 5′ cap modulates protein expression in living cells
    Nucleic Acids Res. (IF 11.147) Pub Date : 2020-01-27
    Sikorski P, Warminski M, Kubacka D, et al.

    7-Methylguanosine 5′ cap on mRNA is necessary for efficient protein expression in vitro and in vivo. Recent studies revealed structural diversity of endogenous mRNA caps, which carry different 5′-terminal nucleotides and additional methylations (2′-O-methylation and m6A). Currently available 5′-capping methods do not address this diversity. We report trinucleotide 5′ cap analogs (m7GpppN(m)pG), which are utilized by RNA polymerase T7 to initiate transcription from templates carrying Φ6.5 promoter and enable production of mRNAs differing in the identity of the first transcribed nucleotide (N = A, m6A, G, C, U) and its methylation status (±2′-O-methylation). HPLC-purified mRNAs carrying these 5′ caps were used to study protein expression in three mammalian cell lines (3T3-L1, HeLa and JAWS II). The highest expression was observed for mRNAs carrying 5′-terminal A/Am and m6Am, whereas the lowest was observed for G and Gm. The mRNAs carrying 2′-O-methyl at the first transcribed nucleotide (cap 1) had significantly higher expression than unmethylated counterparts (cap 0) only in JAWS II dendritic cells. Further experiments indicated that the mRNA expression characteristic does not correlate with affinity for translation initiation factor 4E or in vitro susceptibility to decapping, but instead depends on mRNA purity and the immune state of the cells.

    更新日期:2020-01-27
  • NHDL, a recombinant VL/VH hybrid antibody control for IgG2/4 antibodies
    mAbs (IF 4.405) Pub Date : 2019-11-27
    Corinna Lau; Martin Berner McAdam; Grethe Bergseth; Algirdas Grevys; Jack Ansgar Bruun; Judith Krey Ludviksen; Hilde Fure; Terje Espevik; Anders Moen; Jan Terje Andersen; Tom Eirik Mollnes

    ABSTRACT The mechanism of action of recombinant IgG2/4 antibodies involves blocking of their target without the induction of effector functions. Examples are eculizumab (Soliris®), which is used clinically to block complement factor C5, as well as anti-human CD14 (r18D11) and anti-porcine CD14 (rMIL2) produced in our laboratory. So far, no proper IgG2/4 control antibody has been available for controlled validation of IgG2/4 antibody functions. Here, we describe the design of a recombinant control antibody (NHDL), which was generated by combining the variable light (VL) and heavy (VH) chains from two unrelated specificities. NHDL was readily expressed and purified as a stable IgG2/4 antibody, and showed no detectable specificity toward any putative antigen present in human or porcine blood. The approach of artificial VL/VH combination may be adopted for the design of other recombinant control antibodies.

    更新日期:2020-01-27
  • Makorin 1 controls embryonic patterning by alleviating Bruno1-mediated repression of oskar translation
    PLOS Genet. (IF 5.224) Pub Date : 2020-01-24
    Annabelle Dold; Hong Han; Niankun Liu; Andrea Hildebrandt; Mirko Brüggemann; Cornelia Rücklé; Heike Hänel; Anke Busch; Petra Beli; Kathi Zarnack; Julian König; Jean-Yves Roignant; Paul Lasko
    更新日期:2020-01-26
  • The derived allele of a novel intergenic variant at chromosome 11 associates with lower body mass index and a favorable metabolic phenotype in Greenlanders
    PLOS Genet. (IF 5.224) Pub Date : 2020-01-24
    Mette K. Andersen; Emil Jørsboe; Line Skotte; Kristian Hanghøj; Camilla H. Sandholt; Ida Moltke; Niels Grarup; Timo Kern; Yuvaraj Mahendran; Bolette Søborg; Peter Bjerregaard; Christina V. L. Larsen; Inger K. Dahl-Petersen; Hemant K. Tiwari; Bjarke Feenstra; Anders Koch; Howard W. Wiener; Scarlett E. Hopkins; Oluf Pedersen; Mads Melbye; Bert B. Boyer; Marit E. Jørgensen; Anders Albrechtsen; Torben Hansen
    更新日期:2020-01-26
  • Cooperation of the NEIL3 and Fanconi anemia/BRCA pathways in interstrand crosslink repair
    Nucleic Acids Res. (IF 11.147) Pub Date : 2020-01-25
    Li N, Wang J, Wallace S, et al.

    The NEIL3 DNA glycosylase is a base excision repair enzyme that excises bulky base lesions from DNA. Although NEIL3 has been shown to unhook interstrand crosslinks (ICL) in Xenopus extracts, how NEIL3 participants in ICL repair in human cells and its corporation with the canonical Fanconi anemia (FA)/BRCA pathway remain unclear. Here we show that the NEIL3 and the FA/BRCA pathways are non-epistatic in psoralen-ICL repair. The NEIL3 pathway is the major pathway for repairing psoralen-ICL, and the FA/BRCA pathway is only activated when NEIL3 is not present. Mechanistically, NEIL3 is recruited to psoralen-ICL in a rapid, PARP-dependent manner. Importantly, the NEIL3 pathway repairs psoralen-ICLs without generating double-strand breaks (DSBs), unlike the FA/BRCA pathway. In addition, we found that the RUVBL1/2 complex physically interact with NEIL3 and function within the NEIL3 pathway in psoralen-ICL repair. Moreover, TRAIP is important for the recruitment of NEIL3 but not FANCD2, and knockdown of TRAIP promotes FA/BRCA pathway activation. Interestingly, TRAIP is non-epistatic with both NEIL3 and FA pathways in psoralen-ICL repair, suggesting that TRAIP may function upstream of the two pathways. Taken together, the NEIL3 pathway is the major pathway to repair psoralen-ICL through a unique DSB-free mechanism in human cells.

    更新日期:2020-01-26
  • circSamd4 represses myogenic transcriptional activity of PUR proteins
    Nucleic Acids Res. (IF 11.147) Pub Date : 2020-01-25
    Pandey P, Yang J, Tsitsipatis D, et al.

    By interacting with proteins and nucleic acids, the vast family of mammalian circRNAs is proposed to influence many biological processes. Here, RNA sequencing analysis of circRNAs differentially expressed during myogenesis revealed that circSamd4 expression increased robustly in mouse C2C12 myoblasts differentiating into myotubes. Moreover, silencing circSamd4, which is conserved between human and mouse, delayed myogenesis and lowered the expression of myogenic markers in cultured myoblasts from both species. Affinity pulldown followed by mass spectrometry revealed that circSamd4 associated with PURA and PURB, two repressors of myogenesis that inhibit transcription of the myosin heavy chain (MHC) protein family. Supporting the hypothesis that circSamd4 might complex with PUR proteins and thereby prevent their interaction with DNA, silencing circSamd4 enhanced the association of PUR proteins with the Mhc promoter, while overexpressing circSamd4 interfered with the binding of PUR proteins to the Mhc promoter. These effects were abrogated when using a mutant circSamd4 lacking the PUR binding site. Our results indicate that the association of PUR proteins with circSamd4 enhances myogenesis by contributing to the derepression of MHC transcription.

    更新日期:2020-01-26
  • Reducing the structure bias of RNA-Seq reveals a large number of non-annotated non-coding RNA
    Nucleic Acids Res. (IF 11.147) Pub Date : 2020-01-25
    Boivin V, Reulet G, Boisvert O, et al.

    The study of RNA expression is the fastest growing area of genomic research. However, despite the dramatic increase in the number of sequenced transcriptomes, we still do not have accurate estimates of the number and expression levels of non-coding RNA genes. Non-coding transcripts are often overlooked due to incomplete genome annotation. In this study, we use annotation-independent detection of RNA reads generated using a reverse transcriptase with low structure bias to identify non-coding RNA. Transcripts between 20 and 500 nucleotides were filtered and crosschecked with non-coding RNA annotations revealing 111 non-annotated non-coding RNAs expressed in different cell lines and tissues. Inspecting the sequence and structural features of these transcripts indicated that 60% of these transcripts correspond to new snoRNA and tRNA-like genes. The identified genes exhibited features of their respective families in terms of structure, expression, conservation and response to depletion of interacting proteins. Together, our data reveal a new group of RNA that are difficult to detect using standard gene prediction and RNA sequencing techniques, suggesting that reliance on actual gene annotation and sequencing techniques distorts the perceived architecture of the human transcriptome.

    更新日期:2020-01-26
  • I-Block: a simple Escherichia coli-based assay for studying sequence-specific DNA binding of proteins
    Nucleic Acids Res. (IF 11.147) Pub Date : 2020-01-25
    Szentes S, Zsibrita N, Koncz M, et al.

    We have developed a simple method called I-Block assay, which can detect sequence-specific binding of proteins to DNA in Escherichia coli. The method works by detecting competition between the protein of interest and RNA polymerase for binding to overlapping target sites in a plasmid-borne lacI promoter variant. The assay utilizes two plasmids and an E. coli host strain, from which the gene of the Lac repressor (lacI) has been deleted. One of the plasmids carries the lacI gene with a unique NheI restriction site created in the lacI promoter. The potential recognition sequences of the tested protein are inserted into the NheI site. Introduction of the plasmids into the E. coliΔlacI host represses the constitutive β-galactosidase synthesis of the host bacterium. If the studied protein expressed from a compatible plasmid binds to its target site in the lacI promoter, it will interfere with lacI transcription and lead to increased β-galactosidase activity. The method was tested with two zinc finger proteins, with the lambda phage cI857 repressor, and with CRISPR-dCas9 targeted to the lacI promoter. The I-Block assay was shown to work with standard liquid cultures, with cultures grown in microplate and with colonies on X-gal indicator plates.

    更新日期:2020-01-26
  • Understanding the effect of controlling phosphorothioate chirality in the DNA gap on the potency and safety of gapmer antisense oligonucleotides
    Nucleic Acids Res. (IF 11.147) Pub Date : 2020-01-25
    Østergaard M, De Hoyos C, Wan W, et al.

    Therapeutic oligonucleotides are often modified using the phosphorothioate (PS) backbone modification which enhances stability from nuclease mediated degradation. However, substituting oxygen in the phosphodiester backbone with sulfur introduce chirality into the backbone such that a full PS 16-mer oligonucleotide is comprised of 215 distinct stereoisomers. As a result, the role of PS chirality on the performance of antisense oligonucleotides (ASOs) has been a subject of debate for over two decades. We carried out a systematic analysis to determine if controlling PS chirality in the DNA gap region can enhance the potency and safety of gapmer ASOs modified with high-affinity constrained Ethyl (cEt) nucleotides in the flanks. As part of this effort, we examined the effect of systematically controlling PS chirality on RNase H1 cleavage patterns, protein mislocalization phenotypes, activity and toxicity in cells and in mice. We found that while controlling PS chirality can dramatically modulate interactions with RNase H1 as evidenced by changes in RNA cleavage patterns, these were insufficient to improve the overall therapeutic profile. We also found that controlling PS chirality of only two PS linkages in the DNA gap was sufficient to modulate RNase H1 cleavage patterns and combining these designs with simple modifications such as 2′-OMe to the DNA gap resulted in dramatic improvements in therapeutic index. However, we were unable to demonstrate improved potency relative to the stereorandom parent ASO or improved safety over the 2′-OMe gap-modified stereorandom parent ASO. Overall, our work shows that while controlling PS chirality can modulate RNase H1 cleavage patterns, ASO sequence and design are the primary drivers which determine the pharmacological and toxicological properties of gapmer ASOs.

    更新日期:2020-01-26
  • Nuclear envelope attachment of telomeres limits TERRA and telomeric rearrangements in quiescent fission yeast cells
    Nucleic Acids Res. (IF 11.147) Pub Date : 2020-01-25
    Maestroni L, Reyes C, Vaurs M, et al.

    Telomere anchoring to nuclear envelope (NE) is a key feature of nuclear genome architecture. Peripheral localization of telomeres is important for chromatin silencing, telomere replication and for the control of inappropriate recombination. Here, we report that fission yeast quiescent cells harbor predominantly a single telomeric cluster anchored to the NE. Telomere cluster association to the NE relies on Rap1–Bqt4 interaction, which is impacted by the length of telomeric sequences. In quiescent cells, reducing telomere length or deleting bqt4, both result in an increase in transcription of the telomeric repeat-containing RNA (TERRA). In the absence of Bqt4, telomere shortening leads to deep increase in TERRA level and the concomitant formation of subtelomeric rearrangements (STEEx) that accumulate massively in quiescent cells. Taken together, our data demonstrate that Rap1–Bqt4-dependent telomere association to NE preserves telomere integrity in post-mitotic cells, preventing telomeric transcription and recombination. This defines the nuclear periphery as an area where recombination is restricted, creating a safe zone for telomeres of post-mitotic cells.

    更新日期:2020-01-26
  • Cas3/I-C mediated target DNA recognition and cleavage during CRISPR interference are independent of the composition and architecture of Cascade surveillance complex
    Nucleic Acids Res. (IF 11.147) Pub Date : 2020-01-25
    Nimkar S, Anand B.

    In type I CRISPR-Cas system, Cas3—a nuclease cum helicase—in cooperation with Cascade surveillance complex cleaves the target DNA. Unlike the Cascade/I-E, which is composed of five subunits, the Cascade/I-C is made of only three subunits lacking the CRISPR RNA processing enzyme Cas6, whose role is assumed by Cas5. How these differences in the composition and organization of Cascade subunits in type I-C influence the Cas3/I-C binding and its target cleavage mechanism is poorly understood. Here, we show that Cas3/I-C is intrinsically a single-strand specific promiscuous nuclease. Apart from the helicase domain, a constellation of highly conserved residues—which are unique to type I-C—located in the uncharacterized C-terminal domain appears to influence the nuclease activity. Recruited by Cascade/I-C, the HD nuclease of Cas3/I-C nicks the single-stranded region of the non-target strand and positions the helicase motor. Powered by ATP, the helicase motor reels in the target DNA, until it encounters the roadblock en route, which stimulates the HD nuclease. Remarkably, we show that Cas3/I-C supplants Cas3/I-E for CRISPR interference in type I-E in vivo, suggesting that the target cleavage mechanism is evolutionarily conserved between type I-C and type I-E despite the architectural difference exhibited by Cascade/I-C and Cascade/I-E.

    更新日期:2020-01-26
  • The C-terminal tail of the yeast mitochondrial transcription factor Mtf1 coordinates template strand alignment, DNA scrunching and timely transition into elongation
    Nucleic Acids Res. (IF 11.147) Pub Date : 2020-01-25
    Basu U, Lee S, Deshpande A, et al.

    Mitochondrial RNA polymerases depend on initiation factors, such as TFB2M in humans and Mtf1 in yeast Saccharomyces cerevisiae, for promoter-specific transcription. These factors drive the melting of promoter DNA, but how they support RNA priming and growth was not understood. We show that the flexible C-terminal tails of Mtf1 and TFB2M play a crucial role in RNA priming by aiding template strand alignment in the active site for high-affinity binding of the initiating nucleotides. Using single-molecule fluorescence approaches, we show that the Mtf1 C-tail promotes RNA growth during initiation by stabilizing the scrunched DNA conformation. Additionally, due to its location in the path of the nascent RNA, the C-tail of Mtf1 serves as a sensor of the RNA–DNA hybrid length. Initially, steric clashes of the Mtf1 C-tail with short RNA–DNA hybrids cause abortive synthesis but clashes with longer RNA-DNA trigger conformational changes for the timely release of the promoter DNA to commence the transition into elongation. The remarkable similarities in the functions of the C-tail and σ3.2 finger of the bacterial factor suggest mechanistic convergence of a flexible element in the transcription initiation factor that engages the DNA template for RNA priming and growth and disengages when needed to generate the elongation complex.

    更新日期:2020-01-26
  • Investigation of the effect of salt additives in Protein L affinity chromatography for the purification of tandem single-chain variable fragment bispecific antibodies
    mAbs (IF 4.405) Pub Date : 2020-01-25
    Serene W. Chen; Darryl Tan; Yuan Sheng Yang; Wei Zhang

    ABSTRACT Tandem single-chain variable fragment (scFv) bispecific antibodies (bsAb) are one of the most promising bsAb formats reported thus far. Yet, because of their increased aggregation propensity, high impurity content due to low expression level, smaller size and lack of the Fc region, it is challenging to isolate these products with high yield and purity within a limited number of purification steps in a scalable fashion. A robust purification process that is able to circumvent these issues is therefore of critical importance to allow effective isolation of this group of antibodies. We investigated the addition of sodium chloride (NaCl), calcium chloride (CaCl2), and L-arginine monohydrochloride (Arg·HCl) to the elution buffer of Protein L affinity chromatography, and propose here a novel mechanism for the modification of Protein L binding avidity that can lead to enhanced high molecular weight (HMW)-monomer separation, a preferential strengthening effect of the HMW-Protein L interaction compared to the monomer-Protein L interaction. In particular, we found Arg·HCl to be the most effective salt additive in terms of purity and recovery. The mechanism we propose is different from the widely reported chaotropic effect exerted by salt additives observed in Protein A chromatography. We also demonstrate here that a final eluate containing <1% HMW species and <100 ppm host cell proteins can be obtained within a two-step process with an overall yield of 65%, highlighting the promising suitability of Protein L affinity chromatography for the purification of kappa light chain-containing tandem scFv bsAb.

    更新日期:2020-01-26
  • In situ antibody phage display yields optimal inhibitors of integrin α11/β1
    mAbs (IF 4.405) Pub Date : 2020-01-24
    Eugenio Gallo; Abdellali Kelil; Peter E. Bayliss; Ajitha Jeganathan; Olga Egorova; Lynda Ploder; Jarret A. Adams; Patricia Giblin; Sachdev S. Sidhu

    ABSTRACT Integrins are transmembrane multi-conformation receptors that mediate interactions with the extracellular matrix. In cancer, integrins influence metastasis, proliferation, and survival. Collagen-binding integrin-α11/β1, a marker of aggressive tumors that is involved in stroma-tumor crosstalk, may be an attractive target for anti-cancer therapeutic antibodies. We performed selections with phage-displayed synthetic antibody libraries for binding to either purified integrin-α11/β1 or in situ on live cells. The in-situ strategy yielded many diverse antibodies, and strikingly, most of these antibodies did not recognize purified integrin-α11/β1. Conversely, none of the antibodies selected for binding to purified integrin-α11/β1 were able to efficiently recognize native cell-surface antigen. Most importantly, only the in-situ selection yielded functional antibodies that were able to compete with collagen-I for binding to cell-surface integrin-α11/β1, and thus inhibited cell adhesion. In-depth characterization of a subset of in situ-derived clones as full-length immunoglobulins revealed high affinity cellular binding and inhibitory activities in the single-digit nanomolar range. Moreover, the antibodies showed high selectivity for integrin-α11/β1 with minimal cross-reactivity for close homologs. Taken together, our findings highlight the advantages of in-situ selections for generation of anti-integrin antibodies optimized for recognition and inhibition of native cell-surface proteins, and our work establishes general methods that could be extended to many other membrane proteins.

    更新日期:2020-01-26
  • Characterization of the plant homeodomain (PHD) reader family for their histone tail interactions
    Epigenet. Chromatin (IF 4.185) Pub Date : 2020-01-24
    Kanishk Jain; Caroline S. Fraser; Matthew R. Marunde; Madison M. Parker; Cari Sagum; Jonathan M. Burg; Nathan Hall; Irina K. Popova; Keli L. Rodriguez; Anup Vaidya; Krzysztof Krajewski; Michael-Christopher Keogh; Mark T. Bedford; Brian D. Strahl

    Plant homeodomain (PHD) fingers are central “readers” of histone post-translational modifications (PTMs) with > 100 PHD finger-containing proteins encoded by the human genome. Many of the PHDs studied to date bind to unmodified or methylated states of histone H3 lysine 4 (H3K4). Additionally, many of these domains, and the proteins they are contained in, have crucial roles in the regulation of gene expression and cancer development. Despite this, the majority of PHD fingers have gone uncharacterized; thus, our understanding of how these domains contribute to chromatin biology remains incomplete. We expressed and screened 123 of the annotated human PHD fingers for their histone binding preferences using reader domain microarrays. A subset (31) of these domains showed strong preference for the H3 N-terminal tail either unmodified or methylated at H3K4. These H3 readers were further characterized by histone peptide microarrays and/or AlphaScreen to comprehensively define their H3 preferences and PTM cross-talk. The high-throughput approaches utilized in this study establish a compendium of binding information for the PHD reader family with regard to how they engage histone PTMs and uncover several novel reader domain–histone PTM interactions (i.e., PHRF1 and TRIM66). This study highlights the usefulness of high-throughput analyses of histone reader proteins as a means of understanding how chromatin engagement occurs biochemically.

    更新日期:2020-01-24
  • Co-opted transposons help perpetuate conserved higher-order chromosomal structures
    Genome Biol. (IF 14.028) Pub Date : 2020-01-24
    Mayank NK Choudhary; Ryan Z. Friedman; Julia T. Wang; Hyo Sik Jang; Xiaoyu Zhuo; Ting Wang

    Transposable elements (TEs) make up half of mammalian genomes and shape genome regulation by harboring binding sites for regulatory factors. These include binding sites for architectural proteins, such as CTCF, RAD21, and SMC3, that are involved in tethering chromatin loops and marking domain boundaries. The 3D organization of the mammalian genome is intimately linked to its function and is remarkably conserved. However, the mechanisms by which these structural intricacies emerge and evolve have not been thoroughly probed. Here, we show that TEs contribute extensively to both the formation of species-specific loops in humans and mice through deposition of novel anchoring motifs, as well as to the maintenance of conserved loops across both species through CTCF binding site turnover. The latter function demonstrates the ability of TEs to contribute to genome plasticity and reinforce conserved genome architecture as redundant loop anchors. Deleting such candidate TEs in human cells leads to the collapse of conserved loop and domain structures. These TEs are also marked by reduced DNA methylation and bear mutational signatures of hypomethylation through evolutionary time. TEs have long been considered a source of genetic innovation. By examining their contribution to genome topology, we show that TEs can contribute to regulatory plasticity by inducing redundancy and potentiating genetic drift locally while conserving genome architecture globally, revealing a paradigm for defining regulatory conservation in the noncoding genome beyond classic sequence-level conservation.

    更新日期:2020-01-24
  • scMAGeCK links genotypes with multiple phenotypes in single-cell CRISPR screens
    Genome Biol. (IF 14.028) Pub Date : 2020-01-24
    Lin Yang; Yuqing Zhu; Hua Yu; Xiaolong Cheng; Sitong Chen; Yulan Chu; He Huang; Jin Zhang; Wei Li

    We present scMAGeCK, a computational framework to identify genomic elements associated with multiple expression-based phenotypes in CRISPR/Cas9 functional screening that uses single-cell RNA-seq as readout. scMAGeCK outperforms existing methods, identifies genes and enhancers with known and novel functions in cell proliferation, and enables an unbiased construction of genotype-phenotype network. Single-cell CRISPR screening on mouse embryonic stem cells identifies key genes associated with different pluripotency states. Applying scMAGeCK on multiple datasets, we identify key factors that improve the power of single-cell CRISPR screening. Collectively, scMAGeCK is a novel tool to study genotype-phenotype relationships at a single-cell level.

    更新日期:2020-01-24
  • CUBIC: an atlas of genetic architecture promises directed maize improvement
    Genome Biol. (IF 14.028) Pub Date : 2020-01-24
    Hai-Jun Liu; Xiaqing Wang; Yingjie Xiao; Jingyun Luo; Feng Qiao; Wenyu Yang; Ruyang Zhang; Yijiang Meng; Jiamin Sun; Shijuan Yan; Yong Peng; Luyao Niu; Liumei Jian; Wei Song; Jiali Yan; Chunhui Li; Yanxin Zhao; Ya Liu; Marilyn L. Warburton; Jiuran Zhao; Jianbing Yan

    Identifying genotype-phenotype links and causative genes from quantitative trait loci (QTL) is challenging for complex agronomically important traits. To accelerate maize gene discovery and breeding, we present the Complete-diallel design plus Unbalanced Breeding-like Inter-Cross (CUBIC) population, consisting of 1404 individuals created by extensively inter-crossing 24 widely used Chinese maize founders. Hundreds of QTL for 23 agronomic traits are uncovered with 14 million high-quality SNPs and a high-resolution identity-by-descent map, which account for an average of 75% of the heritability for each trait. We find epistasis contributes to phenotypic variance widely. Integrative cross-population analysis and cross-omics mapping allow effective and rapid discovery of underlying genes, validated here with a case study on leaf width. Through the integration of experimental genetics and genomics, our study provides useful resources and gene mining strategies to explore complex quantitative traits.

    更新日期:2020-01-24
  • Molecular feature and therapeutic perspectives of the immune dysregulation, polyendocrinopathy, enteropathy, X-linked syndrome (IPEX)
    J. Genet. Genomics (IF 4.650) Pub Date : 2020-01-24
    Qianru Huang; Xu Liu; Yujia Zhang; Jingyao Huang; Dan Li; Bin Li

    Regulatory T (Treg) cells, a subtype of CD4+ T cells with distinct immunosuppressive, are vital for maintaining immune homeostasis in healthy people. FOXP3 (Forkhead box protein P3), a member of the forkhead–winged-helix family, is the pivotal transcriptional factor of Treg. The expression, post-translational modifications and protein complex of FOXP3 present a great impact on the functional stability and immune plasticity of Treg in vivo. In particular, the mutation of FOXP3 can result in immune dysregulation polyendocrinopathy enteropathy X-linked syndrome, IPEX, which is a rare genetic disease mostly diagnosed in early childhood and soon be fatal. IPEX syndrome is related to several manifestations, including dermatitis, enteropathy, type 1 diabetes, thyroiditis and so on. Here, we summarize some recent findings on FOXP3 regulation and Treg cell function. We also review the current knowledge about the underlying mechanism of FOXP3 mutant-induced IPEX syndrome and some latest clinical prospects. At last, this review offers a novel insight into the role of FOXP3 complex played in potential therapeutic applications on IPEX syndrome.

    更新日期:2020-01-24
  • Identification of new mutations in patients with hereditary spherocytosis by next-generation sequencing
    J. Hum. Genet. (IF 3.545) Pub Date : 2020-01-24
    Li Qin; Yanbo Nie; Hong Zhang; Long Chen; Donglei Zhang; Yani Lin; Kun Ru
    更新日期:2020-01-24
  • Uncovering tissue-specific binding features from differential deep learning
    Nucleic Acids Res. (IF 11.147) Pub Date : 2020-01-24
    Phuycharoen M, Zarrineh P, Bridoux L, et al.

    Transcription factors (TFs) can bind DNA in a cooperative manner, enabling a mutual increase in occupancy. Through this type of interaction, alternative binding sites can be preferentially bound in different tissues to regulate tissue-specific expression programmes. Recently, deep learning models have become state-of-the-art in various pattern analysis tasks, including applications in the field of genomics. We therefore investigate the application of convolutional neural network (CNN) models to the discovery of sequence features determining cooperative and differential TF binding across tissues. We analyse ChIP-seq data from MEIS, TFs which are broadly expressed across mouse branchial arches, and HOXA2, which is expressed in the second and more posterior branchial arches. By developing models predictive of MEIS differential binding in all three tissues, we are able to accurately predict HOXA2 co-binding sites. We evaluate transfer-like and multitask approaches to regularizing the high-dimensional classification task with a larger regression dataset, allowing for the creation of deeper and more accurate models. We test the performance of perturbation and gradient-based attribution methods in identifying the HOXA2 sites from differential MEIS data. Our results show that deep regularized models significantly outperform shallow CNNs as well as k-mer methods in the discovery of tissue-specific sites bound in vivo.

    更新日期:2020-01-24
  • Comprehensive identification of alternative back-splicing in human tissue transcriptomes
    Nucleic Acids Res. (IF 11.147) Pub Date : 2020-01-24
    Zhang P, Zhang X, Jiang T, et al.

    Circular RNAs (circRNAs) are covalently closed RNAs derived from back-splicing of genes across eukaryotes. Through alternative back-splicing (ABS), a single gene produces multiple circRNAs sharing the same back-splice site. Although many ABS events have recently been discovered, to what extent ABS involves in circRNA biogenesis and how it is regulated in different human tissues still remain elusive. Here, we reported an in-depth analysis of ABS events in 90 human tissue transcriptomes. We observed that ABS occurred for about 84% circRNAs. Interestingly, alternative 5′ back-splicing occurs more prevalently than alternative 3′ back-splicing, and both of them are tissue-specific, especially enriched in brain tissues. In addition, the patterns of ABS events in different brain regions are similar to each other and are more complex than the patterns in non-brain tissues. Finally, the intron length and abundance of Alu elements positively correlated with ABS event complexity, and the predominant circRNAs had longer flanking introns and more Alu elements than other circRNAs in the same ABS event. Together, our results represent a resource for circRNA research—we expanded the repertoire of ABS events of circRNAs in human tissue transcriptomes and provided insights into the complexity of circRNA biogenesis, expression, and regulation.

    更新日期:2020-01-24
  • Measuring mRNA translation in neuronal processes and somata by tRNA-FRET
    Nucleic Acids Res. (IF 11.147) Pub Date : 2020-01-24
    Koltun B, Ironi S, Gershoni-Emek N, et al.

    In neurons, the specific spatial and temporal localization of protein synthesis is of great importance for function and survival. Here, we visualized tRNA and protein synthesis events in fixed and live mouse primary cortical culture using fluorescently-labeled tRNAs. We were able to characterize the distribution and transport of tRNAs in different neuronal sub-compartments and to study their association with the ribosome. We found that tRNA mobility in neural processes is lower than in somata and corresponds to patterns of slow transport mechanisms, and that larger tRNA puncta co-localize with translational machinery components and are likely the functional fraction. Furthermore, chemical induction of long-term potentiation (LTP) in culture revealed up-regulation of mRNA translation with a similar effect in dendrites and somata, which appeared to be GluR-dependent 6 h post-activation. Importantly, measurement of protein synthesis in neurons with high resolutions offers new insights into neuronal function in health and disease states.

    更新日期:2020-01-24
  • Dynamics of strand slippage in DNA hairpins formed by CAG repeats: roles of sequence parity and trinucleotide interrupts
    Nucleic Acids Res. (IF 11.147) Pub Date : 2020-01-24
    Xu P, Pan F, Roland C, et al.

    DNA trinucleotide repeats (TRs) can exhibit dynamic expansions by integer numbers of trinucleotides that lead to neurodegenerative disorders. Strand slipped hairpins during DNA replication, repair and/or recombination may contribute to TR expansion. Here, we combine single-molecule FRET experiments and molecular dynamics studies to elucidate slipping dynamics and conformations of (CAG)n TR hairpins. We directly resolve slipping by predominantly two CAG units. The slipping kinetics depends on the even/odd repeat parity. The populated states suggest greater stability for 5′-AGCA-3′ tetraloops, compared with alternative 5′-CAG-3′ triloops. To accommodate the tetraloop, even(odd)-numbered repeats have an even(odd) number of hanging bases in the hairpin stem. In particular, a paired-end tetraloop (no hanging TR) is stable in (CAG)n = even, but such situation cannot occur in (CAG)n = odd, where the hairpin is “frustrated” and slips back and forth between states with one TR hanging at the 5′ or 3′ end. Trinucleotide interrupts in the repeating CAG pattern associated with altered disease phenotypes select for specific conformers with favorable loop sequences. Molecular dynamics provide atomic-level insight into the loop configurations. Reducing strand slipping in TR hairpins by sequence interruptions at the loop suggests disease-associated variations impact expansion mechanisms at the level of slipped hairpins.

    更新日期:2020-01-24
  • DNA-mediated coupling of ATPase, translocase and nuclease activities of a Type ISP restriction-modification enzyme
    Nucleic Acids Res. (IF 11.147) Pub Date : 2020-01-24
    Chand M, Carle V, Anuvind K, et al.

    Enzymes involved in nucleic acid transactions often have a helicase-like ATPase coordinating and driving their functional activities, but our understanding of the mechanistic details of their coordination is limited. For example, DNA cleavage by the antiphage defense system Type ISP restriction-modification enzyme requires convergence of two such enzymes that are actively translocating on DNA powered by Superfamily 2 ATPases. The ATPase is activated when the enzyme recognizes a DNA target sequence. Here, we show that the activation is a two-stage process of partial ATPase stimulation upon recognition of the target sequence by the methyltransferase and the target recognition domains, and complete stimulation that additionally requires the DNA to interact with the ATPase domain. Mutagenesis revealed that a β-hairpin loop and motif V of the ATPase couples DNA translocation to ATP hydrolysis. Deletion of the loop inhibited translocation, while mutation of motif V slowed the rate of translocation. Both the mutations inhibited the double-strand (ds) DNA cleavage activity of the enzyme. However, a translocating motif V mutant cleaved dsDNA on encountering a translocating wild-type enzyme. Based on these results, we conclude that the ATPase-driven translocation not only brings two nucleases spatially close to catalyze dsDNA break, but that the rate of translocation influences dsDNA cleavage.

    更新日期:2020-01-24
  • HopPER: an adaptive model for probability estimation of influenza reassortment through host prediction
    BMC Med. Genomics (IF 2.568) Pub Date : 2020-01-23
    Rui Yin; Xinrui Zhou; Shamima Rashid; Chee Keong Kwoh

    Influenza reassortment, a mechanism where influenza viruses exchange their RNA segments by co-infecting a single cell, has been implicated in several major pandemics since 19th century. Owing to the significant impact on public health and social stability, great attention has been received on the identification of influenza reassortment. We proposed a novel computational method named HopPER (Host-prediction-based Probability Estimation of Reassortment), that sturdily estimates reassortment probabilities through host tropism prediction using 147 new features generated from seven physicochemical properties of amino acids. We conducted the experiments on a range of real and synthetic datasets and compared HopPER with several state-of-the-art methods. It is shown that 280 out of 318 candidate reassortants have been successfully identified. Additionally, not only can HopPER be applied to complete genomes but its effectiveness on incomplete genomes is also demonstrated. The analysis of evolutionary success of avian, human and swine viruses generated through reassortment across different years using HopPER further revealed the reassortment history of the influenza viruses. Our study presents a novel method for the prediction of influenza reassortment. We hope this method could facilitate rapid reassortment detection and provide novel insights into the evolutionary patterns of influenza viruses.

    更新日期:2020-01-23
  • Genome-wide investigation of calcium-dependent protein kinase gene family in pineapple: evolution and expression profiles during development and stress
    BMC Genomics (IF 3.501) Pub Date : 2020-01-23
    Man Zhang; Yanhui Liu; Qing He; Mengnan Chai; Youmei Huang; Fangqian Chen; Xiaomei Wang; Yeqiang Liu; Hanyang Cai; Yuan Qin

    Calcium-dependent protein kinase (CPK) is one of the main Ca2+ combined protein kinase that play significant roles in plant growth, development and response to multiple stresses. Despite an important member of the stress responsive gene family, little is known about the evolutionary history and expression patterns of CPK genes in pineapple. Herein, we identified and characterized 17 AcoCPK genes from pineapple genome, which were unevenly distributed across eight chromosomes. Based on the gene structure and phylogenetic tree analyses, AcoCPKs were divided into four groups with conserved domain. Synteny analysis identified 7 segmental duplication events of AcoCPKs and 5 syntenic blocks of CPK genes between pineapple and Arabidopsis, and 8 between pineapple and rice. Expression pattern of different tissues and development stages suggested that several genes are involved in the functional development of plants. Different expression levels under various abiotic stresses also indicated that the CPK family underwent functional divergence during long-term evolution. AcoCPK1, AcoCPK3 and AcoCPK6, which were repressed by the abiotic stresses, were shown to be function in regulating pathogen resistance. 17 AcoCPK genes from pineapple genome were identified. Our analyses provide an important foundation for understanding the potential roles of AcoCPKs in regulating pineapple response to biotic and abiotic stresses

    更新日期:2020-01-23
  • Transcriptome profiling of laser-captured germ cells and functional characterization of zbtb40 during 17alpha-methyltestosterone-induced spermatogenesis in orange-spotted grouper (Epinephelus coioides)
    BMC Genomics (IF 3.501) Pub Date : 2020-01-23
    Xi Wu; Yang Yang; Chaoyue Zhong; Yin Guo; Shuisheng Li; Haoran Lin; Xiaochun Liu

    Spermatogenesis is an intricate process regulated by a finely organized network. The orange-spotted grouper (Epinephelus coioides) is a protogynous hermaphroditic fish, but the regulatory mechanism of its spermatogenesis is not well-understood. In the present study, transcriptome sequencing of the male germ cells isolated from orange-spotted grouper was performed to explore the molecular mechanism underlying spermatogenesis. In this study, the orange-spotted grouper was induced to change sex from female to male by 17alpha-methyltestosterone (MT) implantation. During the spermatogenesis, male germ cells (spermatogonia, spermatocytes, spermatids, and spermatozoa) were isolated by laser capture microdissection. Transcriptomic analysis for the isolated cells was performed. A total of 244,984,338 clean reads were generated from four cDNA libraries. Real-time PCR results of 13 genes related to sex differentiation and hormone metabolism indicated that transcriptome data are reliable. RNA-seq data showed that the female-related genes and genes involved in hormone metabolism were highly expressed in spermatogonia and spermatozoa, suggesting that these genes participate in the spermatogenesis. Interestingly, the expression of zbtb family genes showed significantly changes in the RNA-seq data, and their expression patterns were further examined during spermatogenesis. The analysis of cellular localization of Eczbtb40 and the co-localization of Eczbtb40 and Eccyp17a1 in different gonadal stages suggested that Eczbtb40 might interact with Eccyp17a1 during spermatogenesis. Our study, for the first time, investigated the transcriptome of the male germ cells from orange-spotted grouper, and identified functional genes, GO terms, and KEGG pathways involved in spermatogenesis. Furthermore, Eczbtb40 was first characterized and its role during spermatogenesis was predicted. These data will contribute to future studies on the molecular mechanism of spermatogenesis in teleosts.

    更新日期:2020-01-23
  • The primordial tRNA acceptor stem code from theoretical minimal RNA ring clusters
    BMC Genet. (IF 2.547) Pub Date : 2020-01-23
    Jacques Demongeot; Hervé Seligmann

    Theoretical minimal RNA rings code by design over the shortest length once for each of the 20 amino acids, a start and a stop codon, and form stem-loop hairpins. This defines at most 25 RNA rings of 22 nucleotides. As a group, RNA rings mimick numerous prebiotic and early life biomolecular properties: tRNAs, deamination gradients and replication origins, emergence of codon preferences for the natural circular code, and contents of early protein coding genes. These properties result from the RNA ring’s in silico design, based mainly on coding nonredundancy among overlapping translation frames, as the genetic code’s codon-amino acid assignments determine. RNA rings resemble ancestral tRNAs, defining RNA ring anticodons and corresponding cognate amino acids. Surprisingly, all examined RNA ring properties coevolve with genetic code integration ranks of RNA ring cognates, as if RNA rings mimick prebiotic and early life evolution. Distances between RNA rings were calculated using different evolutionary models. Associations between these distances and genetic code evolutionary hypotheses detect evolutionary models best describing RNA ring diversification. Here pseudo-phylogenetic analyses of RNA rings produce clusters corresponding to the primordial code in tRNA acceptor stems, more so when substitution matrices from neutrally evolving pseudogenes are used rather than from functional protein coding genes reflecting selection for conserving amino acid properties. Results indicate RNA rings with recent cognates evolved from those with early cognates. Hence RNA rings, as designed by the genetic code’s structure, simulate tRNA stem evolution and prebiotic history along neutral chemistry-driven mutation regimes.

    更新日期:2020-01-23
  • Distribution of allele frequencies for genes associated with physical activity and/or physical capacity in a homogenous Norwegian cohort- a cross-sectional study
    BMC Genet. (IF 2.547) Pub Date : 2020-01-23
    Sannija Goleva-Fjellet; Anne Mari Bjurholt; Elin H. Kure; Inger Kristin Larsen; Øyvind Støren; Mona Sæbø

    There are large individual differences in physical activity (PA) behavior as well as trainability of physical capacity. Heritability studies have shown that genes may have as much impact on exercise participation behavior as environmental factors. Genes that favor both trainability and participation may increase the levels of PA. The present study aimed to assess the allele frequencies in genes associated with PA and/or physical capacity, and to see if there is any association between these polymorphisms and self-reported PA levels in a cohort of middle-aged Norwegians of Scandinavian descent (n = 831; mean age mean age (± SD) 55.5 ± 3.8 years). The genotype distributions of the ACTN3 R577X, ACE I/D and MAOA uVNTR polymorphisms were similar to other populations of European descent. When comparing the genotype distribution between the low/medium level PA group (LMPA) and high level PA groups (HPA), a significant difference in ACTN3 577X allele distribution was found. The X allele frequency was 10% lower in the HPA level group (P = 0.006). There were no differences in the genotype distribution of the ACE I/D or MAOA uVNTR polymorphism. Education and previous participation in sports or outdoor activities was positively associated with the self-reported PA levels (P ≤ 0.001). To the best of our knowledge, this is the first study to report association between ACTN3 R577X genotype and PA level in middle-aged Scandinavians. Nevertheless, the contribution of a single polymorphism to a complex trait, like PA level, is likely small. Socioeconomic variables, as education and previous participation in sports or outdoor activities, are positively associated with the self-reported PA levels.

    更新日期:2020-01-23
  • Lysine acetylation of the housekeeping sigma factor enhances the activity of the RNA polymerase holoenzyme
    Nucleic Acids Res. (IF 11.147) Pub Date : 2020-01-23
    Kim J, Choi J, Kim J, et al.

    Protein lysine acetylation, one of the most abundant post-translational modifications in eukaryotes, occurs in prokaryotes as well. Despite the evidence of lysine acetylation in bacterial RNA polymerases (RNAPs), its function remains unknown. We found that the housekeeping sigma factor (HrdB) was acetylated throughout the growth of an actinobacterium, Streptomyces venezuelae, and the acetylated HrdB was enriched in the RNAP holoenzyme complex. The lysine (K259) located between 1.2 and 2 regions of the sigma factor, was determined to be the acetylated residue of HrdB in vivo by LC–MS/MS analyses. Specifically, the label-free quantitative analysis revealed that the K259 residues of all the HrdB subunits were acetylated in the RNAP holoenzyme. Using mutations that mimic or block acetylation (K259Q and K259R), we found that K259 acetylation enhances the interaction of HrdB with the RNAP core enzyme as well as the binding activity of the RNAP holoenzyme to target promoters in vivo. Taken together, these findings provide a novel insight into an additional layer of modulation of bacterial RNAP activity.

    更新日期:2020-01-23
  • Cockayne syndrome group A and B proteins function in rRNA transcription through nucleolin regulation
    Nucleic Acids Res. (IF 11.147) Pub Date : 2020-01-23
    Okur M, Lee J, Osmani W, et al.

    Cockayne Syndrome (CS) is a rare neurodegenerative disease characterized by short stature, accelerated aging and short lifespan. Mutations in two human genes, ERCC8/CSA and ERCC6/CSB, are causative for CS and their protein products, CSA and CSB, while structurally unrelated, play roles in DNA repair and other aspects of DNA metabolism in human cells. Many clinical and molecular features of CS remain poorly understood, and it was observed that CSA and CSB regulate transcription of ribosomal DNA (rDNA) genes and ribosome biogenesis. Here, we investigate the dysregulation of rRNA synthesis in CS. We report that Nucleolin (Ncl), a nucleolar protein that regulates rRNA synthesis and ribosome biogenesis, interacts with CSA and CSB. In addition, CSA induces ubiquitination of Ncl, enhances binding of CSB to Ncl, and CSA and CSB both stimulate the binding of Ncl to rDNA and subsequent rRNA synthesis. CSB and CSA also increase RNA Polymerase I loading to the coding region of the rDNA and this is Ncl dependent. These findings suggest that CSA and CSB are positive regulators of rRNA synthesis via Ncl regulation. Most CS patients carry mutations in CSA and CSB and present with similar clinical features, thus our findings provide novel insights into disease mechanism.

    更新日期:2020-01-23
  • HDAC8 cooperates with SMAD3/4 complex to suppress SIRT7 and promote cell survival and migration
    Nucleic Acids Res. (IF 11.147) Pub Date : 2020-01-23
    Tang X, Li G, Su F, et al.

    NAD+-dependent SIRT7 deacylase plays essential roles in ribosome biogenesis, stress response, genome integrity, metabolism and aging, while how it is transcriptionally regulated is still largely unclear. TGF-β signaling is highly conserved in multicellular organisms, regulating cell growth, cancer stemness, migration and invasion. Here, we demonstrate that histone deacetylase HDAC8 forms complex with SMAD3/4 heterotrimer and occupies SIRT7 promoter, wherein it deacetylates H4 and thus suppresses SIRT7 transcription. Treatment with HDAC8 inhibitor compromises TGF-β signaling via SIRT7-SMAD4 axis and consequently, inhibits lung metastasis and improves chemotherapy efficacy in breast cancer. Our data establish a regulatory feedback loop of TGF-β signaling, wherein HDAC8 as a novel cofactor of SMAD3/4 complex, transcriptionally suppresses SIRT7 via local chromatin remodeling and thus further activates TGF-β signaling. Targeting HDAC8 exhibits therapeutic potential for TGF-β signaling related diseases.

    更新日期:2020-01-23
  • SIRT6 coordinates with CHD4 to promote chromatin relaxation and DNA repair
    Nucleic Acids Res. (IF 11.147) Pub Date : 2020-01-23
    Hou T, Cao Z, Zhang J, et al.

    Genomic instability is an underlying hallmark of cancer and is closely associated with defects in DNA damage repair (DDR). Chromatin relaxation is a prerequisite for DDR, but how chromatin accessibility is regulated remains elusive. Here we report that the histone deacetylase SIRT6 coordinates with the chromatin remodeler CHD4 to promote chromatin relaxation in response to DNA damage. Upon DNA damage, SIRT6 rapidly translocates to DNA damage sites, where it interacts with and recruits CHD4. Once at the damage sites, CHD4 displaces heterochromatin protein 1 (HP1) from histone H3 lysine 9 trimethylation (H3K9me3). Notably, loss of SIRT6 or CHD4 leads to impaired chromatin relaxation and disrupted DNA repair protein recruitment. These molecular changes, in-turn, lead to defective homologous recombination (HR) and cancer cell hypersensitivity to DNA damaging agents. Furthermore, we show that SIRT6-mediated CHD4 recruitment has a specific role in DDR within compacted chromatin by HR in G2 phase, which is an ataxia telangiectasia mutated (ATM)-dependent process. Taken together, our results identify a novel function for SIRT6 in recruiting CHD4 onto DNA double-strand breaks. This newly identified novel molecular mechanism involves CHD4-dependent chromatin relaxation and competitive release of HP1 from H3K9me3 within the damaged chromatin, which are both essential for accurate HR.

    更新日期:2020-01-23
  • Genome-wide analysis reveals a switch in the translational program upon oocyte meiotic resumption
    Nucleic Acids Res. (IF 11.147) Pub Date : 2020-01-23
    Luong X, Daldello E, Rajkovic G, et al.

    During oocyte maturation, changes in gene expression depend exclusively on translation and degradation of maternal mRNAs rather than transcription. Execution of this translation program is essential for assembling the molecular machinery required for meiotic progression, fertilization, and embryo development. With the present study, we used a RiboTag/RNA-Seq approach to explore the timing of maternal mRNA translation in quiescent oocytes as well as in oocytes progressing through the first meiotic division. This genome-wide analysis reveals a global switch in maternal mRNA translation coinciding with oocyte re-entry into the meiotic cell cycle. Messenger RNAs whose translation is highly active in quiescent oocytes invariably become repressed during meiotic re-entry, whereas transcripts repressed in quiescent oocytes become activated. Experimentally, we have defined the exact timing of the switch and the repressive function of CPE elements, and identified a novel role for CPEB1 in maintaining constitutive translation of a large group of maternal mRNAs during maturation.

    更新日期:2020-01-23
  • A Multi-tissue Transcriptome Analysis of Human Metabolites Guides Interpretability of Associations Based on Multi-SNP Models for Gene Expression
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2020-01-23
    Anne Ndungu; Anthony Payne; Jason M. Torres; Martijn van de Bunt; Mark I. McCarthy

    There is particular interest in transcriptome-wide association studies (TWAS) gene-level tests based on multi-SNP predictive models of gene expression—for identifying causal genes at loci associated with complex traits. However, interpretation of TWAS associations may be complicated by divergent effects of model SNPs on phenotype and gene expression. We developed an iterative modeling scheme for obtaining multi-SNP models of gene expression and applied this framework to generate expression models for 43 human tissues from the Genotype-Tissue Expression (GTEx) Project. We characterized the performance of single- and multi-SNP models for identifying causal genes in GWAS data for 46 circulating metabolites. We show that: (A) multi-SNP models captured more variation in expression than did the top cis-eQTL (median 2-fold improvement); (B) predicted expression based on multi-SNP models was associated (false discovery rate < 0.01) with metabolite levels for 826 unique gene-metabolite pairs, but, after stepwise conditional analyses, 90% were dominated by a single eQTL SNP; (C) among the 35% of associations where a SNP in the expression model was a significant cis-eQTL and metabolomic-QTL (met-QTL), 92% demonstrated colocalization between these signals, but interpretation was often complicated by incomplete overlap of QTLs in multi-SNP models; and (D) using a “truth” set of causal genes at 61 met-QTLs, the sensitivity was high (67%), but the positive predictive value was low, as only 8% of TWAS associations (19% when restricted to colocalized associations at met-QTLs) involved true causal genes. These results guide the interpretation of TWAS and highlight the need for corroborative data to provide confident assignment of causality.

    更新日期:2020-01-23
  • TTC12 Loss-of-Function Mutations Cause Primary Ciliary Dyskinesia and Unveil Distinct Dynein Assembly Mechanisms in Motile Cilia Versus Flagella
    Am. J. Hum. Genet. (IF 9.924) Pub Date : 2020-01-23
    Lucie Thomas; Khaled Bouhouche; Marjorie Whitfield; Guillaume Thouvenin; Andre Coste; Bruno Louis; Claire Szymanski; Emilie Bequignon; Jean-François Papon; Manon Castelli; Michel Lemullois; Xavier Dhalluin; Valérie Drouin-Garraud; Guy Montantin; Sylvie Tissier; Philippe Duquesnoy; Bruno Copin; Florence Dastot; Marie Legendre

    Cilia and flagella are evolutionarily conserved organelles whose motility relies on the outer and inner dynein arm complexes (ODAs and IDAs). Defects in ODAs and IDAs result in primary ciliary dyskinesia (PCD), a disease characterized by recurrent airway infections and male infertility. PCD mutations in assembly factors have been shown to cause a combined ODA-IDA defect, affecting both cilia and flagella. We identified four loss-of-function mutations in TTC12, which encodes a cytoplasmic protein, in four independent families in which affected individuals displayed a peculiar PCD phenotype characterized by the absence of ODAs and IDAs in sperm flagella, contrasting with the absence of only IDAs in respiratory cilia. Analyses of both primary cells from individuals carrying TTC12 mutations and human differentiated airway cells invalidated for TTC12 by a CRISPR-Cas9 approach revealed an IDA defect restricted to a subset of single-headed IDAs that are different in flagella and cilia, whereas TTC12 depletion in the ciliate Paramecium tetraurelia recapitulated the sperm phenotype. Overall, our study, which identifies TTC12 as a gene involved in PCD, unveils distinct dynein assembly mechanisms in human motile cilia versus flagella.

    更新日期:2020-01-23
  • An integrated analysis of public genomic data unveils a possible functional mechanism of psoriasis risk via a long-range ERRFI1 enhancer
    BMC Med. Genomics (IF 2.568) Pub Date : 2020-01-22
    Naoto Kubota; Mikita Suyama

    Psoriasis is a chronic inflammatory skin disease, for which genome-wide association studies (GWAS) have identified many genetic variants as risk markers. However, the details of underlying molecular mechanisms, especially which variants are functional, are poorly understood. We utilized a computational approach to survey psoriasis-associated functional variants that might affect protein functions or gene expression levels. We developed a pipeline by integrating publicly available datasets provided by GWAS Catalog, FANTOM5, GTEx, SNP2TFBS, and DeepBlue. To identify functional variants on exons or splice sites, we used a web-based annotation tool in the Ensembl database. To search for noncoding functional variants within promoters or enhancers, we used eQTL data calculated by GTEx. The data of variants lying on transcription factor binding sites provided by SNP2TFBS were used to predict detailed functions of the variants. We discovered 22 functional variant candidates, of which 8 were in noncoding regions. We focused on the enhancer variant rs72635708 (T > C) in the 1p36.23 region; this variant is within the enhancer region of the ERRFI1 gene, which regulates lipid metabolism in the liver and skin morphogenesis via EGF signaling. Further analysis showed that the ERRFI1 promoter spatially contacts with the enhancer, despite the 170 kb distance between them. We found that this variant lies on the AP-1 complex binding motif and may modulate binding levels. The minor allele rs72635708 (rs72635708-C) might affect the ERRFI1 promoter activity, which results in unstable expression of ERRFI1, enhancing the risk of psoriasis via disruption of lipid metabolism and skin cell proliferation. Our study represents a successful example of predicting molecular pathogenesis by integration and reanalysis of public data.

    更新日期:2020-01-23
  • Familial autosomal recessive bestrophinopathy: identification of a novel variant in BEST1 gene and the specific metabolomic profile
    BMC Med. Genet. (IF 1.74) Pub Date : 2020-01-22
    Panpan Ye; Jia Xu; Yueqiu Luo; Zhitao Su; Ke Yao

    Autosomal recessive bestrophinopathy (ARB) is a retinal degenerative disorder caused by BEST1 mutations with autosomal recessive inheritance. We aim to map a comprehensive genomic and metabolomic profile of a consanguineous Chinese family with ARB. Ophthalmic examinations were performed on the affected patients with ARB. The proband was screened for potential causative mutations in a panel with 256 known retinal disease genes by using target capture sequencing. The related mutation was further validated and segregated in the family members by Sanger sequencing. In silico prediction tools were used for pathogenicity assessment. A UHPLC-MS/MS metabolomic analysis was performed to explore the disease-associated metabolic feature. The affected patients from this family were characterized by low vision, the presence of subretinal fluid, macular edema, and hyperopia with coincidental angle closure. DNA sequencing identified a novel missense mutation in the BEST1 gene c.646G > A (p.Val216Ile) of the proband. Sanger sequencing further confirmed the mutation. The missense mutation was co-segregation across the pedigree and predicted to be deleterious by SIFT (0.017). The blood metabolic profiles were highly similar among all family members probably because of the same lifestyle, habitat and genomic background. However, ARB patients presented a significant deregulation of metabolites, such as citric acid, L-Threonic acid, and eicosapentaenoic acid. We identified a novel disease-associated variant in the BEST1 gene as well as a disease-specific metabolic feature in familial ARB. Our findings helped improve the understanding of ARB mechanisms.

    更新日期:2020-01-23
  • Genome-wide identification and analyses of the AHL gene family in cotton (Gossypium)
    BMC Genomics (IF 3.501) Pub Date : 2020-01-22
    Lanjie Zhao; Youjun Lü; Wei Chen; Jinbo Yao; Yan Li; Qiulin Li; Jingwen Pan; Shengtao Fang; Jie Sun; Yongshan Zhang

    Members of the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) family are involved in various plant biological processes via protein-DNA and protein-protein interaction. However, no the systematic identification and analysis of AHL gene family have been reported in cotton. To investigate the potential functions of AHLs in cotton, genome-wide identification, expressions and structure analysis of the AHL gene family were performed in this study. 48, 51 and 99 AHL genes were identified from the G.raimondii, G.arboreum and G.hirsutum genome, respectively. Phylogenetic analysis revealed that the AHLs in cotton evolved into 2 clades, Clade-A with 4–5 introns and Clade-B with intronless (excluding AHL20–2). Based on the composition of the AT-hook motif(s) and PPC/DUF 296 domain, AHL proteins were classified into three types (Type-I/−II/−III), with Type-I AHLs forming Clade-B, and the other two types together diversifying in Clade-A. The detection of synteny and collinearity showed that the AHLs expanded with the specific WGD in cotton, and the sequence structure of AHL20–2 showed the tendency of increasing intron in three different Gossypium spp. The ratios of non-synonymous (Ka) and synonymous (Ks) substitution rates of orthologous gene pairs revealed that the AHL genes of G.hirsutum had undergone through various selection pressures, purifying selection mainly in A-subgenome and positive selection mainly in D-subgenome. Examination of their expression patterns showed most of AHLs of Clade-B expressed predominantly in stem, while those of Clade-A in ovules, suggesting that the AHLs within each clade shared similar expression patterns with each other. qRT-PCR analysis further confirmed that some GhAHLs higher expression in stems and ovules. In this study, 48, 51 and 99 AHL genes were identified from three cotton genomes respectively. AHLs in cotton were classified into two clades by phylogenetic relationship and three types based on the composition of motif and domain. The AHLs expanded with segmental duplication, not tandem duplication. The expression profiles of GhAHLs revealed abundant differences in expression levels in various tissues and at different stages of ovules development. Our study provided significant insights into the potential functions of AHLs in regulating the growth and development in cotton.

    更新日期:2020-01-23
  • Genomics-based epidemiology of bovine Mycoplasma bovis strains in Israel
    BMC Genomics (IF 3.501) Pub Date : 2020-01-22
    Yael Yair; Ilya Borovok; Inna Mikula; Rama Falk; Larry K. Fox; Uri Gophna; Inna Lysnyansky

    Mycoplasma bovis is an important etiologic agent of bovine mycoplasmosis affecting cattle production and animal welfare. In the past in Israel, M. bovis has been most frequently associated with bovine respiratory disease (BRD) and was rarely isolated from mastitis. This situation changed in 2008 when M. bovis-associated mastitis emerged in Israel. The aim of this study was to utilize whole genome sequencing to evaluate the molecular epidemiology and genomic diversity of M. bovis mastitis-associated strains and their genetic relatedness to M. bovis strains isolated from BRD in local feedlot calves and those imported to Israel from different European countries and Australia. Phylogeny based on total single nucleotide polymorphism (SNP) analysis of 225 M. bovis genomes clearly showed clustering of isolates on the basis of geographical origin: strains isolated from European countries clustered together and separately from Australian and Chinese isolates, while Israeli isolates were found in the both groups. The dominant genotype was identified among local mastitis-associated M. bovis isolates. This genotype showed a close genomic relatedness to M. bovis strains isolated from calves imported to Israel from Australia, to original Australian M. bovis strains, as well as to strains isolated in China. This study represents the first comprehensive high-resolution genome-based epidemiological analysis of M. bovis in Israel and illustrates the possible dissemination of the pathogen across the globe by cattle trade.

    更新日期:2020-01-23
  • miR-147b-modulated expression of vestigial regulates wing development in the bird cherry-oat aphid Rhopalosiphum padi
    BMC Genomics (IF 3.501) Pub Date : 2020-01-22
    Yinjun Fan; Xiuxia Li; Abd Allah A. H. Mohammed; Ying Liu; Xiwu Gao

    Most aphids exhibit wing polyphenism in which wingless and winged morphs produce depending on the population density and host plant quality. Although the influence of environmental factors on wing polyphenism of aphids have been extensively investigated, molecular mechanisms underlining morph differentiation (i.e. wing development /degeneration), one downstream aspect of the wing polyphenism, has been poorly understood. We examined the expression levels of the twenty genes involved in wing development network, and only vestigial (vg) showed significantly different expression levels in both whole-body and wall-body of third instar nymphs, with 5.4- and 16.14- fold higher expression in winged lines compared to wingless lines, respectively in Rhopalosiphum padi. vg expression was higher in winged lines compared to wingless lines in third, fourth instar nymphs and adults. Larger difference expression was observed in third (21.38-fold) and fourth (20.91-fold) instar nymphs relative to adults (3.12-fold). Suppression of vg using RNAi repressed the wing development of third winged morphs. Furthermore, dual luciferase reporter assay revealed that the miR-147 can target the vg mRNA. Modulation of miR-147b levels by microinjection of its agomir (mimic) decreased vg expression levels and repressed wing development. Our findings suggest that vg is essential for wing development in R. padi and that miR-147b modulates its expression.

    更新日期:2020-01-23
  • A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods
    Genome Biol. (IF 14.028) Pub Date : 2020-01-22
    Jill E. Moore; Henry E. Pratt; Michael J. Purcaro; Zhiping Weng

    Many genome-wide collections of candidate cis-regulatory elements (cCREs) have been defined using genomic and epigenomic data, but it remains a major challenge to connect these elements to their target genes. To facilitate the development of computational methods for predicting target genes, we develop a Benchmark of candidate Enhancer-Gene Interactions (BENGI) by integrating the recently developed Registry of cCREs with experimentally derived genomic interactions. We use BENGI to test several published computational methods for linking enhancers with genes, including signal correlation and the TargetFinder and PEP supervised learning methods. We find that while TargetFinder is the best-performing method, it is only modestly better than a baseline distance method for most benchmark datasets when trained and tested with the same cell type and that TargetFinder often does not outperform the distance method when applied across cell types. Our results suggest that current computational methods need to be improved and that BENGI presents a useful framework for method development and testing.

    更新日期:2020-01-23
  • Gene content evolution in the arthropods
    Genome Biol. (IF 14.028) Pub Date : 2020-01-23
    Gregg W. C. Thomas; Elias Dohmen; Daniel S. T. Hughes; Shwetha C. Murali; Monica Poelchau; Karl Glastad; Clare A. Anstead; Nadia A. Ayoub; Phillip Batterham; Michelle Bellair; Greta J. Binford; Hsu Chao; Yolanda H. Chen; Christopher Childers; Huyen Dinh; Harsha Vardhan Doddapaneni; Jian J. Duan; Shannon Dugan; Lauren A. Esposito; Markus Friedrich; Jessica Garb; Robin B. Gasser; Michael A. D. Goodisman; Dawn E. Gundersen-Rindal; Yi Han; Alfred M. Handler; Masatsugu Hatakeyama; Lars Hering; Wayne B. Hunter; Panagiotis Ioannidis; Joy C. Jayaseelan; Divya Kalra; Abderrahman Khila; Pasi K. Korhonen; Carol Eunmi Lee; Sandra L. Lee; Yiyuan Li; Amelia R. I. Lindsey; Georg Mayer; Alistair P. McGregor; Duane D. McKenna; Bernhard Misof; Mala Munidasa; Monica Munoz-Torres; Donna M. Muzny; Oliver Niehuis; Nkechinyere Osuji-Lacy; Subba R. Palli; Kristen A. Panfilio; Matthias Pechmann; Trent Perry; Ralph S. Peters; Helen C. Poynton; Nikola-Michael Prpic; Jiaxin Qu; Dorith Rotenberg; Coby Schal; Sean D. Schoville; Erin D. Scully; Evette Skinner; Daniel B. Sloan; Richard Stouthamer; Michael R. Strand; Nikolaus U. Szucsich; Asela Wijeratne; Neil D. Young; Eduardo E. Zattara; Joshua B. Benoit; Evgeny M. Zdobnov; Michael E. Pfrender; Kevin J. Hackett; John H. Werren; Kim C. Worley; Richard A. Gibbs; Ariel D. Chipman; Robert M. Waterhouse; Erich Bornberg-Bauer; Matthew W. Hahn; Stephen Richards

    Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods. Using 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality, and chemoperception. These analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity.

    更新日期:2020-01-23
  • Genomic prediction for hastening and improving efficiency of forward selection in conifer polycross mating designs: an example from white spruce
    Heredity (IF 3.179) Pub Date : 2020-01-22
    Patrick R. N. Lenz; Simon Nadeau; Aïda Azaiez; Sébastien Gérardi; Marie Deslauriers; Martin Perron; Nathalie Isabel; Jean Beaulieu; Jean Bousquet
    更新日期:2020-01-23
  • The landscape of chimeric RNAs in non-diseased tissues and cells
    Nucleic Acids Res. (IF 11.147) Pub Date : 2020-01-22
    Singh S, Qin F, Kumar S, et al.

    Chimeric RNAs and their encoded proteins have been traditionally viewed as unique features of neoplasia, and have been used as biomarkers and therapeutic targets for multiple cancers. Recent studies have demonstrated that chimeric RNAs also exist in non-cancerous cells and tissues, although large-scale, genome-wide studies of chimeric RNAs in non-diseased tissues have been scarce. Here, we explored the landscape of chimeric RNAs in 9495 non-diseased human tissue samples of 53 different tissues from the GTEx project. Further, we established means for classifying chimeric RNAs, and observed enrichment for particular classifications as more stringent filters are applied. We experimentally validated a subset of chimeric RNAs from each classification and demonstrated functional relevance of two chimeric RNAs in non-cancerous cells. Importantly, our list of chimeric RNAs in non-diseased tissues overlaps with some entries in several cancer fusion databases, raising concerns for some annotations. The data from this study provides a large repository of chimeric RNAs present in non-diseased tissues, which can be used as a control dataset to facilitate the identification of true cancer-specific chimeras.

    更新日期:2020-01-23
  • AON-induced splice-switching and DMPK pre-mRNA degradation as potential therapeutic approaches for Myotonic Dystrophy type 1
    Nucleic Acids Res. (IF 11.147) Pub Date : 2020-01-22
    Stepniak-Konieczna E, Konieczny P, Cywoniuk P, et al.

    Expansion of an unstable CTG repeat in the 3′UTR of the DMPK gene causes Myotonic Dystrophy type 1 (DM1). CUG-expanded DMPK transcripts (CUGexp) sequester Muscleblind-like (MBNL) alternative splicing regulators in ribonuclear inclusions (foci), leading to abnormalities in RNA processing and splicing. To alleviate the burden of CUGexp, we tested therapeutic approach utilizing antisense oligonucleotides (AONs)-mediated DMPK splice-switching and degradation of mutated pre-mRNA. Experimental design involved: (i) skipping of selected constitutive exons to induce frameshifting and decay of toxic mRNAs by an RNA surveillance mechanism, and (ii) exclusion of the alternative exon 15 (e15) carrying CUGexp from DMPK mRNA. While first strategy failed to stimulate DMPK mRNA decay, exclusion of e15 enhanced DMPK nuclear export but triggered accumulation of potentially harmful spliced out pre-mRNA fragment containing CUGexp. Neutralization of this fragment with antisense gapmers complementary to intronic sequences preceding e15 failed to diminish DM1-specific spliceopathy due to AONs’ chemistry-related toxicity. However, intronic gapmers alone reduced the level of DMPK mRNA and mitigated DM1-related cellular phenotypes including spliceopathy and nuclear foci. Thus, a combination of the correct chemistry and experimental approach should be carefully considered to design a safe AON-based therapeutic strategy for DM1.

    更新日期:2020-01-23
  • Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase
    Nucleic Acids Res. (IF 11.147) Pub Date : 2020-01-22
    Shin Y, Hedglin M, Murakami K.

    Reiterative transcription is a non-canonical form of RNA synthesis by RNA polymerase in which a ribonucleotide specified by a single base in the DNA template is repetitively added to the nascent RNA transcript. We previously determined the X-ray crystal structure of the bacterial RNA polymerase engaged in reiterative transcription from the pyrG promoter, which contains eight poly-G RNA bases synthesized using three C bases in the DNA as a template and extends RNA without displacement of the promoter recognition σ factor from the core enzyme. In this study, we determined a series of transcript initiation complex structures from the pyrG promoter using soak–trigger–freeze X-ray crystallography. We also performed biochemical assays to monitor template DNA translocation during RNA synthesis from the pyrG promoter and in vitro transcription assays to determine the length of poly-G RNA from the pyrG promoter variants. Our study revealed how RNA slips on template DNA and how RNA polymerase and template DNA determine length of reiterative RNA product. Lastly, we determined a structure of a transcript initiation complex at the pyrBI promoter and proposed an alternative mechanism of RNA slippage and extension requiring the σ dissociation from the core enzyme.

    更新日期:2020-01-23
  • Poly(ADP-ribosyl)ation mediates early phase histone eviction at DNA lesions
    Nucleic Acids Res. (IF 11.147) Pub Date : 2020-01-22
    Yang G, Chen Y, Wu J, et al.

    Nucleosomal histones are barriers to the DNA repair process particularly at DNA double-strand breaks (DSBs). However, the molecular mechanism by which these histone barriers are removed from the sites of DNA damage remains elusive. Here, we have generated a single specific inducible DSB in the cells and systematically examined the histone removal process at the DNA lesion. We found that histone removal occurred immediately following DNA damage and could extend up to a range of few kilobases from the lesion. To examine the molecular mechanism underlying DNA damage-induced histone removal, we screened histone modifications and found that histone ADP-ribosylation was associated with histone removal at DNA lesions. PARP inhibitor treatment suppressed the immediate histone eviction at DNA lesions. Moreover, we examined histone chaperones and found that the FACT complex recognized ADP-ribosylated histones and mediated the removal of histones in response to DNA damage. Taken together, our results reveal a pathway that regulates early histone barrier removal at DNA lesions. It may also explain the mechanism by which PARP inhibitor regulates early DNA damage repair.

    更新日期:2020-01-23
  • Correlation between equi-partition of aminoacyl-tRNA synthetases and amino-acid biosynthesis pathways
    Nucleic Acids Res. (IF 11.147) Pub Date : 2020-01-22
    Takénaka A, Moras D.

    The partition of aminoacyl-tRNA synthetases (aaRSs) into two classes of equal size and the correlated amino acid distribution is a puzzling still unexplained observation. We propose that the time scale of the amino-acid synthesis, assumed to be proportional to the number of reaction steps (NE) involved in the biosynthesis pathway, is one of the parameters that controlled the timescale of aaRSs appearance. Because all pathways are branched at fructose-6-phosphate on the metabolic pathway, this product is defined as the common origin for the NE comparison. For each amino-acid, the NE value, counted from the origin to the final product, provides a timescale for the pathways to be established. An archeological approach based on NE reveals that aaRSs of the two classes are generated in pair along this timescale. The results support the coevolution theory for the origin of the genetic code with an earlier appearance of class II aaRSs.

    更新日期:2020-01-23
  • Application of N-palmitoyl-O-phosphocholineserine for diagnosis and assessment of response to treatment in Niemann-Pick type C disease
    Mol. Genet. Metab. (IF 3.610) Pub Date : 2020-01-22
    Rohini Sidhu; Pamela Kell; Dennis J. Dietzen; Nicole Y. Farhat; An Ngoc Dang Do; Forbes D. Porter; Elizabeth Berry-Kravis; Charles H. Vite; Janine Reunert; Thorsten Marquardt; Roberto Giugliani; Charles M. Lourenço; Olaf Bodamer; Raymond Y. Wang; Ellen Plummer; Jean E. Schaffer; Daniel S. Ory; Xuntian Jiang

    Niemann-Pick type C (NPC) disease is a rare lysosomal storage disorder caused by mutations in either the NPC1 or the NPC2 gene. A new class of lipids, N-acyl-O-phosphocholineserines were recently identified as NPC biomarkers. The most abundant species in this class of lipid, N-palmitoyl-O-phosphocholineserine (PPCS), was evaluated for diagnosis of NPC disease and treatment efficacy assessment with 2-hydroxypropyl-β-cyclodextrin (HPβCD) in NPC. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) methods were developed and validated to measure PPCS in human plasma and cerebrospinal fluid (CSF). A cutoff of 248 ng/mL in plasma provided a sensitivity of 100.0% and specificity of 96.6% in identifying NPC1 patients from control and NPC1 carrier subjects. PPCS was significantly elevated in CSF from NPC1 patients, and CSF PPCS levels were significantly correlated with NPC neurological disease severity scores. Plasma and CSF PPCS did not change significantly in response to intrathetical (IT) HPβCD treatment. In an intravenous (IV) HPβCD trial, plasma PPCS in all patients was significantly reduced. These results demonstrate that plasma PPCS was able to diagnose NPC1 patients with high sensitivity and specificity, and to evaluate the peripheral treatment efficacy of IV HPβCD treatment.

    更新日期:2020-01-22
  • Therapeutic Germline Editing: Sense and Sensibility
    Trends Genet. (IF 10.627) Pub Date : 2020-01-22
    Eli Y. Adashi; I. Glenn Cohen

    Safe and effective heritable editing of the human genome is years away from the clinic because of formidable technical, statutory, regulatory, and societal challenges. In particular, we note the fledgling state of the science, the imperatives of editing efficiency, specificity, and uniformity, and the extant legal roadblock.

    更新日期:2020-01-22
  • 5-Hydroxymethylcytosine signatures in circulating cell-free DNA as diagnostic and predictive biomarkers for coronary artery disease
    Clin. Epigenet. (IF 5.496) Pub Date : 2020-01-21
    Chaoran Dong; Jiemei Chen; Jilin Zheng; Yiming Liang; Tao Yu; Yupeng Liu; Feng Gao; Jie Long; Hangyu Chen; Qianhui Zhu; Zilong He; Songnian Hu; Chuan He; Jian Lin; Yida Tang; Haibo Zhu

    The 5-hydroxymethylcytosine (5hmC) DNA modification is an epigenetic marker involved in a range of biological processes. Its function has been studied extensively in tumors, neurodegenerative diseases, and atherosclerosis. Studies have reported that 5hmC modification is closely related to the phenotype transformation of vascular smooth muscle cells and endothelial dysfunction. However, its role in coronary artery disease (CAD) has not been fully studied. To investigate whether 5hmC modification correlates with CAD pathogenesis and whether 5hmC can be used as a biomarker, we used a low-input whole-genome sequencing technology based on selective chemical capture (hmC-Seal) to firstly generate the 5hmC profiles in the circulating cell-free DNA(cfDNA) of CAD patients, including stable coronary artery disease (sCAD) patients and acute myocardial infarction (AMI) patients. We detected a significant difference of 5hmC enrichment in gene bodies from CAD patients compared with normal coronary artery (NCA) individuals. Our results showed that CAD patients can be well separated from NCA individuals by 5hmC markers. The prediction performance of the model established by differentially regulated 5hmc modified genes were superior to common clinical indicators for the diagnosis of CAD (AUC = 0.93) and sCAD (AUC = 0.93). Specially, we found that 5hmC markers in cfDNA showed prediction potential for AMI (AUC = 0.95), which was superior to that of cardiac troponin I, muscle/brain creatine kinase, and myoglobin. Our results suggest that 5hmC markers derived from cfDNA can serve as effective epigenetic biomarkers for minimally noninvasive diagnosis and prediction of CAD.

    更新日期:2020-01-22
  • Comprehensive molecular characterization of inhibitors of apoptosis proteins (IAPs) for therapeutic targeting in cancer
    BMC Med. Genomics (IF 2.568) Pub Date : 2020-01-21
    Jianfeng Liang; Wanni Zhao; Pan Tong; Ping Li; Yuanli Zhao; Hua Li; Jun Liang

    Inhibitors of apoptosis proteins (IAPs) are a family of antiapoptotic proteins modulating cell cycle, signal transduction and apoptosis. Dysregulated IAPs have been reported to contribute to tumor progression and chemoresistance in various cancers. However, existing studies were sporadic and only focus on one specific cancer with one particular gene in the IAPs family. A systematic investigation on the co-expression pattern, regulation frameworks on various pathways, prognostic utility on patient outcomes, and predictive value on drug sensitivity among all the IAPs across multiple tumor types was lacking. Leveraging The Cancer Genome Atlas data with comprehensive genomic characterizations on 9714 patients across 32 tumor types and the Genomics of Drug Sensitivity in Cancer data with both genomic characterizations and drug sensitivity data on > 1000 cell lines, we investigated the co-expression pattern of IAPs, their regulations of apoptosis as well as other pathways and clinical relevance of IAPs for therapeutics development. We discovered diverse expression pattern among IAPs, varied spectrum of apoptosis regulations through IAPs and extensive regulations beyond apoptosis involving immune response, cell cycle, gene expression and DNA damage repair. Importantly, IAPs were strong prognostic factors for patient survival and tumor stage in several tumor types including brain, liver, kidney, breast and lung cancer. Further, several IAPs were found to be predictive of sensitivity to BCL-2 inhibitors (BIRC3, BIRC5, BIRC6, and BIRC7) as well as RIPK1 inhibitors (BIRC3 and BIRC6). Together, our work revealed the landscape of regulations, prognostic utilities and therapeutic relevance of IAPs across multiple tumor types.

    更新日期:2020-01-22
  • A case report of Proteus syndrome (PS)
    BMC Med. Genet. (IF 1.74) Pub Date : 2020-01-21
    Xiaoyun Zeng; Xiaoming Wen; Xinxin Liang; Lina Wang; Lingling Xu

    Proteus syndrome (PS) is an extremely rare disease characterized by excessive chimeric growth of cells, and progressive and irregular asymmetrical hyperplasia. Herein, a PS case with atypical clinical features and syndromes was reported, to improve the understanding of the diagnosis and treatment of the disease. The case was a 3-year-and-11-month-old male child. He was admitted due to a primary diagnosis of McCune-Albright syndrome. After admission, the lesion samples from the milk coffee spots, and nodular thickening skin at hands and feet were subjected to genetic screening. Genetic testing results confirmed the diagnosis of PS. Based on the clinical manifestations, laboratory tests, imaging data, and literature reviewing, the etiology, diagnosis, treatment and prognosis of PS have been analyzed and discussed.

    更新日期:2020-01-22
  • Integrated genome-wide investigations of the housefly, a global vector of diseases reveal unique dispersal patterns and bacterial communities across farms
    BMC Genomics (IF 3.501) Pub Date : 2020-01-21
    Simon Bahrndorff; Aritz Ruiz-González; Nadieh de Jonge; Jeppe Lund Nielsen; Henrik Skovgård; Cino Pertoldi

    Houseflies (Musca domestica L.) live in intimate association with numerous microorganisms and is a vector of human pathogens. In temperate areas, houseflies will overwinter in environments constructed by humans and recolonize surrounding areas in early summer. However, the dispersal patterns and associated bacteria across season and location are unclear. We used genotyping-by-sequencing (GBS) for the simultaneous identification and genotyping of thousands of Single Nucleotide Polymorphisms (SNPs) to establish dispersal patterns of houseflies across farms. Secondly, we used 16S rRNA gene amplicon sequencing to establish the variation and association between bacterial communities and the housefly across farms. Using GBS we identified 18,000 SNPs across 400 individuals sampled within and between 11 dairy farms in Denmark. There was evidence for sub-structuring of Danish housefly populations and with genetic structure that differed across season and sex. Further, there was a strong isolation by distance (IBD) effect, but with large variation suggesting that other hidden geographic barriers are important. Large individual variations were observed in the community structure of the microbiome and it was found to be dependent on location, sex, and collection time. Furthermore, the relative prevalence of putative pathogens was highly dependent on location and collection time. We were able to identify SNPs for the determination of the spatiotemporal housefly genetic structure, and to establish the variation and association between bacterial communities and the housefly across farms using novel next-generation sequencing (NGS) techniques. These results are important for disease prevention given the fine-scale population structure and IBD for the housefly, and that individual houseflies carry location specific bacteria including putative pathogens.

    更新日期:2020-01-22
  • CRISPR/Cas9-mediated precise genome modification by a long ssDNA template in zebrafish
    BMC Genomics (IF 3.501) Pub Date : 2020-01-21
    Haipeng Bai; Lijun Liu; Ke An; Xiaochan Lu; Michael Harrison; Yanqiu Zhao; Ruibin Yan; Zhijie Lu; Song Li; Shuo Lin; Fang Liang; Wei Qin

    Gene targeting by homology-directed repair (HDR) can precisely edit the genome and is a versatile tool for biomedical research. However, the efficiency of HDR-based modification is still low in many model organisms including zebrafish. Recently, long single-stranded DNA (lssDNA) molecules have been developed as efficient alternative donor templates to mediate HDR for the generation of conditional mouse alleles. Here we report a method, zLOST (zebrafish long single-stranded DNA template), which utilises HDR with a long single-stranded DNA template to produce more efficient and precise mutations in zebrafish. The efficiency of knock-ins was assessed by phenotypic rescue at the tyrosinase (tyr) locus and confirmed by sequencing. zLOST was found to be a successful optimised rescue strategy: using zLOST containing a tyr repair site, we restored pigmentation in at least one melanocyte in close to 98% of albino tyr25del/25del embryos, although more than half of the larvae had only a small number of pigmented cells. Sequence analysis showed that there was precise HDR dependent repair of the tyr locus in these rescued pigmented embryos. Furthermore, quantification of zLOST knock-in efficiency at the rps14, nop56 and th loci by next generation sequencing demonstrated that zLOST showed a clear improvement. We utilised the HDR efficiency of zLOST to precisely model specific human disease mutations in zebrafish with ease. Finally, we determined that this method can achieve a germline transmission rate of up to 31.8%. In summary, these results show that zLOST is a useful method of zebrafish genome editing, particularly for generating desired mutations by targeted DNA knock-in through HDR.

    更新日期:2020-01-22
  • Insights into high-pressure acclimation: comparative transcriptome analysis of sea cucumber Apostichopus japonicus at different hydrostatic pressure exposures
    BMC Genomics (IF 3.501) Pub Date : 2020-01-21
    Linying Liang; Jiawei Chen; Yanan Li; Haibin Zhang

    Global climate change is predicted to force the bathymetric migrations of shallow-water marine invertebrates. Hydrostatic pressure is proposed to be one of the major environmental factors limiting the vertical distribution of extant marine invertebrates. However, the high-pressure acclimation mechanisms are not yet fully understood. In this study, the shallow-water sea cucumber Apostichopus japonicus was incubated at 15 and 25 MPa at 15 °C for 24 h, and subjected to comparative transcriptome analysis. Nine samples were sequenced and assembled into 553,507 unigenes with a N50 length of 1204 bp. Three groups of differentially expressed genes (DEGs) were identified according to their gene expression patterns, including 38 linearly related DEGs whose expression patterns were linearly correlated with hydrostatic pressure, 244 pressure-sensitive DEGs which were up-regulated at both 15 and 25 MPa, and 257 high-pressure-induced DEGs which were up-regulated at 25 MPa but not up-regulated at 15 MPa. Our results indicated that the genes and biological processes involving high-pressure acclimation are similar to those related to deep-sea adaptation. In addition to representative biological processes involving deep-sea adaptation (such as antioxidation, immune response, genetic information processing, and DNA repair), two biological processes, namely, ubiquitination and endocytosis, which can collaborate with each other and regulate the elimination of misfolded proteins, also responded to high-pressure exposure in our study. The up-regulation of these two processes suggested that high hydrostatic pressure would lead to the increase of misfolded protein synthesis, and this may result in the death of shallow-water sea cucumber under high-pressure exposure.

    更新日期:2020-01-22
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