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Reese F, Williams B, Balderrama-Gutierrez G, Wyman D, Çelik MH, Rebboah E, Rezaie N, Trout D, Razavi-Mohseni M, Jiang Y, Borsari B, Morabito S, Liang HY, McGill CJ, Rahmanian S, Sakr J, Jiang S, Zeng W, Carvalho K, Weimer AK, Dionne LA, McShane A, Bedi K, Elhajjajy SI, Upchurch S, Jou J, Youngworth I, Gabdank I, Sud P, Jolanki O, Strattan JS, Kagda MS, Snyder MP, Hitz BC, Moore JE, Weng Z, Bennett D, Reinholdt L, Ljungman M, Beer MA, Gerstein MB, Pachter L, Guigó R, Wold BJ, Mortazavi A. The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity. bioRxiv 2023:2023.05.15.540865. [PMID: 37292896 PMCID: PMC10245583 DOI: 10.1101/2023.05.15.540865] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The majority of mammalian genes encode multiple transcript isoforms that result from differential promoter use, changes in exonic splicing, and alternative 3' end choice. Detecting and quantifying transcript isoforms across tissues, cell types, and species has been extremely challenging because transcripts are much longer than the short reads normally used for RNA-seq. By contrast, long-read RNA-seq (LR-RNA-seq) gives the complete structure of most transcripts. We sequenced 264 LR-RNA-seq PacBio libraries totaling over 1 billion circular consensus reads (CCS) for 81 unique human and mouse samples. We detect at least one full-length transcript from 87.7% of annotated human protein coding genes and a total of 200,000 full-length transcripts, 40% of which have novel exon junction chains. To capture and compute on the three sources of transcript structure diversity, we introduce a gene and transcript annotation framework that uses triplets representing the transcript start site, exon junction chain, and transcript end site of each transcript. Using triplets in a simplex representation demonstrates how promoter selection, splice pattern, and 3' processing are deployed across human tissues, with nearly half of multi-transcript protein coding genes showing a clear bias toward one of the three diversity mechanisms. Evaluated across samples, the predominantly expressed transcript changes for 74% of protein coding genes. In evolution, the human and mouse transcriptomes are globally similar in types of transcript structure diversity, yet among individual orthologous gene pairs, more than half (57.8%) show substantial differences in mechanism of diversification in matching tissues. This initial large-scale survey of human and mouse long-read transcriptomes provides a foundation for further analyses of alternative transcript usage, and is complemented by short-read and microRNA data on the same samples and by epigenome data elsewhere in the ENCODE4 collection.
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Affiliation(s)
- Fairlie Reese
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Brian Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
| | - Gabriela Balderrama-Gutierrez
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Dana Wyman
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Muhammed Hasan Çelik
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Elisabeth Rebboah
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Narges Rezaie
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Diane Trout
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
| | - Milad Razavi-Mohseni
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, USA
| | - Yunzhe Jiang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, USA
| | - Beatrice Borsari
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, USA
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Samuel Morabito
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Heidi Yahan Liang
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Cassandra J McGill
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Sorena Rahmanian
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Jasmine Sakr
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, USA
| | - Shan Jiang
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Weihua Zeng
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Klebea Carvalho
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Annika K Weimer
- Department of Genetics, Stanford University School of Medicine, Palo Alto, USA
| | - Louise A Dionne
- The Jackson Laboratory, The Jackson Laboratory, Bar Harbor, USA
| | - Ariel McShane
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, USA
- Department of Radiation Oncology, University of Michigan, Ann Arbor, USA
| | - Karan Bedi
- Department of Biostatistics, University of Michigan, Ann Arbor, USA
- Center for RNA Biomedicine and Rogel Cancer Center, University of Michigan, Ann Arbor, USA
| | - Shaimae I Elhajjajy
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, USA
| | - Sean Upchurch
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
| | - Jennifer Jou
- Department of Genetics, Stanford University School of Medicine, Palo Alto, USA
| | - Ingrid Youngworth
- Department of Genetics, Stanford University School of Medicine, Palo Alto, USA
| | - Idan Gabdank
- Department of Genetics, Stanford University School of Medicine, Palo Alto, USA
| | - Paul Sud
- Department of Genetics, Stanford University School of Medicine, Palo Alto, USA
| | - Otto Jolanki
- Department of Genetics, Stanford University School of Medicine, Palo Alto, USA
| | - J Seth Strattan
- Department of Genetics, Stanford University School of Medicine, Palo Alto, USA
| | - Meenakshi S Kagda
- Department of Genetics, Stanford University School of Medicine, Palo Alto, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Palo Alto, USA
| | - Ben C Hitz
- Department of Genetics, Stanford University School of Medicine, Palo Alto, USA
| | - Jill E Moore
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, USA
| | - David Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, USA
| | - Laura Reinholdt
- The Jackson Laboratory, The Jackson Laboratory, Bar Harbor, USA
| | - Mats Ljungman
- Center for RNA Biomedicine and Rogel Cancer Center, University of Michigan, Ann Arbor, USA
- Departments of Radiation Oncology and Environmental Health Sciences, University of Michigan, Ann Arbor, USA
| | - Michael A Beer
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, USA
| | - Mark B Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, USA
- Section on Biomedical Informatics and Data Science, Yale University, New Haven, USA
- Department of Statistics and Data Science, Yale University, New Haven, USA
- Department of Computer Science, Yale University, New Haven, USA
| | - Lior Pachter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, USA
| | - Roderic Guigó
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Barbara J Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
| | - Ali Mortazavi
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
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Rozowsky J, Gao J, Borsari B, Yang YT, Galeev T, Gürsoy G, Epstein CB, Xiong K, Xu J, Li T, Liu J, Yu K, Berthel A, Chen Z, Navarro F, Sun MS, Wright J, Chang J, Cameron CJF, Shoresh N, Gaskell E, Drenkow J, Adrian J, Aganezov S, Aguet F, Balderrama-Gutierrez G, Banskota S, Corona GB, Chee S, Chhetri SB, Cortez Martins GC, Danyko C, Davis CA, Farid D, Farrell NP, Gabdank I, Gofin Y, Gorkin DU, Gu M, Hecht V, Hitz BC, Issner R, Jiang Y, Kirsche M, Kong X, Lam BR, Li S, Li B, Li X, Lin KZ, Luo R, Mackiewicz M, Meng R, Moore JE, Mudge J, Nelson N, Nusbaum C, Popov I, Pratt HE, Qiu Y, Ramakrishnan S, Raymond J, Salichos L, Scavelli A, Schreiber JM, Sedlazeck FJ, See LH, Sherman RM, Shi X, Shi M, Sloan CA, Strattan JS, Tan Z, Tanaka FY, Vlasova A, Wang J, Werner J, Williams B, Xu M, Yan C, Yu L, Zaleski C, Zhang J, Ardlie K, Cherry JM, Mendenhall EM, Noble WS, Weng Z, Levine ME, Dobin A, Wold B, Mortazavi A, Ren B, Gillis J, Myers RM, Snyder MP, Choudhary J, Milosavljevic A, Schatz MC, Bernstein BE, Guigó R, Gingeras TR, Gerstein M. The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell 2023; 186:1493-1511.e40. [PMID: 37001506 PMCID: PMC10074325 DOI: 10.1016/j.cell.2023.02.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 10/16/2022] [Accepted: 02/10/2023] [Indexed: 04/03/2023]
Abstract
Understanding how genetic variants impact molecular phenotypes is a key goal of functional genomics, currently hindered by reliance on a single haploid reference genome. Here, we present the EN-TEx resource of 1,635 open-access datasets from four donors (∼30 tissues × ∼15 assays). The datasets are mapped to matched, diploid genomes with long-read phasing and structural variants, instantiating a catalog of >1 million allele-specific loci. These loci exhibit coordinated activity along haplotypes and are less conserved than corresponding, non-allele-specific ones. Surprisingly, a deep-learning transformer model can predict the allele-specific activity based only on local nucleotide-sequence context, highlighting the importance of transcription-factor-binding motifs particularly sensitive to variants. Furthermore, combining EN-TEx with existing genome annotations reveals strong associations between allele-specific and GWAS loci. It also enables models for transferring known eQTLs to difficult-to-profile tissues (e.g., from skin to heart). Overall, EN-TEx provides rich data and generalizable models for more accurate personal functional genomics.
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Affiliation(s)
- Joel Rozowsky
- Section on Biomedical Informatics and Data Science, Yale University, New Haven, CT, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jiahao Gao
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Beatrice Borsari
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Yucheng T Yang
- Institute of Science and Technology for Brain-Inspired Intelligence; MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence; MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200433, China; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Timur Galeev
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Gamze Gürsoy
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | | | - Kun Xiong
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jinrui Xu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Tianxiao Li
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jason Liu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Keyang Yu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ana Berthel
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Zhanlin Chen
- Department of Statistics and Data Science, Yale University, New Haven, CT, USA
| | - Fabio Navarro
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Maxwell S Sun
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | | | - Justin Chang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Christopher J F Cameron
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Noam Shoresh
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Jorg Drenkow
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Jessika Adrian
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Sergey Aganezov
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA
| | | | | | | | | | - Sora Chee
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
| | - Surya B Chhetri
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Gabriel Conte Cortez Martins
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Cassidy Danyko
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Carrie A Davis
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Daniel Farid
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | | | - Idan Gabdank
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Yoel Gofin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - David U Gorkin
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
| | - Mengting Gu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Vivian Hecht
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin C Hitz
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Robbyn Issner
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yunzhe Jiang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Melanie Kirsche
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Xiangmeng Kong
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Bonita R Lam
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Shantao Li
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Bian Li
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Xiqi Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Khine Zin Lin
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Ruibang Luo
- Department of Computer Science, The University of Hong Kong, Hong Kong, CHN
| | - Mark Mackiewicz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Ran Meng
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jill E Moore
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jonathan Mudge
- European Bioinformatics Institute, Cambridge, Cambridgeshire, GB
| | | | - Chad Nusbaum
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ioann Popov
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Henry E Pratt
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Yunjiang Qiu
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
| | - Srividya Ramakrishnan
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Joe Raymond
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Leonidas Salichos
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Department of Biological and Chemical Sciences, New York Institute of Technology, Old Westbury, NY, USA
| | - Alexandra Scavelli
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Jacob M Schreiber
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Fritz J Sedlazeck
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA; Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Lei Hoon See
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Rachel M Sherman
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Xu Shi
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Minyi Shi
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Cricket Alicia Sloan
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - J Seth Strattan
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Zhen Tan
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Forrest Y Tanaka
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Anna Vlasova
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain; Comparative Genomics Group, Life Science Programme, Barcelona Supercomputing Centre, Barcelona, Spain; Institute of Research in Biomedicine, Barcelona, Spain
| | - Jun Wang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jonathan Werner
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Brian Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Min Xu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Chengfei Yan
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Lu Yu
- Institute of Cancer Research, London, UK
| | - Christopher Zaleski
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Jing Zhang
- Department of Computer Science, University of California, Irvine, Irvine, CA, USA
| | | | - J Michael Cherry
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | | | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Morgan E Levine
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Alexander Dobin
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Barbara Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
| | - Jesse Gillis
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Michael P Snyder
- Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA
| | | | | | - Michael C Schatz
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA; Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
| | - Bradley E Bernstein
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Roderic Guigó
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain; Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.
| | - Thomas R Gingeras
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
| | - Mark Gerstein
- Section on Biomedical Informatics and Data Science, Yale University, New Haven, CT, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Department of Statistics and Data Science, Yale University, New Haven, CT, USA; Department of Computer Science, Yale University, New Haven, CT, USA.
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3
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Borsari B, Villegas-Mirón P, Pérez-Lluch S, Turpin I, Laayouni H, Segarra-Casas A, Bertranpetit J, Guigó R, Acosta S. Enhancers with tissue-specific activity are enriched in intronic regions. Genome Res 2021; 31:1325-1336. [PMID: 34290042 PMCID: PMC8327915 DOI: 10.1101/gr.270371.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 06/23/2021] [Indexed: 01/07/2023]
Abstract
Tissue function and homeostasis reflect the gene expression signature by which the combination of ubiquitous and tissue-specific genes contribute to the tissue maintenance and stimuli-responsive function. Enhancers are central to control this tissue-specific gene expression pattern. Here, we explore the correlation between the genomic location of enhancers and their role in tissue-specific gene expression. We find that enhancers showing tissue-specific activity are highly enriched in intronic regions and regulate the expression of genes involved in tissue-specific functions, whereas housekeeping genes are more often controlled by intergenic enhancers, common to many tissues. Notably, an intergenic-to-intronic active enhancers continuum is observed in the transition from developmental to adult stages: the most differentiated tissues present higher rates of intronic enhancers, whereas the lowest rates are observed in embryonic stem cells. Altogether, our results suggest that the genomic location of active enhancers is key for the tissue-specific control of gene expression.
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Affiliation(s)
- Beatrice Borsari
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Catalonia, Spain
| | - Pablo Villegas-Mirón
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona 08003, Catalonia, Spain
| | - Sílvia Pérez-Lluch
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Catalonia, Spain
| | - Isabel Turpin
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona 08003, Catalonia, Spain
| | - Hafid Laayouni
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona 08003, Catalonia, Spain.,Bioinformatic Studies, ESCI-UPF, 08003, Barcelona, Spain
| | - Alba Segarra-Casas
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona 08003, Catalonia, Spain
| | - Jaume Bertranpetit
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona 08003, Catalonia, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona 08003, Catalonia, Spain
| | - Sandra Acosta
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona 08003, Catalonia, Spain.,Department of Pathology and Experimental Therapeutics, Medical School, University of Barcelona, 08907, L'Hospitalet de Llobregat, Catalonia, Spain
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4
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Garrido-Martín D, Borsari B, Calvo M, Reverter F, Guigó R. Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome. Nat Commun 2021; 12:727. [PMID: 33526779 PMCID: PMC7851174 DOI: 10.1038/s41467-020-20578-2] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 12/02/2020] [Indexed: 12/13/2022] Open
Abstract
Alternative splicing (AS) is a fundamental step in eukaryotic mRNA biogenesis. Here, we develop an efficient and reproducible pipeline for the discovery of genetic variants that affect AS (splicing QTLs, sQTLs). We use it to analyze the GTEx dataset, generating a comprehensive catalog of sQTLs in the human genome. Downstream analysis of this catalog provides insight into the mechanisms underlying splicing regulation. We report that a core set of sQTLs is shared across multiple tissues. sQTLs often target the global splicing pattern of genes, rather than individual splicing events. Many also affect the expression of the same or other genes, uncovering regulatory loci that act through different mechanisms. sQTLs tend to be located in post-transcriptionally spliced introns, which would function as hotspots for splicing regulation. While many variants affect splicing patterns by altering the sequence of splice sites, many more modify the binding sites of RNA-binding proteins. Genetic variants affecting splicing can have a stronger phenotypic impact than those affecting gene expression.
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Affiliation(s)
- Diego Garrido-Martín
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Catalonia, Spain.
| | - Beatrice Borsari
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Catalonia, Spain
| | - Miquel Calvo
- Section of Statistics, Faculty of Biology, Universitat de Barcelona (UB), Av. Diagonal 643, Barcelona, 08028, Spain
| | - Ferran Reverter
- Section of Statistics, Faculty of Biology, Universitat de Barcelona (UB), Av. Diagonal 643, Barcelona, 08028, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Catalonia, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain.
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5
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Ramilowski JA, Yip CW, Agrawal S, Chang JC, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, Petri A, Roos L, Severin J, Yasuzawa K, Abugessaisa I, Akalin A, Antonov IV, Arner E, Bonetti A, Bono H, Borsari B, Brombacher F, Cameron CJ, Cannistraci CV, Cardenas R, Cardon M, Chang H, Dostie J, Ducoli L, Favorov A, Fort A, Garrido D, Gil N, Gimenez J, Guler R, Handoko L, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto K, Hayatsu N, Heutink P, Hirose T, Imada EL, Itoh M, Kaczkowski B, Kanhere A, Kawabata E, Kawaji H, Kawashima T, Kelly ST, Kojima M, Kondo N, Koseki H, Kouno T, Kratz A, Kurowska-Stolarska M, Kwon ATJ, Leek J, Lennartsson A, Lizio M, López-Redondo F, Luginbühl J, Maeda S, Makeev VJ, Marchionni L, Medvedeva YA, Minoda A, Müller F, Muñoz-Aguirre M, Murata M, Nishiyori H, Nitta KR, Noguchi S, Noro Y, Nurtdinov R, Okazaki Y, Orlando V, Paquette D, Parr CJ, Rackham OJ, Rizzu P, Martinez DFS, Sandelin A, Sanjana P, Semple CA, Shibayama Y, Sivaraman DM, Suzuki T, Szumowski SC, Tagami M, Taylor MS, Terao C, Thodberg M, Thongjuea S, Tripathi V, Ulitsky I, Verardo R, Vorontsov IE, Yamamoto C, Young RS, Baillie JK, Forrest AR, Guigó R, Hoffman MM, Hon CC, Kasukawa T, Kauppinen S, Kere J, Lenhard B, Schneider C, Suzuki H, Yagi K, de Hoon MJ, Shin JW, Carninci P. Corrigendum: Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Res 2020. [DOI: 10.1101/gr.270330.120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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6
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Ramilowski JA, Yip CW, Agrawal S, Chang JC, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, Petri A, Roos L, Severin J, Yasuzawa K, Abugessaisa I, Akalin A, Antonov IV, Arner E, Bonetti A, Bono H, Borsari B, Brombacher F, Cameron CJF, Cannistraci CV, Cardenas R, Cardon M, Chang H, Dostie J, Ducoli L, Favorov A, Fort A, Garrido D, Gil N, Gimenez J, Guler R, Handoko L, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto K, Hayatsu N, Heutink P, Hirose T, Imada EL, Itoh M, Kaczkowski B, Kanhere A, Kawabata E, Kawaji H, Kawashima T, Kelly ST, Kojima M, Kondo N, Koseki H, Kouno T, Kratz A, Kurowska-Stolarska M, Kwon ATJ, Leek J, Lennartsson A, Lizio M, López-Redondo F, Luginbühl J, Maeda S, Makeev VJ, Marchionni L, Medvedeva YA, Minoda A, Müller F, Muñoz-Aguirre M, Murata M, Nishiyori H, Nitta KR, Noguchi S, Noro Y, Nurtdinov R, Okazaki Y, Orlando V, Paquette D, Parr CJC, Rackham OJL, Rizzu P, Sánchez Martinez DF, Sandelin A, Sanjana P, Semple CAM, Shibayama Y, Sivaraman DM, Suzuki T, Szumowski SC, Tagami M, Taylor MS, Terao C, Thodberg M, Thongjuea S, Tripathi V, Ulitsky I, Verardo R, Vorontsov IE, Yamamoto C, Young RS, Baillie JK, Forrest ARR, Guigó R, Hoffman MM, Hon CC, Kasukawa T, Kauppinen S, Kere J, Lenhard B, Schneider C, Suzuki H, Yagi K, de Hoon MJL, Shin JW, Carninci P. Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Res 2020; 30:1060-1072. [PMID: 32718982 PMCID: PMC7397864 DOI: 10.1101/gr.254219.119] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 06/24/2020] [Indexed: 12/12/2022]
Abstract
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 oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.
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Affiliation(s)
- Jordan A Ramilowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Chi Wai Yip
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Saumya Agrawal
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jen-Chien Chang
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Yari Ciani
- Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie (CIB), Trieste 34127, Italy
| | - Ivan V Kulakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.,Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Mickaël Mendez
- Department of Computer Science, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | | | - John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Nick Parkinson
- Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, United Kingdom
| | - Andreas Petri
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen 9220, Denmark
| | - Leonie Roos
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom
| | - Jessica Severin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Kayoko Yasuzawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Imad Abugessaisa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Altuna Akalin
- Berlin Institute for Medical Systems Biology, Max Delbrük Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | - Ivan V Antonov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 117312, Russia
| | - Erik Arner
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Alessandro Bonetti
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Hidemasa Bono
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima City 739-0046, Japan
| | - Beatrice Borsari
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Frank Brombacher
- International Centre for Genetic Engineering and Biotechnology (ICGEB), University of Cape Town, Cape Town 7925, South Africa.,Institute of Infectious Diseases and Molecular Medicine (IDM), Department of Pathology, Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Christopher JF Cameron
- School of Computer Science, McGill University, Montréal, Québec H3G 1Y6, Canada.,Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, Québec H3G 1Y6, Canada.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06510, USA
| | - Carlo Vittorio Cannistraci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Cluster of Excellence Physics of Life (PoL), Department of Physics, Technische Universität Dresden, Dresden 01062, Germany.,Center for Complex Network Intelligence (CCNI) at the Tsinghua Laboratory of Brain and Intelligence (THBI), Department of Bioengineering, Tsinghua University, Beijing 100084, China
| | - Ryan Cardenas
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Melissa Cardon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Howard Chang
- Center for Personal Dynamic Regulome, Stanford University, Stanford, California 94305, USA
| | - Josée Dostie
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Luca Ducoli
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, Zurich 8093, Switzerland
| | - Alexander Favorov
- Department of Computational Systems Biology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.,Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Alexandre Fort
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Diego Garrido
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Noa Gil
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Juliette Gimenez
- Epigenetics and Genome Reprogramming Laboratory, IRCCS Fondazione Santa Lucia, Rome 00179, Italy
| | - Reto Guler
- International Centre for Genetic Engineering and Biotechnology (ICGEB), University of Cape Town, Cape Town 7925, South Africa.,Institute of Infectious Diseases and Molecular Medicine (IDM), Department of Pathology, Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Lusy Handoko
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jayson Harshbarger
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Akira Hasegawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Yuki Hasegawa
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Kosuke Hashimoto
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Norihito Hayatsu
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Peter Heutink
- Genome Biology of Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Tübingen 72076, Germany
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Eddie L Imada
- Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Masayoshi Itoh
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Saitama 351-0198, Japan
| | - Bogumil Kaczkowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Aditi Kanhere
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Emily Kawabata
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Hideya Kawaji
- RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Saitama 351-0198, Japan
| | - Tsugumi Kawashima
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - S Thomas Kelly
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Miki Kojima
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Naoto Kondo
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Haruhiko Koseki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Tsukasa Kouno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Anton Kratz
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Mariola Kurowska-Stolarska
- Institute of Infection, Immunity, and Inflammation, University of Glasgow, Glasgow, Scotland G12 8QQ, United Kingdom
| | - Andrew Tae Jun Kwon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jeffrey Leek
- Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14157, Sweden
| | - Marina Lizio
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Fernando López-Redondo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Joachim Luginbühl
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Shiori Maeda
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Vsevolod J Makeev
- Department of Computational Systems Biology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Luigi Marchionni
- Department of Oncology, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Yulia A Medvedeva
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow 117312, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Aki Minoda
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Manuel Muñoz-Aguirre
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Mitsuyoshi Murata
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Hiromi Nishiyori
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Kazuhiro R Nitta
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Shuhei Noguchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Yukihiko Noro
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Ramil Nurtdinov
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
| | - Yasushi Okazaki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Valerio Orlando
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Denis Paquette
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Callum J C Parr
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Patrizia Rizzu
- Genome Biology of Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Tübingen 72076, Germany
| | | | - Albin Sandelin
- Department of Biology and BRIC, University of Copenhagen, Denmark, Copenhagen N DK2200, Denmark
| | - Pillay Sanjana
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Colin A M Semple
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Youtaro Shibayama
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Divya M Sivaraman
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Takahiro Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | | | - Michihira Tagami
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Martin S Taylor
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Chikashi Terao
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Malte Thodberg
- Department of Biology and BRIC, University of Copenhagen, Denmark, Copenhagen N DK2200, Denmark
| | - Supat Thongjuea
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Vidisha Tripathi
- National Centre for Cell Science, Pune, Maharashtra 411007, India
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Roberto Verardo
- Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie (CIB), Trieste 34127, Italy
| | - Ilya E Vorontsov
- Department of Computational Systems Biology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Chinatsu Yamamoto
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Robert S Young
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, United Kingdom
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, United Kingdom
| | - Alistair R R Forrest
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, Western Australia 6009, Australia
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Catalonia 08002, Spain
| | | | - Chung Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Sakari Kauppinen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen 9220, Denmark
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14157, Sweden.,Stem Cells and Metabolism Research Program, University of Helsinki and Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Boris Lenhard
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom.,Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen N-5008, Norway
| | - Claudio Schneider
- Laboratorio Nazionale Consorzio Interuniversitario Biotecnologie (CIB), Trieste 34127, Italy.,Department of Medicine and Consorzio Interuniversitario Biotecnologie p.zle Kolbe 1 University of Udine, Udine 33100, Italy
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Ken Yagi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Michiel J L de Hoon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jay W Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
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7
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Stik G, Vidal E, Barrero M, Cuartero S, Vila-Casadesús M, Mendieta-Esteban J, Tian TV, Choi J, Berenguer C, Abad A, Borsari B, le Dily F, Cramer P, Marti-Renom MA, Stadhouders R, Graf T. CTCF is dispensable for immune cell transdifferentiation but facilitates an acute inflammatory response. Nat Genet 2020; 52:655-661. [DOI: 10.1038/s41588-020-0643-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 05/08/2020] [Indexed: 11/09/2022]
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8
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Pervouchine D, Popov Y, Berry A, Borsari B, Frankish A, Guigó R. Integrative transcriptomic analysis suggests new autoregulatory splicing events coupled with nonsense-mediated mRNA decay. Nucleic Acids Res 2019; 47:5293-5306. [PMID: 30916337 PMCID: PMC6547761 DOI: 10.1093/nar/gkz193] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/12/2019] [Indexed: 11/12/2022] Open
Abstract
Nonsense-mediated decay (NMD) is a eukaryotic mRNA surveillance system that selectively degrades transcripts with premature termination codons (PTC). Many RNA-binding proteins (RBP) regulate their expression levels by a negative feedback loop, in which RBP binds its own pre-mRNA and causes alternative splicing to introduce a PTC. We present a bioinformatic analysis integrating three data sources, eCLIP assays for a large RBP panel, shRNA inactivation of NMD pathway, and shRNA-depletion of RBPs followed by RNA-seq, to identify novel such autoregulatory feedback loops. We show that RBPs frequently bind their own pre-mRNAs, their exons respond prominently to NMD pathway disruption, and that the responding exons are enriched with nearby eCLIP peaks. We confirm previously proposed models of autoregulation in SRSF7 and U2AF1 genes and present two novel models, in which (i) SFPQ binds its mRNA and promotes switching to an alternative distal 3'-UTR that is targeted by NMD, and (ii) RPS3 binding activates a poison 5'-splice site in its pre-mRNA that leads to a frame shift and degradation by NMD. We also suggest specific splicing events that could be implicated in autoregulatory feedback loops in RBM39, HNRNPM, and U2AF2 genes. The results are available through a UCSC Genome Browser track hub.
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Affiliation(s)
- Dmitri Pervouchine
- Skolkovo Institute of Science and Technology, Ulitsa Nobelya 3, Moscow 121205, Russia
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Leninskiye Gory 1-73, 119234 Moscow, Russia
| | - Yaroslav Popov
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Leninskiye Gory 1-73, 119234 Moscow, Russia
| | - Andy Berry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, CB10 1SA Hinxton, Cambridge, UK
| | - Beatrice Borsari
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, CB10 1SA Hinxton, Cambridge, UK
| | - Roderic Guigó
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
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9
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Hustad JTP, Borsari B. Web-based screening and brief motivational intervention reduces alcohol use in heavy-drinking undergraduates at up to 6 months. ACTA ACUST UNITED AC 2010. [DOI: 10.1136/ebm1015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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10
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Abstract
Peer pressure is consistently implicated in the excessive drinking of college students. However, both theory and empirical findings suggest that peer pressure is a combination of three distinct influences: overt offers of alcohol, modeling, and social norms. Overt offers of alcohol can range from polite gestures to intense goading or commands to drink. Modeling occurs when the student's behavior corresponds to another student's concurrent drinking behavior. Perceived social norms can serve to make excessive alcohol use appear common and acceptable to the student. This review critically examines the literature on each form of peer influence and provides suggestions for future research.
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Affiliation(s)
- B Borsari
- Center for Health and Behavior, Syracuse University, NY 13244-2340, USA.
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11
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Borsari B, Neal DJ, Collins SE, Carey KB. Differential utility of three indexes of risky drinking for predicting alcohol problems in college students. Psychol Addict Behav 2002. [PMID: 11767264 DOI: 10.1037//0893-164x.15.4.321] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This study evaluated the relationship between alcohol-related problems and 3 indexes of risky drinking in college student drinkers: number of drinks consumed per week, frequency of binge drinking, and estimated blood alcohol levels (BALs). Use of 2 independent samples (N1 = 204, N2 = 181) allowed a cross-validation of obtained associations. Results indicated that neither binge drinking frequency nor BAL were more highly related to alcohol-related problems than was weekly drinking. Furthermore, BAL did not provide unique explanatory power in accounting for alcohol-related problems; mixed results were obtained regarding the relationship of binge drinking estimates with problems.
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Affiliation(s)
- B Borsari
- Department of Psychology, Syracuse University, New York 13244-2340, USA.
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12
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Borsari B, Neal DJ, Collins SE, Carey KB. Differential utility of three indexes of risky drinking for predicting alcohol problems in college students. Psychol Addict Behav 2001; 15:321-4. [PMID: 11767264 PMCID: PMC2635061 DOI: 10.1037/0893-164x.15.4.321] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This study evaluated the relationship between alcohol-related problems and 3 indexes of risky drinking in college student drinkers: number of drinks consumed per week, frequency of binge drinking, and estimated blood alcohol levels (BALs). Use of 2 independent samples (N1 = 204, N2 = 181) allowed a cross-validation of obtained associations. Results indicated that neither binge drinking frequency nor BAL were more highly related to alcohol-related problems than was weekly drinking. Furthermore, BAL did not provide unique explanatory power in accounting for alcohol-related problems; mixed results were obtained regarding the relationship of binge drinking estimates with problems.
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Affiliation(s)
- B Borsari
- Department of Psychology, Syracuse University, New York 13244-2340, USA.
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13
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Borsari B, Carey KB. Peer influences on college drinking: a review of the research. J Subst Abuse 2001. [PMID: 11775073 DOI: 10.1016/s08993289(01)00098-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Peer pressure is consistently implicated in the excessive drinking of college students. However, both theory and empirical findings suggest that peer pressure is a combination of three distinct influences: overt offers of alcohol, modeling, and social norms. Overt offers of alcohol can range from polite gestures to intense goading or commands to drink. Modeling occurs when the student's behavior corresponds to another student's concurrent drinking behavior. Perceived social norms can serve to make excessive alcohol use appear common and acceptable to the student. This review critically examines the literature on each form of peer influence and provides suggestions for future research.
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Affiliation(s)
- B Borsari
- Center for Health and Behavior, Syracuse University, NY 13244-2340, USA.
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14
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Borsari B, Carey KB. Effects of a brief motivational intervention with college student drinkers. J Consult Clin Psychol 2000; 68:728-33. [PMID: 10965648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
This study consisted of a randomized controlled trial of a 1-session motivational intervention for college student binge drinkers. Sixty students who reported binge drinking 2 or more times in the past 30 days were randomly assigned to either a no-treatment control or a brief intervention group. The intervention provided students with feedback regarding personal consumption, perceived drinking norms, alcohol-related problems, situations associated with heavy drinking, and alcohol expectancies. At 6-week follow-up, the brief intervention group exhibited significant reductions on number of drinks consumed per week, number of times drinking alcohol in the past month, and frequency of binge drinking in the past month. Estimates of typical student drinking mediated these reductions. This study replicates earlier research on the efficacy of brief interventions with college students and extends previous work regarding potential mechanisms of change.
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Affiliation(s)
- B Borsari
- Department of Psychology, Syracuse University, New York 13244-2340, USA.
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15
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Campioli O, Borsari B, Villani M. [Fibroangioma of the small intestine. Description of a case]. MINERVA CHIR 1979; 34:889-92. [PMID: 225699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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