当前期刊: Genome Research Go to current issue    加入关注   
显示样式:        排序: IF: - GO 导出
我的关注
我的收藏
您暂时未登录!
登录
  • Corrigendum: Functional annotation of human long noncoding RNAs via molecular phenotyping
    Genome Res. (IF 11.093) Pub Date : 2020-09-01
    Jordan A. Ramilowski; Chi Wai Yip; Saumya Agrawal; Jen-Chien Chang; Yari Ciani; Ivan V. Kulakovskiy; Mickaël Mendez; Jasmine Li Ching Ooi; John F. Ouyang; Nick Parkinson; Andreas Petri; Leonie Roos; Jessica Severin; Kayoko Yasuzawa; Imad Abugessaisa; Altuna Akalin; Ivan V. Antonov; Erik Arner; Alessandro Bonetti; Hidemasa Bono; Beatrice Borsari; Frank Brombacher; Christopher J.F. Cameron; Carlo Vittorio

    Genome Research 30: 1060–1072 (2020)

    更新日期:2020-09-15
  • Corrigendum: 3′ UTR lengthening as a novel mechanism in regulating cellular senescence
    Genome Res. (IF 11.093) Pub Date : 2020-09-01
    Meng Chen; Guoliang Lyu; Miao Han; Hongbo Nie; Ting Shen; Wei Chen; Yichi Niu; Yifan Song; Xueping Li; Huan Li; Xinyu Chen; Ziyue Wang; Zheng Xia; Wei Li; Xiao-Li Tian; Chen Ding; Jun Gu; Yufang Zheng; Xinhua Liu; Jinfeng Hu; Gang Wei; Wei Tao; Ting Ni

    Genome Research 28: 285–294 (2018)

    更新日期:2020-09-15
  • The Nubeam reference-free approach to analyze metagenomic sequencing reads.
    Genome Res. (IF 11.093) Pub Date : 2020-09-01
    Hang Dai,Yongtao Guan

    We present Nubeam (nucleotide be a matrix) as a novel reference-free approach to analyze short sequencing reads. Nubeam represents nucleotides by matrices, transforms a read into a product of matrices, and assigns numbers to reads based on the product matrix. Nubeam capitalizes on the noncommutative property of matrix multiplication, such that different reads are assigned different numbers and similar

    更新日期:2020-09-15
  • High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing.
    Genome Res. (IF 11.093) Pub Date : 2020-09-01
    Nicholas D Sanderson,Jeremy Swann,Leanne Barker,James Kavanagh,Sarah Hoosdally,Derrick Crook,,Teresa L Street,David W Eyre

    The rise of antimicrobial-resistant Neisseria gonorrhoeae is a significant public health concern. Against this background, rapid culture-independent diagnostics may allow targeted treatment and prevent onward transmission. We have previously shown metagenomic sequencing of urine samples from men with urethral gonorrhea can recover near-complete N. gonorrhoeae genomes. However, disentangling the N.

    更新日期:2020-09-15
  • Molecular barcoding of native RNAs using nanopore sequencing and deep learning
    Genome Res. (IF 11.093) Pub Date : 2020-09-01
    Martin A. Smith; Tansel Ersavas; James M. Ferguson; Huanle Liu; Morghan C. Lucas; Oguzhan Begik; Lilly Bojarski; Kirston Barton; Eva Maria Novoa

    Nanopore sequencing enables direct measurement of RNA molecules without conversion to cDNA, thus opening the gates to a new era for RNA biology. However, the lack of molecular barcoding of direct RNA nanopore sequencing data sets severely affects the applicability of this technology to biological samples, where RNA availability is often limited. Here, we provide the first experimental protocol and

    更新日期:2020-09-15
  • Native molecule sequencing by nano-ID reveals synthesis and stability of RNA isoforms.
    Genome Res. (IF 11.093) Pub Date : 2020-09-01
    Kerstin C Maier,Saskia Gressel,Patrick Cramer,Björn Schwalb

    Eukaryotic genes often generate a variety of RNA isoforms that can lead to functionally distinct protein variants. The synthesis and stability of RNA isoforms is poorly characterized because current methods to quantify RNA metabolism use short-read sequencing and cannot detect RNA isoforms. Here we present nanopore sequencing–based isoform dynamics (nano-ID), a method that detects newly synthesized

    更新日期:2020-09-15
  • High-throughput single-cell functional elucidation of neurodevelopmental disease-associated genes reveals convergent mechanisms altering neuronal differentiation.
    Genome Res. (IF 11.093) Pub Date : 2020-09-01
    Matthew A Lalli,Denis Avey,Joseph D Dougherty,Jeffrey Milbrandt,Robi D Mitra

    The overwhelming success of exome- and genome-wide association studies in discovering thousands of disease-associated genes necessitates developing novel high-throughput functional genomics approaches to elucidate the molecular mechanisms of these genes. Here, we have coupled multiplexed repression of neurodevelopmental disease–associated genes to single-cell transcriptional profiling in differentiating

    更新日期:2020-09-15
  • Background-suppressed live visualization of genomic loci with an improved CRISPR system based on a split fluorophore.
    Genome Res. (IF 11.093) Pub Date : 2020-09-01
    Narendra Chaudhary,Si-Hyeong Nho,Hayoon Cho,Narangerel Gantumur,Jae Sun Ra,Kyungjae Myung,Hajin Kim

    The higher-order structural organization and dynamics of the chromosomes play a central role in gene regulation. To explore this structure–function relationship, it is necessary to directly visualize genomic elements in living cells. Genome imaging based on the CRISPR system is a powerful approach but has limited applicability due to background signals and nonspecific aggregation of fluorophores within

    更新日期:2020-09-15
  • HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads.
    Genome Res. (IF 11.093) Pub Date : 2020-09-01
    Sergey Nurk,Brian P Walenz,Arang Rhie,Mitchell R Vollger,Glennis A Logsdon,Robert Grothe,Karen H Miga,Evan E Eichler,Adam M Phillippy,Sergey Koren

    Complete and accurate genome assemblies form the basis of most downstream genomic analyses and are of critical importance. Recent genome assembly projects have relied on a combination of noisy long-read sequencing and accurate short-read sequencing, with the former offering greater assembly continuity and the latter providing higher consensus accuracy. The recently introduced Pacific Biosciences (PacBio)

    更新日期:2020-09-15
  • Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples.
    Genome Res. (IF 11.093) Pub Date : 2020-09-01
    Sergey Aganezov,Benjamin J Raphael

    Many cancer genomes are extensively rearranged with aberrant chromosomal karyotypes. Deriving these karyotypes from high-throughput DNA sequencing of bulk tumor samples is complicated because most tumors are a heterogeneous mixture of normal cells and subpopulations of cancer cells, or clones, that harbor distinct somatic mutations. We introduce a new algorithm, Reconstructing Cancer Karyotypes (RCK)

    更新日期:2020-09-15
  • Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing.
    Genome Res. (IF 11.093) Pub Date : 2020-09-01
    Sergey Aganezov,Sara Goodwin,Rachel M Sherman,Fritz J Sedlazeck,Gayatri Arun,Sonam Bhatia,Isac Lee,Melanie Kirsche,Robert Wappel,Melissa Kramer,Karen Kostroff,David L Spector,Winston Timp,W Richard McCombie,Michael C Schatz

    Improved identification of structural variants (SVs) in cancer can lead to more targeted and effective treatment options as well as advance our basic understanding of the disease and its progression. We performed whole-genome sequencing of the SKBR3 breast cancer cell line and patient-derived tumor and normal organoids from two breast cancer patients using Illumina/10x Genomics, Pacific Biosciences

    更新日期:2020-09-15
  • Long-read sequencing for non-small-cell lung cancer genomes.
    Genome Res. (IF 11.093) Pub Date : 2020-09-01
    Yoshitaka Sakamoto,Liu Xu,Masahide Seki,Toshiyuki T Yokoyama,Masahiro Kasahara,Yukie Kashima,Akihiro Ohashi,Yoko Shimada,Noriko Motoi,Katsuya Tsuchihara,Susumu S Kobayashi,Takashi Kohno,Yuichi Shiraishi,Ayako Suzuki,Yutaka Suzuki

    Here, we report the application of a long-read sequencer, PromethION, for analyzing human cancer genomes. We first conducted whole-genome sequencing on lung cancer cell lines. We found that it is possible to genotype known cancerous mutations, such as point mutations. We also found that long-read sequencing is particularly useful for precisely identifying and characterizing structural aberrations,

    更新日期:2020-09-15
  • Somatic structural variation targets neurodevelopmental genes and identifies SHANK2 as a tumor suppressor in neuroblastoma.
    Genome Res. (IF 11.093) Pub Date : 2020-09-01
    Gonzalo Lopez,Karina L Conkrite,Miriam Doepner,Komal S Rathi,Apexa Modi,Zalman Vaksman,Lance M Farra,Eric Hyson,Moataz Noureddine,Jun S Wei,Malcolm A Smith,Shahab Asgharzadeh,Robert C Seeger,Javed Khan,Jaime Guidry Auvil,Daniela S Gerhard,John M Maris,Sharon J Diskin

    Neuroblastoma is a malignancy of the developing sympathetic nervous system that accounts for 12% of childhood cancer deaths. Like many childhood cancers, neuroblastoma shows a relative paucity of somatic single-nucleotide variants (SNVs) and small insertions and deletions (indels) compared to adult cancers. Here, we assessed the contribution of somatic structural variation (SV) in neuroblastoma using

    更新日期:2020-09-15
  • Chromatin activation as a unifying principle underlying pathogenic mechanisms in multiple myeloma.
    Genome Res. (IF 11.093) Pub Date : 2020-09-01
    Raquel Ordoñez,Marta Kulis,Nuria Russiñol,Vicente Chapaprieta,Arantxa Carrasco-Leon,Beatriz García-Torre,Stella Charalampopoulou,Guillem Clot,Renée Beekman,Cem Meydan,Martí Duran-Ferrer,Núria Verdaguer-Dot,Roser Vilarrasa-Blasi,Paula Soler-Vila,Leire Garate,Estíbaliz Miranda,Edurne San José-Enériz,Juan R Rodriguez-Madoz,Teresa Ezponda,Rebeca Martínez-Turrilas,Amaia Vilas-Zornoza,David Lara-Astiaso

    Multiple myeloma (MM) is a plasma cell neoplasm associated with a broad variety of genetic lesions. In spite of this genetic heterogeneity, MMs share a characteristic malignant phenotype whose underlying molecular basis remains poorly characterized. In the present study, we examined plasma cells from MM using a multi-epigenomics approach and demonstrated that, when compared to normal B cells, malignant

    更新日期:2020-09-15
  • Mapping genome variation of SARS-CoV-2 worldwide highlights the impact of COVID-19 super-spreaders.
    Genome Res. (IF 11.093) Pub Date : 2020-09-02
    Alberto Gomez-Carballa,Xabi Bello,Jacobo Pardo-Seco,Federico Martinon-Torres,Antonio Salas

    The human pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the major pandemic of the 21st century. We analyzed >4,700 SARS-CoV-2 genomes and associated meta-data retrieved from public repositories. SARS-CoV-2 sequences have a high sequence identity (>99.9%), which drops to >96% when compared to bat coronavirus genome. We built a mutation-annotated reference SARS-CoV-2

    更新日期:2020-09-02
  • Pooled analysis of radiation hybrids identifies loci for growth and drug action in mammalian cells.
    Genome Res. (IF 11.093) Pub Date : 2020-09-02
    Arshad H Khan,Andy Lin,Richard T Wang,Joshua S Bloom,Kenneth Lange,Desmond J Smith

    Genetic screens in mammalian cells commonly focus on loss-of-function methodologies. To evaluate the phenotypic consequences of extra gene copies, we used bulk segregant analysis (BSA) of radiation hybrid (RH) cells. We constructed six pools of RH cells, each consisting of ~2500 independent clones, and placed the pools under selection in media with or without paclitaxel. Low pass sequencing identified

    更新日期:2020-09-02
  • LEMMI: a continuous benchmarking platform for metagenomics classifiers.
    Genome Res. (IF 11.093) Pub Date : 2020-08-01
    Mathieu Seppey,Mosè Manni,Evgeny M Zdobnov

    Studies of microbiomes are booming, along with the diversity of computational approaches to make sense out of the sequencing data and the volumes of accumulated microbial genotypes. A swift evaluation of newly published methods and their improvements against established tools is necessary to reduce the time between the methods' release and their adoption in microbiome analyses. The LEMMI platform offers

    更新日期:2020-08-27
  • SNP-based quantitative deconvolution of biological mixtures: application to the detection of cows with subclinical mastitis by whole-genome sequencing of tank milk.
    Genome Res. (IF 11.093) Pub Date : 2020-08-01
    Wouter Coppieters,Latifa Karim,Michel Georges

    Biological products of importance in food (e.g., milk) and medical (e.g., donor blood-derived products) sciences often correspond to mixtures of samples contributed by multiple individuals. Identifying which individuals contributed to the mixture and in what proportions may be of interest in several circumstances. We herein present a method that allows to do this by shallow whole-genome sequencing

    更新日期:2020-08-27
  • RNA-Bloom enables reference-free and reference-guided sequence assembly for single-cell transcriptomes.
    Genome Res. (IF 11.093) Pub Date : 2020-08-01
    Ka Ming Nip,Readman Chiu,Chen Yang,Justin Chu,Hamid Mohamadi,René L Warren,Inanc Birol

    Despite the rapid advance in single-cell RNA sequencing (scRNA-seq) technologies within the last decade, single-cell transcriptome analysis workflows have primarily used gene expression data while isoform sequence analysis at the single-cell level still remains fairly limited. Detection and discovery of isoforms in single cells is difficult because of the inherent technical shortcomings of scRNA-seq

    更新日期:2020-08-27
  • TransBorrow: genome-guided transcriptome assembly by borrowing assemblies from different assemblers.
    Genome Res. (IF 11.093) Pub Date : 2020-08-01
    Ting Yu,Zengchao Mu,Zhaoyuan Fang,Xiaoping Liu,Xin Gao,Juntao Liu

    RNA-seq technology is widely used in various transcriptomic studies and provides great opportunities to reveal the complex structures of transcriptomes. To effectively analyze RNA-seq data, we introduce a novel transcriptome assembler, TransBorrow, which borrows the assemblies from different assemblers to search for reliable subsequences by building a colored graph from those borrowed assemblies. Then

    更新日期:2020-08-27
  • A pedigree-based prediction model identifies carriers of deleterious de novo mutations in families with Li-Fraumeni syndrome.
    Genome Res. (IF 11.093) Pub Date : 2020-08-01
    Fan Gao,Xuedong Pan,Elissa B Dodd-Eaton,Carlos Vera Recio,Matthew D Montierth,Jasmina Bojadzieva,Phuong L Mai,Kristin Zelley,Valen E Johnson,Danielle Braun,Kim E Nichols,Judy E Garber,Sharon A Savage,Louise C Strong,Wenyi Wang

    De novo mutations (DNMs) are increasingly recognized as rare disease causal factors. Identifying DNM carriers will allow researchers to study the likely distinct molecular mechanisms of DNMs. We developed Famdenovo to predict DNM status (DNM or familial mutation [FM]) of deleterious autosomal dominant germline mutations for any syndrome. We introduce Famdenovo.TP53 for Li-Fraumeni syndrome (LFS) and

    更新日期:2020-08-27
  • Detection of simple and complex de novo mutations with multiple reference sequences.
    Genome Res. (IF 11.093) Pub Date : 2020-08-01
    Kiran V Garimella,Zamin Iqbal,Michael A Krause,Susana Campino,Mihir Kekre,Eleanor Drury,Dominic Kwiatkowski,Juliana M Sá,Thomas E Wellems,Gil McVean

    The characterization of de novo mutations in regions of high sequence and structural diversity from whole-genome sequencing data remains highly challenging. Complex structural variants tend to arise in regions of high repetitiveness and low complexity, challenging both de novo assembly, in which short reads do not capture the long-range context required for resolution, and mapping approaches, in which

    更新日期:2020-08-27
  • Detection and characterization of jagged ends of double-stranded DNA in plasma.
    Genome Res. (IF 11.093) Pub Date : 2020-08-01
    Peiyong Jiang,Tingting Xie,Spencer C Ding,Ze Zhou,Suk Hang Cheng,Rebecca W Y Chan,Wing-Shan Lee,Wenlei Peng,John Wong,Vincent W S Wong,Henry L Y Chan,Stephen L Chan,Liona C Y Poon,Tak Y Leung,K C Allen Chan,Rossa W K Chiu,Y M Dennis Lo

    Cell-free DNA in plasma has been used for noninvasive prenatal testing and cancer liquid biopsy. The physical properties of cell-free DNA fragments in plasma, such as fragment sizes and ends, have attracted much recent interest, leading to the emerging field of cell-free DNA fragmentomics. However, one aspect of plasma DNA fragmentomics as to whether double-stranded plasma molecules might carry single-stranded

    更新日期:2020-08-27
  • Xylem systems genetics analysis reveals a key regulator of lignin biosynthesis in Populus deltoides.
    Genome Res. (IF 11.093) Pub Date : 2020-08-01
    Kelly M Balmant,Jerald D Noble,Filipe C Alves,Christopher Dervinis,Daniel Conde,Henry W Schmidt,Ana I Vazquez,William B Barbazuk,Gustavo de Los Campos,Marcio F R Resende,Matias Kirst

    Despite the growing resources and tools for high-throughput characterization and analysis of genomic information, the discovery of the genetic elements that regulate complex traits remains a challenge. Systems genetics is an emerging field that aims to understand the flow of biological information that underlies complex traits from genotype to phenotype. In this study, we used a systems genetics approach

    更新日期:2020-08-27
  • PR-DUB maintains the expression of critical genes through FOXK1/2- and ASXL1/2/3-dependent recruitment to chromatin and H2AK119ub1 deubiquitination.
    Genome Res. (IF 11.093) Pub Date : 2020-08-01
    Petros Kolovos,Koutarou Nishimura,Aditya Sankar,Simone Sidoli,Paul A Cloos,Kristian Helin,Jesper Christensen

    Polycomb group proteins are important for maintaining gene expression patterns and cell identity in metazoans. The mammalian Polycomb repressive deubiquitinase (PR-DUB) complexes catalyze removal of monoubiquitination on lysine 119 of histone H2A (H2AK119ub1) through a multiprotein core comprised of BAP1, HCFC1, FOXK1/2, and OGT in combination with either of ASXL1, 2, or 3. Mutations in PR-DUB components

    更新日期:2020-08-27
  • ADAR-deficiency perturbs the global splicing landscape in mouse tissues.
    Genome Res. (IF 11.093) Pub Date : 2020-08-01
    Utkarsh Kapoor,Konstantin Licht,Fabian Amman,Tobias Jakobi,David Martin,Christoph Dieterich,Michael F Jantsch

    Adenosine-to-inosine RNA editing and pre-mRNA splicing largely occur cotranscriptionally and influence each other. Here, we use mice deficient in either one of the two editing enzymes ADAR (ADAR1) or ADARB1 (ADAR2) to determine the transcriptome-wide impact of RNA editing on splicing across different tissues. We find that ADAR has a 100× higher impact on splicing than ADARB1, although both enzymes

    更新日期:2020-08-27
  • Diploid genome architecture revealed by multi-omic data of hybrid mice.
    Genome Res. (IF 11.093) Pub Date : 2020-08-01
    Zhijun Han,Kairong Cui,Katarzyna Placek,Ni Hong,Chengqi Lin,Wei Chen,Keji Zhao,Wenfei Jin

    Although mammalian genomes are diploid, previous studies extensively investigated the average chromatin architectures without considering the differences between homologous chromosomes. We generated Hi-C, ChIP-seq, and RNA-seq data sets from CD4 T cells of B6, Cast, and hybrid mice, to investigate the diploid chromatin organization and epigenetic regulation. Our data indicate that inter-chromosomal

    更新日期:2020-08-27
  • LCM-seq reveals unique transcriptional adaptation mechanisms of resistant neurons and identifies protective pathways in spinal muscular atrophy.
    Genome Res. (IF 11.093) Pub Date : 2020-08-01
    Susanne Nichterwitz,Jik Nijssen,Helena Storvall,Christoph Schweingruber,Laura Helen Comley,Ilary Allodi,Mirjam van der Lee,Qiaolin Deng,Rickard Sandberg,Eva Hedlund

    Somatic motor neurons are selectively vulnerable in spinal muscular atrophy (SMA), which is caused by a deficiency of the ubiquitously expressed survival of motor neuron protein. However, some motor neuron groups, including oculomotor and trochlear (ocular), which innervate eye muscles, are for unknown reasons spared. To reveal mechanisms of vulnerability and resistance in SMA, we investigate the transcriptional

    更新日期:2020-08-27
  • Metabolic labeling of RNA using multiple ribonucleoside analogs enables the simultaneous evaluation of RNA synthesis and degradation rates.
    Genome Res. (IF 11.093) Pub Date : 2020-08-25
    Kentaro Kawata,Hiroyasu Wakida,Toshimichi Yamada,Kenzui Taniue,Han Han,Masahide Seki,Yutaka Suzuki,Nobuyoshi Akimitsu

    Gene expression is determined by a balance between RNA synthesis and RNA degradation. To elucidate the underlying regulatory mechanisms and principles of this, simultaneous measurements of RNA synthesis and degradation are required. Here, we report the development of Dyrec-seq which uses 4-thiouridine and 5-bromouridine to simultaneously quantify RNA synthesis and degradation rates. Dyrec-seq enabled

    更新日期:2020-08-26
  • HDA6 dependent chromatin deacetylation orchestrates mRNA polyadenylation.
    Genome Res. (IF 11.093) Pub Date : 2020-08-05
    Juncheng Lin,Fu-Yu Hung,Congting Ye,Liwei Hong,Yuan-Hsin Shih,Keqiang Wu,Qingshun Quinn Li

    Eukaryotic histone deacetylation, critical for maintaining nucleosome structure and regulating gene expression, is mediated by histone deacetylases (HDACs). While nucleosomes have been reported to regulate mRNA polyadenylation in humans, the role of HDACs in regulating polyadenylation has not been uncovered. Taking the advantage of phenotypic studies on Arabidopsis, HDA6 (one of HDACs) was found to

    更新日期:2020-08-06
  • Cross-species analysis of enhancer logic using deep learning.
    Genome Res. (IF 11.093) Pub Date : 2020-07-30
    Liesbeth Minnoye,Ibrahim Ihsan Taskiran,David Mauduit,Maurizio Fazio,Linde Van Aerschot,Gert Hulselmans,Valerie Christiaens,Samira Makhzami,Monika Seltenhammer,Panagiotis Karras,Aline Primot,Edouard Cadieu,Ellen van Rooijen,Jean-Christophe Marine,Giorgia Egidy,Ghanem Elias Ghanem,Leonard Zon,Jasper Wouters,Stein Aerts

    Deciphering the genomic regulatory code of enhancers is a key challenge in biology as this code underlies cellular identity. A better understanding of how enhancers work will improve the interpretation of noncoding genome variation, and empower the generation of cell type-specific drivers for gene therapy. Here we explore the combination of deep learning and cross-species chromatin accessibility profiling

    更新日期:2020-07-31
  • Recounting the FANTOM CAGE-Associated Transcriptome.
    Genome Res. (IF 11.093) Pub Date : 2020-07-01
    Eddie Luidy Imada,Diego Fernando Sanchez,Leonardo Collado-Torres,Christopher Wilks,Tejasvi Matam,Wikum Dinalankara,Aleksey Stupnikov,Francisco Lobo-Pereira,Chi-Wai Yip,Kayoko Yasuzawa,Naoto Kondo,Masayoshi Itoh,Harukazu Suzuki,Takeya Kasukawa,Chung-Chau Hon,Michiel J L de Hoon,Jay W Shin,Piero Carninci,Andrew E Jaffe,Jeffrey T Leek,Alexander Favorov,Gloria R Franco,Ben Langmead,Luigi Marchionni

    Long noncoding RNAs (lncRNAs) have emerged as key coordinators of biological and cellular processes. Characterizing lncRNA expression across cells and tissues is key to understanding their role in determining phenotypes, including human diseases. We present here FC-R2, a comprehensive expression atlas across a broadly defined human transcriptome, inclusive of over 109,000 coding and noncoding genes

    更新日期:2020-07-30
  • Functional annotation of human long noncoding RNAs via molecular phenotyping.
    Genome Res. (IF 11.093) Pub Date : 2020-07-01
    Jordan A Ramilowski,Chi Wai Yip,Saumya Agrawal,Jen-Chien Chang,Yari Ciani,Ivan V Kulakovskiy,Mickaël Mendez,Jasmine Li Ching Ooi,John F Ouyang,Nick Parkinson,Andreas Petri,Leonie Roos,Jessica Severin,Kayoko Yasuzawa,Imad Abugessaisa,Altuna Akalin,Ivan V Antonov,Erik Arner,Alessandro Bonetti,Hidemasa Bono,Beatrice Borsari,Frank Brombacher,Christopher JF Cameron,Carlo Vittorio Cannistraci,Ryan Cardenas

    Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense

    更新日期:2020-07-30
  • A limited set of transcriptional programs define major cell types.
    Genome Res. (IF 11.093) Pub Date : 2020-07-01
    Alessandra Breschi,Manuel Muñoz-Aguirre,Valentin Wucher,Carrie A Davis,Diego Garrido-Martín,Sarah Djebali,Jesse Gillis,Dmitri D Pervouchine,Anna Vlasova,Alexander Dobin,Chris Zaleski,Jorg Drenkow,Cassidy Danyko,Alexandra Scavelli,Ferran Reverter,Michael P Snyder,Thomas R Gingeras,Roderic Guigó

    We have produced RNA sequencing data for 53 primary cells from different locations in the human body. The clustering of these primary cells reveals that most cells in the human body share a few broad transcriptional programs, which define five major cell types: epithelial, endothelial, mesenchymal, neural, and blood cells. These act as basic components of many tissues and organs. Based on gene expression

    更新日期:2020-07-30
  • TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence.
    Genome Res. (IF 11.093) Pub Date : 2020-07-01
    Ningxin Ouyang,Alan P Boyle

    Transcription is tightly regulated by cis-regulatory DNA elements where transcription factors (TFs) can bind. Thus, identification of TF binding sites (TFBSs) is key to understanding gene expression and whole regulatory networks within a cell. The standard approaches used for TFBS prediction, such as position weight matrices (PWMs) and chromatin immunoprecipitation followed by sequencing (ChIP-seq)

    更新日期:2020-07-30
  • Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility.
    Genome Res. (IF 11.093) Pub Date : 2020-07-01
    Qiao Rui Xing,Chadi A El Farran,Ying Ying Zeng,Yao Yi,Tushar Warrier,Pradeep Gautam,James J Collins,Jian Xu,Peter Dröge,Cheng-Gee Koh,Hu Li,Li-Feng Zhang,Yuin-Han Loh

    Joint profiling of transcriptome and chromatin accessibility within single cells allows for the deconstruction of the complex relationship between transcriptional states and upstream regulatory programs determining different cell fates. Here, we developed an automated method with high sensitivity, assay for single-cell transcriptome and accessibility regions (ASTAR-seq), for simultaneous measurement

    更新日期:2020-07-30
  • System-wide analyses of the fission yeast poly(A)+ RNA interactome reveal insights into organization and function of RNA-protein complexes.
    Genome Res. (IF 11.093) Pub Date : 2020-07-01
    Cornelia Kilchert,Tea Kecman,Emily Priest,Svenja Hester,Ebru Aydin,Krzysztof Kus,Oliver Rossbach,Alfredo Castello,Shabaz Mohammed,Lidia Vasiljeva

    Large RNA-binding complexes play a central role in gene expression and orchestrate production, function, and turnover of mRNAs. The accuracy and dynamics of RNA–protein interactions within these molecular machines are essential for their function and are mediated by RNA-binding proteins (RBPs). Here, we show that fission yeast whole-cell poly(A)+ RNA–protein crosslinking data provide information on

    更新日期:2020-07-30
  • Independent evolution of transcript abundance and gene regulatory dynamics.
    Genome Res. (IF 11.093) Pub Date : 2020-07-01
    Gat Krieger,Offir Lupo,Avraham A Levy,Naama Barkai

    Changes in gene expression drive novel phenotypes, raising interest in how gene expression evolves. In contrast to the static genome, cells modulate gene expression in response to changing environments. Previous comparative studies focused on specific conditions, describing interspecies variation in expression levels, but providing limited information about variation across different conditions. To

    更新日期:2020-07-30
  • Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing.
    Genome Res. (IF 11.093) Pub Date : 2020-07-01
    Alaaddin Bulak Arpat,Angélica Liechti,Mara De Matos,René Dreos,Peggy Janich,David Gatfield

    Translation initiation is the major regulatory step defining the rate of protein production from an mRNA. Meanwhile, the impact of nonuniform ribosomal elongation rates is largely unknown. Using a modified ribosome profiling protocol based on footprints from two closely packed ribosomes (disomes), we have mapped ribosomal collisions transcriptome-wide in mouse liver. We uncover that the stacking of

    更新日期:2020-07-30
  • Translation initiation downstream from annotated start codons in human mRNAs coevolves with the Kozak context.
    Genome Res. (IF 11.093) Pub Date : 2020-07-01
    Maria S Benitez-Cantos,Martina M Yordanova,Patrick B F O'Connor,Alexander V Zhdanov,Sergey I Kovalchuk,Dmitri B Papkovsky,Dmitry E Andreev,Pavel V Baranov

    Eukaryotic translation initiation involves preinitiation ribosomal complex 5′-to-3′ directional probing of mRNA for codons suitable for starting protein synthesis. The recognition of codons as starts depends on the codon identity and on its immediate nucleotide context known as Kozak context. When the context is weak (i.e., nonoptimal), leaky scanning takes place during which a fraction of ribosomes

    更新日期:2020-07-30
  • Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences.
    Genome Res. (IF 11.093) Pub Date : 2020-07-01
    Arttu Jolma,Jilin Zhang,Estefania Mondragón,Ekaterina Morgunova,Teemu Kivioja,Kaitlin U Laverty,Yimeng Yin,Fangjie Zhu,Gleb Bourenkov,Quaid Morris,Timothy R Hughes,Louis James Maher,Jussi Taipale

    RNA-binding proteins (RBPs) regulate RNA metabolism at multiple levels by affecting splicing of nascent transcripts, RNA folding, base modification, transport, localization, translation, and stability. Despite their central role in RNA function, the RNA-binding specificities of most RBPs remain unknown or incompletely defined. To address this, we have assembled a genome-scale collection of RBPs and

    更新日期:2020-07-30
  • Comparative transcriptomics of primary cells in vertebrates.
    Genome Res. (IF 11.093) Pub Date : 2020-07-01
    Tanvir Alam,Saumya Agrawal,Jessica Severin,Robert S Young,Robin Andersson,Erik Arner,Akira Hasegawa,Marina Lizio,Jordan A Ramilowski,Imad Abugessaisa,Yuri Ishizu,Shohei Noma,Hiroshi Tarui,Martin S Taylor,Timo Lassmann,Masayoshi Itoh,Takeya Kasukawa,Hideya Kawaji,Luigi Marchionni,Guojun Sheng,Alistair R R Forrest,Levon M Khachigian,Yoshihide Hayashizaki,Piero Carninci,Michiel J L de Hoon

    Gene expression profiles in homologous tissues have been observed to be different between species, which may be due to differences between species in the gene expression program in each cell type, but may also reflect differences in cell type composition of each tissue in different species. Here, we compare expression profiles in matching primary cells in human, mouse, rat, dog, and chicken using Cap

    更新日期:2020-07-30
  • Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations.
    Genome Res. (IF 11.093) Pub Date : 2020-07-01
    Ryne C Ramaker,Andrew A Hardigan,Say-Tar Goh,E Christopher Partridge,Barbara Wold,Sara J Cooper,Richard M Myers

    DNA-associated proteins (DAPs) classically regulate gene expression by binding to regulatory loci such as enhancers or promoters. As expanding catalogs of genome-wide DAP binding maps reveal thousands of loci that, unlike the majority of conventional enhancers and promoters, associate with dozens of different DAPs with apparently little regard for motif preference, an understanding of DAP association

    更新日期:2020-07-30
  • The multi-comparative 2-n-way genome suite.
    Genome Res. (IF 11.093) Pub Date : 2020-07-29
    Gennady Churakov,Fengjun Zhang,Norbert Grundmann,Wojciech Makalowski,Angela Noll,Liliya Doronina,Juergen Schmitz

    To effectively analyze the increasing amounts of available genomic data, improved comparative analytical tools that are accessible to and applicable by a broad scientific community are essential. We built the "2-n-way" software suite to provide a fundamental and innovative processing framework for revealing and comparing inserted elements among various genomes. The suite is comprised of two user-friendly

    更新日期:2020-07-29
  • Corrigendum: OMA standalone: orthology inference among public and custom genomes and transcriptomes
    Genome Res. (IF 11.093) Pub Date : 2020-06-01
    Adrian M. Altenhoff; Jeremy Levy; Magdalena Zarowiecki; Bartłomiej Tomiczek; Alex Warwick Vesztrocy; Daniel A. Dalquen; Steven Müller; Maximilian J. Telford; Natasha M. Glover; David Dylus; Christophe Dessimoz

    Genome Research 29: 1152–1163 (2019)

    更新日期:2020-07-15
  • Corrigendum: Human auditory ossicles as an alternative optimal source of ancient DNA
    Genome Res. (IF 11.093) Pub Date : 2020-06-01
    Kendra Sirak; Daniel Fernandes; Olivia Cheronet; Eadaoin Harney; Matthew Mah; Swapan Mallick; Nadin Rohland; Nicole Adamski; Nasreen Broomandkhoshbacht; Kimberly Callan; Francesca Candilio; Ann Marie Lawson; Kirsten Mandl; Jonas Oppenheimer; Kristin Stewardson; Fatma Zalzala; Alexandra Anders; Juraj Bartík; Alfredo Coppa; Tumen Dashtseveg; Sándor Évinger; Zdeněk Farkaš; Tamás Hajdu; Jamsranjav Bayarsaikhan;

    Genome Research 30: 427–436 (2020)

    更新日期:2020-07-15
  • Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis.
    Genome Res. (IF 11.093) Pub Date : 2020-06-01
    Yingshu Li,Yongjie Liu,Hang Yang,Ting Zhang,Kiyoshi Naruse,Qiang Tu

    Medaka (Oryzias latipes) has become an important vertebrate model widely used in genetics, developmental biology, environmental sciences, and many other fields. A high-quality genome sequence and a variety of genetic tools are available for this model organism. However, existing genome annotation is still rudimentary, as it was mainly based on computational prediction and short-read RNA-seq data. Here

    更新日期:2020-07-15
  • Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq.
    Genome Res. (IF 11.093) Pub Date : 2020-06-01
    Robert A Policastro,R Taylor Raborn,Volker P Brendel,Gabriel E Zentner

    Accurate mapping of transcription start sites (TSSs) is key for understanding transcriptional regulation. However, current protocols for genome-wide TSS profiling are laborious and/or expensive. We present Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq), a simple, rapid, and cost-effective protocol for sequencing capped RNA 5′ ends from as little

    更新日期:2020-07-15
  • Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information.
    Genome Res. (IF 11.093) Pub Date : 2020-06-01
    Zhoutao Chen,Long Pham,Tsai-Chin Wu,Guoya Mo,Yu Xia,Peter L Chang,Devin Porter,Tan Phan,Huu Che,Hao Tran,Vikas Bansal,Justin Shaffer,Pedro Belda-Ferre,Greg Humphrey,Rob Knight,Pavel Pevzner,Son Pham,Yong Wang,Ming Lei

    Long-range sequencing information is required for haplotype phasing, de novo assembly, and structural variation detection. Current long-read sequencing technologies can provide valuable long-range information but at a high cost with low accuracy and high DNA input requirements. We have developed a single-tube Transposase Enzyme Linked Long-read Sequencing (TELL-seq) technology, which enables a low-cost

    更新日期:2020-07-15
  • A long-read RNA-seq approach to identify novel transcripts of very large genes.
    Genome Res. (IF 11.093) Pub Date : 2020-06-01
    Prech Uapinyoying,Jeremy Goecks,Susan M Knoblach,Karuna Panchapakesan,Carsten G Bonnemann,Terence A Partridge,Jyoti K Jaiswal,Eric P Hoffman

    RNA-seq is widely used for studying gene expression, but commonly used sequencing platforms produce short reads that only span up to two exon junctions per read. This makes it difficult to accurately determine the composition and phasing of exons within transcripts. Although long-read sequencing improves this issue, it is not amenable to precise quantitation, which limits its utility for differential

    更新日期:2020-07-15
  • The evolution of sex-biased gene expression in the Drosophila brain.
    Genome Res. (IF 11.093) Pub Date : 2020-06-01
    Samuel Khodursky,Nicolas Svetec,Sylvia M Durkin,Li Zhao

    Genes with sex-biased expression in Drosophila are thought to underlie sexually dimorphic phenotypes and have been shown to possess unique evolutionary properties. However, the forces and constraints governing the evolution of sex-biased genes in the somatic tissues of Drosophila are largely unknown. By using population-scale RNA sequencing data, we show that sex-biased genes in the Drosophila brain

    更新日期:2020-07-15
  • Quantitative analysis of Y-Chromosome gene expression across 36 human tissues.
    Genome Res. (IF 11.093) Pub Date : 2020-06-01
    Alexander K Godfrey,Sahin Naqvi,Lukáš Chmátal,Joel M Chick,Richard N Mitchell,Steven P Gygi,Helen Skaletsky,David C Page

    Little is known about how human Y-Chromosome gene expression directly contributes to differences between XX (female) and XY (male) individuals in nonreproductive tissues. Here, we analyzed quantitative profiles of Y-Chromosome gene expression across 36 human tissues from hundreds of individuals. Although it is often said that Y-Chromosome genes are lowly expressed outside the testis, we report many

    更新日期:2020-07-15
  • Untangling the effects of cellular composition on coexpression analysis.
    Genome Res. (IF 11.093) Pub Date : 2020-06-01
    Marjan Farahbod,Paul Pavlidis

    Coexpression analysis is widely used for inferring regulatory networks, predicting gene function, and interpretation of transcriptome profiling studies, based on methods such as clustering. The majority of such studies use data collected from bulk tissue, where the effects of cellular composition present a potential confound. However, the impact of composition on coexpression analysis has not been

    更新日期:2020-07-15
  • Coexpression enrichment analysis at the single-cell level reveals convergent defects in neural progenitor cells and their cell-type transitions in neurodevelopmental disorders.
    Genome Res. (IF 11.093) Pub Date : 2020-06-01
    Kaifang Pang,Li Wang,Wei Wang,Jian Zhou,Chao Cheng,Kihoon Han,Huda Y Zoghbi,Zhandong Liu

    A large number of genes have been implicated in neurodevelopmental disorders (NDDs), but their contributions to NDD pathology are difficult to decipher without understanding their diverse roles in different brain cell types. Here, we integrated NDD genetics with single-cell RNA sequencing data to assess coexpression enrichment patterns of various NDD gene sets. We identified midfetal cortical neural

    更新日期:2020-07-15
  • Paternal age in rhesus macaques is positively associated with germline mutation accumulation but not with measures of offspring sociability.
    Genome Res. (IF 11.093) Pub Date : 2020-06-01
    Richard J Wang,Gregg W C Thomas,Muthuswamy Raveendran,R Alan Harris,Harshavardhan Doddapaneni,Donna M Muzny,John P Capitanio,Predrag Radivojac,Jeffrey Rogers,Matthew W Hahn

    Mutation is the ultimate source of all genetic novelty and the cause of heritable genetic disorders. Mutational burden has been linked to complex disease, including neurodevelopmental disorders such as schizophrenia and autism. The rate of mutation is a fundamental genomic parameter and direct estimates of this parameter have been enabled by accurate comparisons of whole-genome sequences between parents

    更新日期:2020-07-15
  • Single-cell analysis of human embryos reveals diverse patterns of aneuploidy and mosaicism.
    Genome Res. (IF 11.093) Pub Date : 2020-06-01
    Margaret R Starostik,Olukayode A Sosina,Rajiv C McCoy

    Less than half of human zygotes survive to birth, primarily due to aneuploidies of meiotic or mitotic origin. Mitotic errors generate chromosomal mosaicism, defined by multiple cell lineages with distinct chromosome complements. The incidence and impacts of mosaicism in human embryos remain controversial, with most previous studies based on bulk DNA assays or comparisons of multiple biopsies of few

    更新日期:2020-07-15
  • Characterization of colibactin-associated mutational signature in an Asian oral squamous cell carcinoma and in other mucosal tumor types.
    Genome Res. (IF 11.093) Pub Date : 2020-06-01
    Arnoud Boot,Alvin W T Ng,Fui Teen Chong,Szu-Chi Ho,Willie Yu,Daniel S W Tan,N Gopalakrishna Iyer,Steven G Rozen

    Mutational signatures can reveal the history of mutagenic processes that cells were exposed to before and during tumorigenesis. We expect that as-yet-undiscovered mutational processes will shed further light on mutagenesis leading to carcinogenesis. With this in mind, we analyzed the mutational spectra of 36 Asian oral squamous cell carcinomas. The mutational spectra of two samples from patients who

    更新日期:2020-07-15
  • Exploring dimension-reduced embeddings with Sleepwalk.
    Genome Res. (IF 11.093) Pub Date : 2020-05-01
    Svetlana Ovchinnikova,Simon Anders

    Dimension-reduction methods, such as t-SNE or UMAP, are widely used when exploring high-dimensional data describing many entities, for example, RNA-seq data for many single cells. However, dimension reduction is commonly prone to introducing artifacts, and we hence need means to see where a dimension-reduced embedding is a faithful representation of the local neighborhood and where it is not. We present

    更新日期:2020-05-01
  • MEDEA: analysis of transcription factor binding motifs in accessible chromatin.
    Genome Res. (IF 11.093) Pub Date : 2020-05-01
    Luca Mariani,Kathryn Weinand,Stephen S Gisselbrecht,Martha L Bulyk

    Deciphering the interplay between chromatin accessibility and transcription factor (TF) binding is fundamental to understanding transcriptional regulation, control of cellular states, and the establishment of new phenotypes. Recent genome-wide chromatin accessibility profiling studies have provided catalogs of putative open regions, where TFs can recognize their motifs and regulate gene expression

    更新日期:2020-05-01
  • Comprehensive analyses of 723 transcriptomes enhance genetic and biological interpretations for complex traits in cattle.
    Genome Res. (IF 11.093) Pub Date : 2020-05-01
    Lingzhao Fang,Wentao Cai,Shuli Liu,Oriol Canela-Xandri,Yahui Gao,Jicai Jiang,Konrad Rawlik,Bingjie Li,Steven G Schroeder,Benjamin D Rosen,Cong-Jun Li,Tad S Sonstegard,Leeson J Alexander,Curtis P Van Tassell,Paul M VanRaden,John B Cole,Ying Yu,Shengli Zhang,Albert Tenesa,Li Ma,George E Liu

    By uniformly analyzing 723 RNA-seq data from 91 tissues and cell types, we built a comprehensive gene atlas and studied tissue specificity of genes in cattle. We demonstrated that tissue-specific genes significantly reflected the tissue-relevant bio