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Experimentally evolving Drosophila erecta populations may fail to establish an effective piRNA based host defense against invading P-elements Genome Res. (IF 7.0) Pub Date : 2024-03-15 Divya Selvaraju, Filip Wierzbicki, Robert Kofler
To prevent the spread of transposable elements (TEs) hosts have developed sophisticated defense mechanisms. In mammals and invertebrates, a major defense mechanism operates through PIWI-interacting RNAs (piRNAs). To investigate the establishment of the host defence we introduced the P-element, one of the most widely studied eukaryotic transposons, into naive lines of Drosophila erecta. We monitored
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Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance Nat. Genet. (IF 30.8) Pub Date : 2024-03-15 Peng-Fei Ma, Yun-Long Liu, Cen Guo, Guihua Jin, Zhen-Hua Guo, Ling Mao, Yi-Zhou Yang, Liang-Zhong Niu, Yu-Jiao Wang, Lynn G. Clark, Elizabeth A. Kellogg, Zu-Chang Xu, Xia-Ying Ye, Jing-Xia Liu, Meng-Yuan Zhou, Yan Luo, Yang Yang, Douglas E. Soltis, Jeffrey L. Bennetzen, Pamela S. Soltis, De-Zhu Li
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MYC activates transcriptional enhancers to drive cancer progression Nat. Genet. (IF 30.8) Pub Date : 2024-03-13
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Multiplex DNA fluorescence in situ hybridization to analyze maternal vs. paternal C. elegans chromosomes Genome Biol. (IF 12.3) Pub Date : 2024-03-14 Silvia Gutnik, Jia Emil You, Ahilya N. Sawh, Aude Andriollo, Susan E. Mango
Recent advances in microscopy have enabled studying chromosome organization at the single-molecule level, yet little is known about inherited chromosome organization. Here we adapt single-molecule chromosome tracing to distinguish two C. elegans strains (N2 and HI) and find that while their organization is similar, the N2 chromosome influences the folding parameters of the HI chromosome, in particular
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Pan-cellular organelles and suborganelles—from common functions to cellular diversity? Genes Dev. (IF 10.5) Pub Date : 2024-03-14 Rico Schieweck, Magdalena Götz
Cell diversification is at the base of increasing multicellular organism complexity in phylogeny achieved during ontogeny. However, there are also functions common to all cells, such as cell division, cell migration, translation, endocytosis, exocytosis, etc. Here we revisit the organelles involved in such common functions, reviewing recent evidence of unexpected differences of proteins at these organelles
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A serine metabolic enzyme is flexing its muscle to help repair skeletal muscle Genes Dev. (IF 10.5) Pub Date : 2024-03-14 Benjámin R. Baráth, Laszlo Nagy
Metabolic reprogramming of stem cells is a targetable pathway to control regeneration. Activation of stem cells results in down-regulation of oxidative phosphorylation (OXPHOS) and fatty acid oxidation (FAO) and turns on glycolysis to provide fuel for proliferation and specific signaling events. How cell type-specific events are regulated is unknown. In this issue of Genes & Development Ciuffoli and
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Substrate specificity of Mycobacterium tuberculosis tRNA terminal nucleotidyltransferase toxin MenT3 Nucleic Acids Res. (IF 14.9) Pub Date : 2024-03-15 Jun Liu, Yuka Yashiro, Yuriko Sakaguchi, Tsutomu Suzuki, Kozo Tomita
Mycobacterium tuberculosis transfer RNA (tRNA) terminal nucleotidyltransferase toxin, MenT3, incorporates nucleotides at the 3′-CCA end of tRNAs, blocking their aminoacylation and inhibiting protein synthesis. Here, we show that MenT3 most effectively adds CMPs to the 3′-CCA end of tRNA. The crystal structure of MenT3 in complex with CTP reveals a CTP-specific nucleotide-binding pocket. The 4-NH2 and
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Competition between sites of meiotic recombination in snakes Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-03-12 Kirsty Minton
A study in Science reports that corn snakes use both PRDM9 and promoter-like features to direct meiotic recombination, indicating that these are not mutually exclusive.
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Genetic contribution to heterogeneity in type 2 diabetes Nat. Genet. (IF 30.8) Pub Date : 2024-03-13 Wei Li
Genome-wide association studies of type 2 diabetes (T2D) have led to the identification of hundreds of risk loci. Through the Type 2 Diabetes Global Genomics Initiative, Suzuki et al. performed a multi-ancestry meta-analysis of T2D in 2,535,601 individuals (428,452 cases of T2D) from diverse ancestry groups: European (60.3%), East Asian (19.8%), admixed African American (10.5%), admixed Hispanic (5
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How transposable elements are spliced out Nat. Genet. (IF 30.8) Pub Date : 2024-03-13 Chiara Anania
A large part of the human genome consists of transposable elements (TEs). Most TEs do not contribute to mature transcripts, which suggests that cells might have evolved a strategy to skip TE sequences by splicing them as introns. In a study published in Nature, Ilık et al. studied 33 RNA-binding proteins involved in splicing, and found that SAFB, hnRNPC and DHX9 associated with sense LINE1 elements
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Implicating XIST in sex-biased autoimmunity Nat. Genet. (IF 30.8) Pub Date : 2024-03-13 Kyle Vogan
Autoimmune diseases exhibit a strong female sex bias in incidence, but the mechanistic basis for this differential susceptibility is poorly understood. Given previous evidence that X chromosome dosage, and specifically the long non-coding RNA XIST produced from the inactive X chromosome and its associated proteins, could be key factors underlying the increased autoimmune disease risk in females and
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Transcription factor binding site affinity and the link to phenotype Nat. Genet. (IF 30.8) Pub Date : 2024-03-13 Michael Fletcher
Genetic variation, such as single-nucleotide variants (SNVs), can alter transcription factor binding and thus phenotypes. However, the exact mechanistic bases of this process remain poorly understood. Lim et al. examine the classic model enhancer, ZRS, which regulates expression of SHH during limb development and contains SNVs that are causal for polydactyly. Using protein-binding microarray data,
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Guidance on use of race, ethnicity, and geographic origin as proxies for genetic ancestry groups in biomedical publications Nat. Genet. (IF 30.8) Pub Date : 2024-03-13 W. Gregory Feero, Robert D. Steiner, Anne Slavotinek, Tiago Faial, Michael J. Bamshad, Jehannine Austin, Bruce R. Korf, Annette Flanagin, Kirsten Bibbins-Domingo
In March 2023, the National Academies of Sciences, Engineering, and Medicine (NASEM) released a consensus study report titled Using Population Descriptors in Genetics and Genomics Research1. Sponsored by the US National Institutes of Health, the report is more than a discussion of the use of terminology; the authors of the NASEM report suggest a tectonic shift away from current models that use race
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Multi-omics provide insights into the regulation of DNA methylation in pear fruit metabolism Genome Biol. (IF 12.3) Pub Date : 2024-03-14 Chao Gu, Mao-Song Pei, Zhi-Hua Guo, Lei Wu, Kai-Jie Qi, Xue-Ping Wang, Hong Liu, Zhongchi Liu, Zhaobo Lang, Shaoling Zhang
Extensive research has been conducted on fruit development in crops, but the metabolic regulatory networks underlying perennial fruit trees remain poorly understood. To address this knowledge gap, we conduct a comprehensive analysis of the metabolome, proteome, transcriptome, DNA methylome, and small RNAome profiles of pear fruit flesh at 11 developing stages, spanning from fruitlet to ripening. Here
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Haplotype-resolved 3D chromatin architecture of the hybrid pig Genome Res. (IF 7.0) Pub Date : 2024-03-13 Yu Lin, Jing Li, Yiren Gu, Long Jin, Jingyi Bai, Jiaman Zhang, Yujie Wang, Pengliang Liu, Keren Long, Mengnan He, Diyan Li, Can Liu, Ziyin Han, Yu Zhang, Xiaokai Li, Bo Zeng, Lu Lu, Fanli Kong, Ying Sun, Yongliang Fan, Xun Wang, Tao Wang, An'an Jiang, Jideng Ma, Linyuan Shen, Li Zhu, Yanzhi Jiang, Guoqing Tang, Xiaolan Fan, Qingyou Liu, Hua Li, Jinyong Wang, Li Chen, Liangpeng Ge, Xuewei Li, Qianzi
In diploid mammals, allele-specific three-dimensional (3D) genome architecture may lead to imbalanced gene expression. Through ultradeep in situ Hi-C sequencing of three representative somatic tissues (liver, skeletal muscle, and brain) from hybrid pigs generated by reciprocal crosses of phenotypically and physiologically divergent Berkshire and Tibetan pigs, we uncover extensive chromatin reorganization
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Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes Genome Res. (IF 7.0) Pub Date : 2024-03-13 Ting-Ying Wu, Ya-Ru Li, Kai-Jyun Chang, Jhen-Cheng Fang, Daisuke Urano, Ming-Jung Liu
mRNA translation relies on identifying translation initiation sites (TISs) in mRNAs. Alternative TISs are prevalent across plant transcriptomes, but the mechanisms for their recognition are unclear. Using ribosome profiling and machine learning, we developed models for predicting alternative TISs in the tomato (Solanum lycopersicum). Distinct feature sets were predictive of AUG and nonAUG TISs in 5′
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Major impacts of widespread structural variation on sorghum Genome Res. (IF 7.0) Pub Date : 2024-03-13 Zhihai Zhang, Joao Paulo Gomes Viana, Bosen Zhang, Kimberly K.O. Walden, Hans Müller Paul, Stephen P. Moose, Geoffrey P. Morris, Chris Daum, Kerrie W. Barry, Nadia Shakoor, Matthew E. Hudson
Genetic diversity is critical to crop breeding and improvement, and dissection of the genomic variation underlying agronomic traits can both assist breeding and give insight into basic biological mechanisms. Although recent genome analyses in plants reveal many structural variants (SVs), most current studies of crop genetic variation are dominated by single-nucleotide polymorphisms (SNPs). The extent
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The structure, function, and evolution of plant centromeres Genome Res. (IF 7.0) Pub Date : 2024-03-14 Matthew Naish, Ian R. Henderson
Centromeres are essential regions of eukaryotic chromosomes responsible for the formation of kinetochore complexes, which connect to spindle microtubules during cell division. Notably, although centromeres maintain a conserved function in chromosome segregation, the underlying DNA sequences are diverse both within and between species and are predominantly repetitive in nature. The repeat content of
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ADNP modulates SINE B2-derived CTCF-binding sites during blastocyst formation in mice Genes Dev. (IF 10.5) Pub Date : 2024-03-13 Wen Wang, Rui Gao, Dongxu Yang, Mingli Ma, Ruge Zang, Xiangxiu Wang, Chuan Chen, Xiaochen Kou, Yanhong Zhao, Jiayu Chen, Xuelian Liu, Jiaxu Lu, Ben Xu, Juntao Liu, Yanxin Huang, Chaoqun Chen, Hong Wang, Shaorong Gao, Yong Zhang, Yawei Gao
CTCF is crucial for chromatin structure and transcription regulation in early embryonic development. However, the kinetics of CTCF chromatin occupation in preimplantation embryos have remained unclear. In this study, we used CUT&RUN technology to investigate CTCF occupancy in mouse preimplantation development. Our findings revealed that CTCF begins binding to the genome prior to zygotic genome activation
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Coordination of histone chaperones for parental histone segregation and epigenetic inheritance Genes Dev. (IF 10.5) Pub Date : 2024-03-13 Yimeng Fang, Xu Hua, Chun-Min Shan, Takenori Toda, Feng Qiao, Zhiguo Zhang, Songtao Jia
Chromatin-based epigenetic memory relies on the accurate distribution of parental histone H3–H4 tetramers to newly replicated DNA strands. Mcm2, a subunit of the replicative helicase, and Dpb3/4, subunits of DNA polymerase ε, govern parental histone H3–H4 deposition to the lagging and leading strands, respectively. However, their contribution to epigenetic inheritance remains controversial. Here, using
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Dynamic DNA N6-adenine methylation (6mA) governs the encystment process, showcased in the unicellular eukaryote Pseudocohnilembus persalinus Genome Res. (IF 7.0) Pub Date : 2024-03-12 Yongqiang Liu, Junhua Niu, Fei Ye, Therese Solberg, Borong Lu, Chundi Wang, Mariusz Nowacki, Shan Gao
The formation of resting cysts commonly found in unicellular eukaryotes is a complex and highly regulated survival strategy against environmental stress that involves drastic physiological and biochemical changes. Although most studies have focused on the morphology and structure of cysts, little is known about the molecular mechanisms that control this process. Recent studies indicate that DNA N6-adenine
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RNA Pol II–dependent transcription efficiency fine-tunes A-to-I editing levels Genome Res. (IF 7.0) Pub Date : 2024-03-12 Brigitta Szabo, Therese C. Mandl, Bernhard Woldrich, Gregor Diensthuber, David Martin, Michael F. Jantsch, Konstantin Licht
A-to-I RNA editing is a widespread epitranscriptomic phenomenon leading to the conversion of adenosines to inosines, which are primarily interpreted as guanosines by cellular machines. Consequently, A-to-I editing can alter splicing or lead to recoding of transcripts. As misregulation of editing can cause a variety of human diseases, A-to-I editing requires tight regulation of the extent of deamination
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Molecular mechanism of the one-component regulator RccR on bacterial metabolism and virulence Nucleic Acids Res. (IF 14.9) Pub Date : 2024-03-13 Yibo Zhu, Xingyu Mou, Yingjie Song, Qianqian Zhang, Bo Sun, Huanxiang Liu, Hong Tang, Rui Bao
The regulation of carbon metabolism and virulence is critical for the rapid adaptation of pathogenic bacteria to host conditions. In Pseudomonas aeruginosa, RccR is a transcriptional regulator of genes involved in primary carbon metabolism and is associated with bacterial resistance and virulence, although the exact mechanism is unclear. Our study demonstrates that PaRccR is a direct repressor of the
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Catalytic residues of microRNA Argonautes play a modest role in microRNA star strand destabilization in C. elegans Nucleic Acids Res. (IF 14.9) Pub Date : 2024-03-13 Kasuen Kotagama, Acadia L Grimme, Leah Braviner, Bing Yang, Rima M Sakhawala, Guoyun Yu, Lars Kristian Benner, Leemor Joshua-Tor, Katherine McJunkin
Many microRNA (miRNA)-guided Argonaute proteins can cleave RNA (‘slicing’), even though miRNA-mediated target repression is generally cleavage-independent. Here we use Caenorhabditis elegans to examine the role of catalytic residues of miRNA Argonautes in organismal development. In contrast to previous work, mutations in presumed catalytic residues did not interfere with development when introduced
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Comprehensive transcriptome analysis reveals altered mRNA splicing and post-transcriptional changes in the aged mouse brain Nucleic Acids Res. (IF 14.9) Pub Date : 2024-03-13 Nisha Hemandhar Kumar, Verena Kluever, Emanuel Barth, Sebastian Krautwurst, Mattia Furlan, Mattia Pelizzola, Manja Marz, Eugenio F Fornasiero
A comprehensive understanding of molecular changes during brain aging is essential to mitigate cognitive decline and delay neurodegenerative diseases. The interpretation of mRNA alterations during brain aging is influenced by the health and age of the animal cohorts studied. Here, we carefully consider these factors and provide an in-depth investigation of mRNA splicing and dynamics in the aging mouse
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Structural basis of how MGME1 processes DNA 5′ ends to maintain mitochondrial genome integrity Nucleic Acids Res. (IF 14.9) Pub Date : 2024-03-13 Eric Y C Mao, Han-Yi Yen, Chyuan-Chuan Wu
Mitochondrial genome maintenance exonuclease 1 (MGME1) helps to ensure mitochondrial DNA (mtDNA) integrity by serving as an ancillary 5′-exonuclease for DNA polymerase γ. Curiously, MGME1 exhibits unique bidirectionality in vitro, being capable of degrading DNA from either the 5′ or 3′ end. The structural basis of this bidirectionally and, particularly, how it processes DNA from the 5′ end to assist
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CRISPR antiphage defence mediated by the cyclic nucleotide-binding membrane protein Csx23 Nucleic Acids Res. (IF 14.9) Pub Date : 2024-03-13 Sabine Grüschow, Stuart McQuarrie, Katrin Ackermann, Stephen McMahon, Bela E Bode, Tracey M Gloster, Malcolm F White
CRISPR-Cas provides adaptive immunity in prokaryotes. Type III CRISPR systems detect invading RNA and activate the catalytic Cas10 subunit, which generates a range of nucleotide second messengers to signal infection. These molecules bind and activate a diverse range of effector proteins that provide immunity by degrading viral components and/or by disturbing key aspects of cellular metabolism to slow
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Tyrosine 1–phosphorylated RNA polymerase II transcribes PROMPTs to facilitate proximal promoter pausing and induce global transcriptional repression in response to DNA damage Genome Res. (IF 7.0) Pub Date : 2024-03-11 Kamal Ajit, Adele Alagia, Kaspar Burger, Monika Gullerova
DNA damage triggers a complex transcriptional response that involves both activation and repression of gene expression. In this study, we investigated global changes in transcription in response to ionizing irradiation (IR), which induces double-strand breaks in DNA. We used mNET-seq to profile nascent transcripts bound to different phosphorylated forms of the RNA polymerase II (RNA Pol II) C-terminal
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Short tandem repeats — how microsatellites became the currency of forensic genetics Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-03-11 Bruce Budowle, Antti Sajantila
Short tandem repeats (STRs), also known as microsatellites, are the primary markers of forensic genetics for developing investigative leads in criminal cases and humanitarian efforts. Their variation in length and sequence provides genetic information even in samples of low quantity and quality, enabling high resolution for identification and attribution purposes, and culminating in the development
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The regulatory landscape of chromatin accessibility Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-03-11 Henry Ertl
A study in Nature Genetics identifies many regulators of genome-wide chromatin accessibility and then reports the mechanistic underpinnings for one of the identified transcription factors.
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Sequence composition changes in short tandem repeats: heterogeneity, detection, mechanisms and clinical implications Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-03-11 Indhu-Shree Rajan-Babu, Egor Dolzhenko, Michael A. Eberle, Jan M. Friedman
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Enhancer–promoter interactions become more instructive in the transition from cell-fate specification to tissue differentiation Nat. Genet. (IF 30.8) Pub Date : 2024-03-11 Tim Pollex, Adam Rabinowitz, Maria Cristina Gambetta, Raquel Marco-Ferreres, Rebecca R. Viales, Aleksander Jankowski, Christoph Schaub, Eileen E. M. Furlong
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A comparison of methods for detecting DNA methylation from long-read sequencing of human genomes Genome Biol. (IF 12.3) Pub Date : 2024-03-11 Brynja D. Sigurpalsdottir, Olafur A. Stefansson, Guillaume Holley, Doruk Beyter, Florian Zink, Marteinn Þ. Hardarson, Sverrir Þ. Sverrisson, Nina Kristinsdottir, Droplaug N. Magnusdottir, Olafur Þ. Magnusson, Daniel F. Gudbjartsson, Bjarni V. Halldorsson, Kari Stefansson
Long-read sequencing can enable the detection of base modifications, such as CpG methylation, in single molecules of DNA. The most commonly used methods for long-read sequencing are nanopore developed by Oxford Nanopore Technologies (ONT) and single molecule real-time (SMRT) sequencing developed by Pacific Bioscience (PacBio). In this study, we systematically compare the performance of CpG methylation
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Seven-chain adaptive immune receptor repertoire analysis in rheumatoid arthritis reveals novel features associated with disease and clinically relevant phenotypes Genome Biol. (IF 12.3) Pub Date : 2024-03-11 Adrià Aterido, María López-Lasanta, Francisco Blanco, Antonio Juan-Mas, María Luz García-Vivar, Alba Erra, Carolina Pérez-García, Simón Ángel Sánchez-Fernández, Raimon Sanmartí, Antonio Fernández-Nebro, Mercedes Alperi-López, Jesús Tornero, Ana María Ortiz, Carlos Marras Fernández-Cid, Núria Palau, Wenjing Pan, Miranda Byrne-Steele, Dmytro Starenki, Daniel Weber, Ivan Rodriguez-Nunez, Jian Han, Richard
In rheumatoid arthritis (RA), the activation of T and B cell clones specific for self-antigens leads to the chronic inflammation of the synovium. Here, we perform an in-depth quantitative analysis of the seven chains that comprise the adaptive immune receptor repertoire (AIRR) in RA. In comparison to controls, we show that RA patients have multiple and strong differences in the B cell receptor repertoire
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Liquid–liquid phase separation of H3K27me3 reader BP1 regulates transcriptional repression Genome Biol. (IF 12.3) Pub Date : 2024-03-11 Guangfei Tang, Haoxue Xia, Yufei Huang, Yuanwen Guo, Yun Chen, Zhonghua Ma, Wende Liu
Bromo-adjacent homology-plant homeodomain domain containing protein 1 (BP1) is a reader of histone post-translational modifications in fungi. BP1 recognizes trimethylation of lysine 27 in histone H3 (H3K27me3), an epigenetic hallmark of gene silencing. However, whether and how BP1 participates in transcriptional repression remains poorly understood. We report that BP1 forms phase-separated liquid condensates
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Prediction of metabolites associated with somatic mutations in cancers by using genome-scale metabolic models and mutation data Genome Biol. (IF 12.3) Pub Date : 2024-03-11 GaRyoung Lee, Sang Mi Lee, Sungyoung Lee, Chang Wook Jeong, Hyojin Song, Sang Yup Lee, Hongseok Yun, Youngil Koh, Hyun Uk Kim
Oncometabolites, often generated as a result of a gene mutation, show pro-oncogenic function when abnormally accumulated in cancer cells. Identification of such mutation-associated metabolites will facilitate developing treatment strategies for cancers, but is challenging due to the large number of metabolites in a cell and the presence of multiple genes associated with cancer development. Here we
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MYC activity at enhancers drives prognostic transcriptional programs through an epigenetic switch Nat. Genet. (IF 30.8) Pub Date : 2024-03-07 Simon T. Jakobsen, Rikke A. M. Jensen, Maria S. Madsen, Tina Ravnsborg, Christian S. Vaagenso, Majken S. Siersbæk, Hjorleifur Einarsson, Robin Andersson, Ole N. Jensen, Rasmus Siersbæk
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Joint analysis of mutational and transcriptional landscapes in human cancer reveals key perturbations during cancer evolution Genome Biol. (IF 12.3) Pub Date : 2024-03-08 Jae-Won Cho, Jingyi Cao, Martin Hemberg
Tumors are able to acquire new capabilities, including traits such as drug resistance and metastasis that are associated with unfavorable clinical outcomes. Single-cell technologies have made it possible to study both mutational and transcriptomic profiles, but as most studies have been conducted on model systems, little is known about cancer evolution in human patients. Hence, a better understanding
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A maternal-effect Padi6 variant causes nuclear and cytoplasmic abnormalities in oocytes, as well as failure of epigenetic reprogramming and zygotic genome activation in embryos Genes Dev. (IF 10.5) Pub Date : 2024-03-07 Carlo Giaccari, Francesco Cecere, Lucia Argenziano, Angela Pagano, Antonio Galvao, Dario Acampora, Gianna Rossi, Bruno Hay Mele, Basilia Acurzio, Scott Coonrod, Maria Vittoria Cubellis, Flavia Cerrato, Simon Andrews, Sandra Cecconi, Gavin Kelsey, Andrea Riccio
Maternal inactivation of genes encoding components of the subcortical maternal complex (SCMC) and its associated member, PADI6, generally results in early embryo lethality. In humans, SCMC gene variants were found in the healthy mothers of children affected by multilocus imprinting disturbances (MLID). However, how the SCMC controls the DNA methylation required to regulate imprinting remains poorly
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Psat1-generated α-ketoglutarate and glutamine promote muscle stem cell activation and regeneration Genes Dev. (IF 10.5) Pub Date : 2024-03-07 Veronica Ciuffoli, Xuesong Feng, Kan Jiang, Natalia Acevedo-Luna, Kyung Dae Ko, A. Hong Jun Wang, Giulia Riparini, Mamduh Khateb, Brian Glancy, Stefania Dell'Orso, Vittorio Sartorelli
By satisfying bioenergetic demands, generating biomass, and providing metabolites serving as cofactors for chromatin modifiers, metabolism regulates adult stem cell biology. Here, we report that a branch of glycolysis, the serine biosynthesis pathway (SBP), is activated in regenerating muscle stem cells (MuSCs). Gene inactivation and metabolomics revealed that Psat1, one of the three SBP enzymes, controls
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Genetics of chronic respiratory disease Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-03-06 Ian Sayers, Catherine John, Jing Chen, Ian P. Hall
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Improved identification of cancer mutational processes Nat. Genet. (IF 30.8) Pub Date : 2024-03-07 Tom L. Kaufmann, Roland F. Schwarz
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DNA fragility at topologically associated domain boundaries is promoted by alternative DNA secondary structure and topoisomerase II activity Nucleic Acids Res. (IF 14.9) Pub Date : 2024-03-07 Heather M Raimer Young, Pei-Chi Hou, Anna R Bartosik, Naomi D Atkin, Lixin Wang, Zhenjia Wang, Aakrosh Ratan, Chongzhi Zang, Yuh-Hwa Wang
CCCTC-binding factor (CTCF) binding sites are hotspots of genome instability. Although many factors have been associated with CTCF binding site fragility, no study has integrated all fragility-related factors to understand the mechanism(s) of how they work together. Using an unbiased, genome-wide approach, we found that DNA double-strand breaks (DSBs) are enriched at strong, but not weak, CTCF binding
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Determinant of m6A regional preference by transcriptional dynamics Nucleic Acids Res. (IF 14.9) Pub Date : 2024-03-07 Yalan Wang, Shen Wang, Zhen Meng, Xiao-Min Liu, Yuanhui Mao
N6-Methyladenosine (m6A) is the most abundant chemical modification occurring on eukaryotic mRNAs, and has been reported to be involved in almost all stages of mRNA metabolism. The distribution of m6A sites is notably asymmetric along mRNAs, with a strong preference toward the 3′ terminus of the transcript. How m6A regional preference is shaped remains incompletely understood. In this study, by performing
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WSB1/2 target chromatin-bound lysine-methylated RelA for proteasomal degradation and NF-κB termination Nucleic Acids Res. (IF 14.9) Pub Date : 2024-03-07 Jie Zhang, Yuanyuan Yu, Xiuqun Zou, Yaning Du, Qiankun Liang, Mengyao Gong, Yurong He, Junqi Luo, Dandan Wu, Xiaoli Jiang, Matt Sinclair, Emad Tajkhorshid, Hong-Zhuan Chen, Zhaoyuan Hou, Yuejuan Zheng, Lin-Feng Chen, Xiao-Dong Yang
Proteasome-mediated degradation of chromatin-bound NF-κB is critical in terminating the transcription of pro-inflammatory genes and can be triggered by Set9-mediated lysine methylation of the RelA subunit. However, the E3 ligase targeting methylated RelA remains unknown. Here, we find that two structurally similar substrate-recognizing components of Cullin-RING E3 ligases, WSB1 and WSB2, can recognize
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Identification of G-quadruplex-interacting proteins in living cells using an artificial G4-targeting biotin ligase Nucleic Acids Res. (IF 14.9) Pub Date : 2024-03-07 Ziang Lu, Shengjie Xie, Haomiao Su, Shaoqing Han, Haiyan Huang, Xiang Zhou
G-quadruplexes (G4s) are noncanonical nucleic acid structures pivotal to cellular processes and disease pathways. Deciphering G4-interacting proteins is imperative for unraveling G4’s biological significance. In this study, we developed a G4-targeting biotin ligase named G4PID, meticulously assessing its binding affinity and specificity both in vitro and in vivo. Capitalizing on G4PID, we devised a
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Implication of nucleotides near the 3′ end of 16S rRNA in guarding the translational reading frame Nucleic Acids Res. (IF 14.9) Pub Date : 2024-03-07 Alexandria Smart, Laura Lancaster, John Paul Donohue, Dustin Niblett, Harry F Noller
Loss of the translational reading frame leads to misincorporation and premature termination, which can have lethal consequences. Based on structural evidence that A1503 of 16S rRNA intercalates between specific mRNA bases, we tested the possibility that it plays a role in maintenance of the reading frame by constructing ribosomes with an abasic nucleotide at position 1503. This was done by specific
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Unveiling the expanding protein universe of life Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-02-29 Hajk-Georg Drost
In this Journal Club, Hajk-Georg Drost highlights a recent study by Pavlopoulos et al. that organizes proteins at tree-of-life scale using massively parallel graph-based clustering.
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Set2 regulates Ccp1 and Swc2 to ensure centromeric stability by retargeting CENP-A Nucleic Acids Res. (IF 14.9) Pub Date : 2024-03-05 Kim Kiat Lim, Ulysses Tsz Fung Lam, Ying Li, Yi Bing Zeng, Henry Yang, Ee Sin Chen
Precise positioning of the histone-H3 variant, CENP-A, ensures centromere stability and faithful chromosomal segregation. Mislocalization of CENP-A to extra-centromeric loci results in aneuploidy and compromised cell viability associated with formation of ectopic kinetochores. The mechanism that retargets mislocalized CENP-A back to the centromere is unclarified. We show here that the downregulation
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An alphacoronavirus polymerase structure reveals conserved replication factor functions Nucleic Acids Res. (IF 14.9) Pub Date : 2024-03-05 Thomas K Anderson, Peter J Hoferle, Kennan J Chojnacki, Kenneth W Lee, Joshua J Coon, Robert N Kirchdoerfer
Coronaviruses are a diverse subfamily of viruses containing pathogens of humans and animals. This subfamily of viruses replicates their RNA genomes using a core polymerase complex composed of viral non-structural proteins: nsp7, nsp8 and nsp12. Most of our understanding of coronavirus molecular biology comes from betacoronaviruses like SARS-CoV and SARS-CoV-2, the latter of which is the causative agent
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Origin, evolution, and maintenance of gene-strand bias in bacteria Nucleic Acids Res. (IF 14.9) Pub Date : 2024-03-05 Malhar Atre, Bharat Joshi, Jebin Babu, Shabduli Sawant, Shreya Sharma, T Sabari Sankar
Gene-strand bias is a characteristic feature of bacterial genome organization wherein genes are preferentially encoded on the leading strand of replication, promoting co-orientation of replication and transcription. This co-orientation bias has evolved to protect gene essentiality, expression, and genomic stability from the harmful effects of head-on replication-transcription collisions. However, the
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How ancient genes form animal body plans Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-03-04 Hajk-Georg Drost
Hajk-Georg Drost recalls a 2010 publication that used a phylotranscriptomic approach to estimate the age of genes that contribute to the developmental transcriptome across animal species and inspired a subsequent study on the embryonic hourglass in plants.
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Early-life ruminal microbiome-derived indole-3-carboxaldehyde and prostaglandin D2 are effective promoters of rumen development Genome Biol. (IF 12.3) Pub Date : 2024-03-04 Daming Sun, Gaorui Bian, Kai Zhang, Ning Liu, Yuyang Yin, Yuanlong Hou, Fei Xie, Weiyun Zhu, Shengyong Mao, Junhua Liu
The function of diverse ruminal microbes is tightly linked to rumen development and host physiology. The system of ruminal microbes is an excellent model to clarify the fundamental ecological relationships among complex nutrient–microbiome–host interactions. Here, neonatal lambs are introduced to different dietary regimes to investigate the influences of early-life crosstalk between nutrients and microbiome
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Three near-complete genome assemblies reveal substantial centromere dynamics from diploid to tetraploid in Brachypodium genus Genome Biol. (IF 12.3) Pub Date : 2024-03-04 Chuanye Chen, Siying Wu, Yishuang Sun, Jingwei Zhou, Yiqian Chen, Jing Zhang, James A. Birchler, Fangpu Han, Ning Yang, Handong Su
Centromeres are critical for maintaining genomic stability in eukaryotes, and their turnover shapes genome architectures and drives karyotype evolution. However, the co-evolution of centromeres from different species in allopolyploids over millions of years remains largely unknown. Here, we generate three near-complete genome assemblies, a tetraploid Brachypodium hybridum and its two diploid ancestors
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scAbsolute: measuring single-cell ploidy and replication status Genome Biol. (IF 12.3) Pub Date : 2024-03-04 Michael P. Schneider, Amy E. Cullen, Justina Pangonyte, Jason Skelton, Harvey Major, Elke Van Oudenhove, Maria J. Garcia, Blas Chaves Urbano, Anna M. Piskorz, James D. Brenton, Geoff Macintyre, Florian Markowetz
Cancer cells often exhibit DNA copy number aberrations and can vary widely in their ploidy. Correct estimation of the ploidy of single-cell genomes is paramount for downstream analysis. Based only on single-cell DNA sequencing information, scAbsolute achieves accurate and unbiased measurement of single-cell ploidy and replication status, including whole-genome duplications. We demonstrate scAbsolute’s
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Changes in cell-cycle rate drive diverging cell fates Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-03-01 Kate E. Galloway
Kate Galloway highlights a paper by Kueh et al., who showed that the cell cycle indirectly influences concentrations of the transcription factor PU.1 to stabilize cell-fate trajectories in mice.
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Targeting and engineering long non-coding RNAs for cancer therapy Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-02-29 Michela Coan, Simon Haefliger, Samir Ounzain, Rory Johnson
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Digenic inheritance involving a muscle-specific protein kinase and the giant titin protein causes a skeletal muscle myopathy Nat. Genet. (IF 30.8) Pub Date : 2024-03-01 Ana Töpf, Dan Cox, Irina T. Zaharieva, Valeria Di Leo, Jaakko Sarparanta, Per Harald Jonson, Ian M. Sealy, Andrei Smolnikov, Richard J. White, Anna Vihola, Marco Savarese, Munise Merteroglu, Neha Wali, Kristen M. Laricchia, Cristina Venturini, Bas Vroling, Sarah L. Stenton, Beryl B. Cummings, Elizabeth Harris, Chiara Marini-Bettolo, Jordi Diaz-Manera, Matt Henderson, Rita Barresi, Jennifer Duff, Eleina
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Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes Genome Res. (IF 7.0) Pub Date : 2024-03-01 Wenjuan Yu, Haohui Luo, Jinbao Yang, Shengchen Zhang, Heling Jiang, Xianjia Zhao, Xingqi Hui, Da Sun, Liang Li, Xiu-qing Wei, Stefano Lonardi, Weihua Pan
Pacific Biosciences (PacBio) HiFi sequencing technology generates long reads (>10 kbp) with very high accuracy (<0.01% sequencing error). Although several de novo assembly tools are available for HiFi reads, there are no comprehensive studies on the evaluation of these assemblers. We evaluated the performance of 11 de novo HiFi assemblers on (1) real data for three eukaryotic genomes; (2) 34 synthetic
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Conserved structures and dynamics in 5′-proximal regions of Betacoronavirus RNA genomes Nucleic Acids Res. (IF 14.9) Pub Date : 2024-03-01 Tales Rocha de Moura, Elżbieta Purta, Agata Bernat, Eva M Martín-Cuevas, Małgorzata Kurkowska, Eugene F Baulin, Sunandan Mukherjee, Jakub Nowak, Artur P Biela, Michał Rawski, Sebastian Glatt, Fernando Moreno-Herrero, Janusz M Bujnicki
Betacoronaviruses are a genus within the Coronaviridae family of RNA viruses. They are capable of infecting vertebrates and causing epidemics as well as global pandemics in humans. Mitigating the threat posed by Betacoronaviruses requires an understanding of their molecular diversity. The development of novel antivirals hinges on understanding the key regulatory elements within the viral RNA genomes