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Childs JE, Morabito S, Das S, Santelli C, Pham V, Kusche K, Vera VA, Reese F, Campbell RR, Matheos DP, Swarup V, Wood MA. Relapse to cocaine seeking is regulated by medial habenula NR4A2/NURR1 in mice. Cell Rep 2024; 43:113956. [PMID: 38489267 PMCID: PMC11100346 DOI: 10.1016/j.celrep.2024.113956] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 09/28/2022] [Revised: 09/11/2023] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
Drugs of abuse can persistently change the reward circuit in ways that contribute to relapse behavior, partly via mechanisms that regulate chromatin structure and function. Nuclear orphan receptor subfamily4 groupA member2 (NR4A2, also known as NURR1) is an important effector of histone deacetylase 3 (HDAC3)-dependent mechanisms in persistent memory processes and is highly expressed in the medial habenula (MHb), a region that regulates nicotine-associated behaviors. Here, expressing the Nr4a2 dominant negative (Nurr2c) in the MHb blocks reinstatement of cocaine seeking in mice. We use single-nucleus transcriptomics to characterize the molecular cascade following Nr4a2 manipulation, revealing changes in transcriptional networks related to addiction, neuroplasticity, and GABAergic and glutamatergic signaling. The network controlled by NR4A2 is characterized using a transcription factor regulatory network inference algorithm. These results identify the MHb as a pivotal regulator of relapse behavior and demonstrate the importance of NR4A2 as a key mechanism driving the MHb component of relapse.
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Affiliation(s)
- Jessica E Childs
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; UC Irvine Center for Addiction Neuroscience, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Samuel Morabito
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, Irvine, CA 92697, USA; Mathematical, Computational, and Systems Biology (MCSB) Program, University of California, Irvine, Irvine, CA 92697, USA; Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Sudeshna Das
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, Irvine, CA 92697, USA
| | - Caterina Santelli
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; UC Irvine Center for Addiction Neuroscience, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Victoria Pham
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; UC Irvine Center for Addiction Neuroscience, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Kelly Kusche
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; UC Irvine Center for Addiction Neuroscience, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Vanessa Alizo Vera
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; UC Irvine Center for Addiction Neuroscience, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Fairlie Reese
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Rianne R Campbell
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; UC Irvine Center for Addiction Neuroscience, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Dina P Matheos
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; UC Irvine Center for Addiction Neuroscience, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Vivek Swarup
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, Irvine, CA 92697, USA.
| | - Marcelo A Wood
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA; UC Irvine Center for Addiction Neuroscience, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA; Center for the Neurobiology of Learning and Memory, School of Biological Sciences, University of California, Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, Irvine, CA 92697, USA.
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Rezaie N, Rebboah E, Williams BA, Liang HY, Reese F, Balderrama-Gutierrez G, Dionne LA, Reinholdt L, Trout D, Wold BJ, Mortazavi A. Identification of robust cellular programs using reproducible LDA that impact sex-specific disease progression in different genotypes of a mouse model of AD. bioRxiv 2024:2024.02.26.582178. [PMID: 38464087 PMCID: PMC10925135 DOI: 10.1101/2024.02.26.582178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The gene expression profiles of distinct cell types reflect complex genomic interactions among multiple simultaneous biological processes within each cell that can be altered by disease progression as well as genetic background. The identification of these active cellular programs is an open challenge in the analysis of single-cell RNA-seq data. Latent Dirichlet Allocation (LDA) is a generative method used to identify recurring patterns in counts data, commonly referred to as topics that can be used to interpret the state of each cell. However, LDA's interpretability is hindered by several key factors including the hyperparameter selection of the number of topics as well as the variability in topic definitions due to random initialization. We developed Topyfic, a Reproducible LDA (rLDA) package, to accurately infer the identity and activity of cellular programs in single-cell data, providing insights into the relative contributions of each program in individual cells. We apply Topyfic to brain single-cell and single-nucleus datasets of two 5xFAD mouse models of Alzheimer's disease crossed with C57BL6/J or CAST/EiJ mice to identify distinct cell types and states in different cell types such as microglia. We find that 8-month 5xFAD/Cast F1 males show higher level of microglial activation than matching 5xFAD/BL6 F1 males, whereas female mice show similar levels of microglial activation. We show that regulatory genes such as TFs, microRNA host genes, and chromatin regulatory genes alone capture cell types and cell states. Our study highlights how topic modeling with a limited vocabulary of regulatory genes can identify gene expression programs in single-cell data in order to quantify similar and divergent cell states in distinct genotypes.
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Affiliation(s)
- Narges Rezaie
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Elisabeth Rebboah
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Brian A Williams
- Division of Biology, California Institute of Technology, Pasadena, CA, USA
| | - Heidi Yahan Liang
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Fairlie Reese
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Gabriela Balderrama-Gutierrez
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | | | | | - Diane Trout
- Division of Biology, California Institute of Technology, Pasadena, CA, USA
| | - Barbara J Wold
- Division of Biology, California Institute of Technology, Pasadena, CA, USA
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
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3
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Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G, Behera AK, Gonzalez JM, Hunt T, Lagarde J, Liang CE, Li H, Jerryd Meade M, Moraga Amador DA, Prjibelski AD, Birol I, Bostan H, Brooks AM, Hasan Çelik M, Chen Y, Du MR, Felton C, Göke J, Hafezqorani S, Herwig R, Kawaji H, Lee J, Liang Li J, Lienhard M, Mikheenko A, Mulligan D, Ming Nip K, Pertea M, Ritchie ME, Sim AD, Tang AD, Kei Wan Y, Wang C, Wong BY, Yang C, Barnes I, Berry A, Capella S, Dhillon N, Fernandez-Gonzalez JM, Ferrández-Peral L, Garcia-Reyero N, Goetz S, Hernández-Ferrer C, Kondratova L, Liu T, Martinez-Martin A, Menor C, Mestre-Tomás J, Mudge JM, Panayotova NG, Paniagua A, Repchevsky D, Rouchka E, Saint-John B, Sapena E, Sheynkman L, Laird Smith M, Suner MM, Takahashi H, Youngworth IA, Carninci P, Denslow ND, Guigó R, Hunter ME, Tilgner HU, Wold BJ, Vollmers C, Frankish A, Fai Au K, Sheynkman GM, Mortazavi A, Conesa A, Brooks AN. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. bioRxiv 2023:2023.07.25.550582. [PMID: 37546854 PMCID: PMC10402094 DOI: 10.1101/2023.07.25.550582] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from cDNA and direct RNA datasets, encompassing human, mouse, and manatee species, using different protocols and sequencing platforms. These data were utilized by developers to address challenges in transcript isoform detection and quantification, as well as de novo transcript isoform identification. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. When aiming to detect rare and novel transcripts or when using reference-free approaches, incorporating additional orthogonal data and replicate samples are advised. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis.
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Affiliation(s)
- Francisco J. Pardo-Palacios
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
- These authors contributed equally to this work
| | - Dingjie Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA
- These authors contributed equally to this work
| | - Fairlie Reese
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
- These authors contributed equally to this work
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, USA
- These authors contributed equally to this work
| | - Sílvia Carbonell-Sala
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- These authors contributed equally to this work
| | - Brian Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
- These authors contributed equally to this work
| | - Jane E. Loveland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- These authors contributed equally to this work
| | - Maite De María
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, USA
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, USA
- These authors contributed equally to this work
| | - Matthew S. Adams
- Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, USA
- These authors contributed equally to this work
| | - Gabriela Balderrama-Gutierrez
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
- These authors contributed equally to this work
| | - Amit K. Behera
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
- These authors contributed equally to this work
| | - Jose M. Gonzalez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- These authors contributed equally to this work
| | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- These authors contributed equally to this work
| | - Julien Lagarde
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Flomics Biotech, Dr Aiguader 88, Barcelona 08003, Spain
- These authors contributed equally to this work
| | - Cindy E. Liang
- Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, USA
- These authors contributed equally to this work
| | - Haoran Li
- Department of Biomedical Informatics, The Ohio State University, Columbus, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA
- These authors contributed equally to this work
| | - Marcus Jerryd Meade
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA
- These authors contributed equally to this work
| | - David A. Moraga Amador
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, USA
- These authors contributed equally to this work
| | - Andrey D. Prjibelski
- Department of Computer Science, University of Helsinki, Helsinki, Finland
- Center for Bioinformatics and Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
- These authors contributed equally to this work
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Hamed Bostan
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA
| | - Ashley M. Brooks
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA
| | - Muhammed Hasan Çelik
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Ying Chen
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Mei R,M. Du
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Colette Felton
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Jonathan Göke
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Statistics and Data Science, National University of Singapore, Singapore, Singapore
| | - Saber Hafezqorani
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Ralf Herwig
- Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Hideya Kawaji
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Joseph Lee
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jian Liang Li
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA
| | - Matthias Lienhard
- Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Alla Mikheenko
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Dennis Mulligan
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Ka Ming Nip
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Mihaela Pertea
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, USA
| | - Matthew E. Ritchie
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Andre D. Sim
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Alison D. Tang
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Yuk Kei Wan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Changqing Wang
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Brandon Y. Wong
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, USA
| | - Chen Yang
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - If Barnes
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrew Berry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Namrita Dhillon
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | | | - Luis Ferrández-Peral
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
| | - Natàlia Garcia-Reyero
- Environmental Laboratory, US Army Engineer Research & Development Center, Vicksburg, USA
| | | | | | | | | | | | | | - Jorge Mestre-Tomás
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
| | - Jonathan M. Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nedka G. Panayotova
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, USA
| | - Alejandro Paniagua
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
| | | | - Eric Rouchka
- Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, USA
| | - Brandon Saint-John
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Enrique Sapena
- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK, UK
| | - Leon Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA
| | - Melissa Laird Smith
- Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, USA
| | - Marie-Marthe Suner
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Hazuki Takahashi
- Center for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan
| | | | - Piero Carninci
- Center for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan
- Human Technopole, Milano, Italy
| | - Nancy D. Denslow
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, USA
- Center for Environmental and Human Toxicology, Department of Physiological Sciences,, University of Florida, Gainesville, USA
| | - 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
| | - Margaret E. Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, USA
| | - Hagen U. Tilgner
- Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York City, USA
| | - Barbara J. Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kin Fai Au
- Department of Biomedical Informatics, The Ohio State University, Columbus, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA
| | - Gloria M. Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA
- Center for Public Health Genomics
- UVA Cancer Center, University of Virginia, Charlottesville, USA
| | - Ali Mortazavi
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Ana Conesa
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
- Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, USA
| | - Angela N. Brooks
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, USA
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
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4
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Miyoshi E, Morabito S, Henningfield CM, Rahimzadeh N, Kiani Shabestari S, Das S, Michael N, Reese F, Shi Z, Cao Z, Scarfone V, Arreola MA, Lu J, Wright S, Silva J, Leavy K, Lott IT, Doran E, Yong WH, Shahin S, Perez-Rosendahl M, Head E, Green KN, Swarup V. Spatial and single-nucleus transcriptomic analysis of genetic and sporadic forms of Alzheimer's Disease. bioRxiv 2023:2023.07.24.550282. [PMID: 37546983 PMCID: PMC10402031 DOI: 10.1101/2023.07.24.550282] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The pathogenesis of Alzheimer's disease (AD) depends on environmental and heritable factors, with remarkable differences evident between individuals at the molecular level. Here we present a transcriptomic survey of AD using spatial transcriptomics (ST) and single-nucleus RNA-seq in cortical samples from early-stage AD, late-stage AD, and AD in Down Syndrome (AD in DS) donors. Studying AD in DS provides an opportunity to enhance our understanding of the AD transcriptome, potentially bridging the gap between genetic mouse models and sporadic AD. Our analysis revealed spatial and cell-type specific changes in disease, with broad similarities in these changes between sAD and AD in DS. We performed additional ST experiments in a disease timecourse of 5xFAD and wildtype mice to facilitate cross-species comparisons. Finally, amyloid plaque and fibril imaging in the same tissue samples used for ST enabled us to directly link changes in gene expression with accumulation and spread of pathology.
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Affiliation(s)
- Emily Miyoshi
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
| | - Samuel Morabito
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
- Mathematical, Computational, and Systems Biology (MCSB) Program, University of California Irvine, Irvine, CA, USA
- Center for Complex Biological Systems (CCBS), University of California Irvine, Irvine, CA, USA
| | - Caden M Henningfield
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
| | - Negin Rahimzadeh
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
- Mathematical, Computational, and Systems Biology (MCSB) Program, University of California Irvine, Irvine, CA, USA
- Center for Complex Biological Systems (CCBS), University of California Irvine, Irvine, CA, USA
| | - Sepideh Kiani Shabestari
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
- Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA, USA
| | - Sudeshna Das
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
| | - Neethu Michael
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
| | - Fairlie Reese
- Center for Complex Biological Systems (CCBS), University of California Irvine, Irvine, CA, USA
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA
| | - Zechuan Shi
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
| | - Zhenkun Cao
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
| | - Vanessa Scarfone
- Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA, USA
| | - Miguel A Arreola
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
| | - Jackie Lu
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
| | - Sierra Wright
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
| | - Justine Silva
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
| | - Kelsey Leavy
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
| | - Ira T Lott
- Department of Pediatrics, University of California Irvine School of Medicine, Orange, CA, USA
| | - Eric Doran
- Department of Pediatrics, University of California Irvine School of Medicine, Orange, CA, USA
| | - William H Yong
- Department of Pathology and Laboratory Medicine, University of California Irvine , Irvine, CA, USA
| | - Saba Shahin
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
| | - Mari Perez-Rosendahl
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
- Department of Pathology and Laboratory Medicine, University of California Irvine , Irvine, CA, USA
| | - Elizabeth Head
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
- Department of Pathology and Laboratory Medicine, University of California Irvine , Irvine, CA, USA
| | - Kim N Green
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
| | - Vivek Swarup
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California Irvine, Irvine, CA, USA
- Center for Complex Biological Systems (CCBS), University of California Irvine, Irvine, CA, USA
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5
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Liu Z, Quinones-Valdez G, Fu T, Huang E, Choudhury M, Reese F, Mortazavi A, Xiao X. L-GIREMI uncovers RNA editing sites in long-read RNA-seq. Genome Biol 2023; 24:171. [PMID: 37474948 PMCID: PMC10360234 DOI: 10.1186/s13059-023-03012-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 03/22/2022] [Accepted: 07/12/2023] [Indexed: 07/22/2023] Open
Abstract
Although long-read RNA-seq is increasingly applied to characterize full-length transcripts it can also enable detection of nucleotide variants, such as genetic mutations or RNA editing sites, which is significantly under-explored. Here, we present an in-depth study to detect and analyze RNA editing sites in long-read RNA-seq. Our new method, L-GIREMI, effectively handles sequencing errors and read biases. Applied to PacBio RNA-seq data, L-GIREMI affords a high accuracy in RNA editing identification. Additionally, our analysis uncovered novel insights about RNA editing occurrences in single molecules and double-stranded RNA structures. L-GIREMI provides a valuable means to study nucleotide variants in long-read RNA-seq.
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Affiliation(s)
- Zhiheng Liu
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA
| | - Giovanni Quinones-Valdez
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA
| | - Ting Fu
- Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, CA, USA
| | - Elaine Huang
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
| | - Mudra Choudhury
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
| | - Fairlie Reese
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Xinshu Xiao
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA.
- Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, CA, USA.
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA.
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6
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Hitz BC, Lee JW, Jolanki O, Kagda MS, Graham K, Sud P, Gabdank I, Strattan JS, Sloan CA, Dreszer T, Rowe LD, Podduturi NR, Malladi VS, Chan ET, Davidson JM, Ho M, Miyasato S, Simison M, Tanaka F, Luo Y, Whaling I, Hong EL, Lee BT, Sandstrom R, Rynes E, Nelson J, Nishida A, Ingersoll A, Buckley M, Frerker M, Kim DS, Boley N, Trout D, Dobin A, Rahmanian S, Wyman D, Balderrama-Gutierrez G, Reese F, Durand NC, Dudchenko O, Weisz D, Rao SSP, Blackburn A, Gkountaroulis D, Sadr M, Olshansky M, Eliaz Y, Nguyen D, Bochkov I, Shamim MS, Mahajan R, Aiden E, Gingeras T, Heath S, Hirst M, Kent WJ, Kundaje A, Mortazavi A, Wold B, Cherry JM. The ENCODE Uniform Analysis Pipelines. Res Sq 2023:rs.3.rs-3111932. [PMID: 37503119 PMCID: PMC10371165 DOI: 10.21203/rs.3.rs-3111932/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across more than 1000 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the Homo sapiens and Mus musculus genomes. All experimental data, metadata, and associated computational analyses created by the ENCODE consortium are submitted to the Data Coordination Center (DCC) for validation, tracking, storage, and distribution to community resources and the scientific community. The ENCODE project has engineered and distributed uniform processing pipelines in order to promote data provenance and reproducibility as well as allow interoperability between genomic resources and other consortia. All data files, reference genome versions, software versions, and parameters used by the pipelines are captured and available via the ENCODE Portal. The pipeline code, developed using Docker and Workflow Description Language (WDL; https://openwdl.org/) is publicly available in GitHub, with images available on Dockerhub (https://hub.docker.com), enabling access to a diverse range of biomedical researchers. ENCODE pipelines maintained and used by the DCC can be installed to run on personal computers, local HPC clusters, or in cloud computing environments via Cromwell. Access to the pipelines and data via the cloud allows small labs the ability to use the data or software without access to institutional compute clusters. Standardization of the computational methodologies for analysis and quality control leads to comparable results from different ENCODE collections - a prerequisite for successful integrative analyses.
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Affiliation(s)
- Benjamin C Hitz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jin-Wook Lee
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Otto Jolanki
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Meenakshi S Kagda
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Keenan Graham
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Paul Sud
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Idan Gabdank
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - J Seth Strattan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cricket A Sloan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Timothy Dreszer
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laurence D Rowe
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nikhil R Podduturi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Venkat S Malladi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Esther T Chan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jean M Davidson
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marcus Ho
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stuart Miyasato
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matt Simison
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Forrest Tanaka
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yunhai Luo
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ian Whaling
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Eurie L Hong
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brian T Lee
- Genomics Institute, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Richard Sandstrom
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Eric Rynes
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Jemma Nelson
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Andrew Nishida
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Alyssa Ingersoll
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Michael Buckley
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Mark Frerker
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Daniel S Kim
- Department of Genetics, Department of Computer Science, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94304, USA
| | - Nathan Boley
- Department of Genetics, Department of Computer Science, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94304, USA
| | - Diane Trout
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125 USA
| | - Alex Dobin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sorena Rahmanian
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Dana Wyman
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | | | - Fairlie Reese
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Neva C Durand
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
- Department of Computer Science, Rice University, Houston, TX 77030, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Suhas S P Rao
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Alyssa Blackburn
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Dimos Gkountaroulis
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Mahdi Sadr
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Moshe Olshansky
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yossi Eliaz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dat Nguyen
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ivan Bochkov
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muhammad Saad Shamim
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ragini Mahajan
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Erez Aiden
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Tom Gingeras
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Simon Heath
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain
| | - Martin Hirst
- Micheal Smith Laboratories, University of British Columbia, British Columbia, Canada
| | - W James Kent
- Genomics Institute, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Anshul Kundaje
- Department of Genetics, Department of Computer Science, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94304, USA
| | - Ali Mortazavi
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Barbara Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125 USA
| | - J Michael Cherry
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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7
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Morabito S, Reese F, Rahimzadeh N, Miyoshi E, Swarup V. hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data. Cell Rep Methods 2023; 3:100498. [PMID: 37426759 PMCID: PMC10326379 DOI: 10.1016/j.crmeth.2023.100498] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 02/13/2023] [Accepted: 05/16/2023] [Indexed: 07/11/2023]
Abstract
Biological systems are immensely complex, organized into a multi-scale hierarchy of functional units based on tightly regulated interactions between distinct molecules, cells, organs, and organisms. While experimental methods enable transcriptome-wide measurements across millions of cells, popular bioinformatic tools do not support systems-level analysis. Here we present hdWGCNA, a comprehensive framework for analyzing co-expression networks in high-dimensional transcriptomics data such as single-cell and spatial RNA sequencing (RNA-seq). hdWGCNA provides functions for network inference, gene module identification, gene enrichment analysis, statistical tests, and data visualization. Beyond conventional single-cell RNA-seq, hdWGCNA is capable of performing isoform-level network analysis using long-read single-cell data. We showcase hdWGCNA using data from autism spectrum disorder and Alzheimer's disease brain samples, identifying disease-relevant co-expression network modules. hdWGCNA is directly compatible with Seurat, a widely used R package for single-cell and spatial transcriptomics analysis, and we demonstrate the scalability of hdWGCNA by analyzing a dataset containing nearly 1 million cells.
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Affiliation(s)
- Samuel Morabito
- Mathematical, Computational, and Systems Biology (MCSB) Program, University of California, Irvine, Irvine, CA, USA
- Center for Complex Biological Systems (CCBS), University of California, Irvine, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, Irvine, CA, USA
| | - Fairlie Reese
- Center for Complex Biological Systems (CCBS), University of California, Irvine, Irvine, CA, USA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - Negin Rahimzadeh
- Mathematical, Computational, and Systems Biology (MCSB) Program, University of California, Irvine, Irvine, CA, USA
- Center for Complex Biological Systems (CCBS), University of California, Irvine, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, Irvine, CA, USA
| | - Emily Miyoshi
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, Irvine, CA, USA
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA
| | - Vivek Swarup
- Center for Complex Biological Systems (CCBS), University of California, Irvine, Irvine, CA, USA
- Institute for Memory Impairments and Neurological Disorders (MIND), University of California, Irvine, Irvine, CA, USA
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA
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8
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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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9
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Happ HC, Schneider PN, Hong JH, Goes E, Bandouil M, Biar CG, Ramamurthy A, Reese F, Engel K, Weckhuysen S, Scheffer IE, Mefford HC, Calhoun JD, Carvill GL. Long-read sequencing and profiling of RNA-binding proteins reveals the pathogenic mechanism of aberrant splicing of an SCN1A poison exon in epilepsy. bioRxiv 2023:2023.05.04.538282. [PMID: 37205386 PMCID: PMC10187291 DOI: 10.1101/2023.05.04.538282] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Pathogenic loss-of-function SCN1A variants cause a spectrum of seizure disorders. We previously identified variants in individuals with SCN1A -related epilepsy that fall in or near a poison exon (PE) in SCN1A intron 20 (20N). We hypothesized these variants lead to increased PE inclusion, which introduces a premature stop codon, and, therefore, reduced abundance of the full-length SCN1A transcript and Na v 1.1 protein. We used a splicing reporter assay to interrogate PE inclusion in HEK293T cells. In addition, we used patient-specific induced pluripotent stem cells (iPSCs) differentiated into neurons to quantify 20N inclusion by long and short-read sequencing and Na v 1.1 abundance by western blot. We performed RNA-antisense purification with mass spectrometry to identify RNA-binding proteins (RBPs) that could account for the aberrant PE splicing. We demonstrate that variants in/near 20N lead to increased 20N inclusion by long-read sequencing or splicing reporter assay and decreased Na v 1.1 abundance. We also identified 28 RBPs that differentially interact with variant constructs compared to wild-type, including SRSF1 and HNRNPL. We propose a model whereby 20N variants disrupt RBP binding to splicing enhancers (SRSF1) and suppressors (HNRNPL), to favor PE inclusion. Overall, we demonstrate that SCN1A 20N variants cause haploinsufficiency and SCN1A -related epilepsies. This work provides insights into the complex control of RBP-mediated PE alternative splicing, with broader implications for PE discovery and identification of pathogenic PE variants in other genetic conditions.
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10
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Hitz BC, Jin-Wook L, Jolanki O, Kagda MS, Graham K, Sud P, Gabdank I, Strattan JS, Sloan CA, Dreszer T, Rowe LD, Podduturi NR, Malladi VS, Chan ET, Davidson JM, Ho M, Miyasato S, Simison M, Tanaka F, Luo Y, Whaling I, Hong EL, Lee BT, Sandstrom R, Rynes E, Nelson J, Nishida A, Ingersoll A, Buckley M, Frerker M, Kim DS, Boley N, Trout D, Dobin A, Rahmanian S, Wyman D, Balderrama-Gutierrez G, Reese F, Durand NC, Dudchenko O, Weisz D, Rao SSP, Blackburn A, Gkountaroulis D, Sadr M, Olshansky M, Eliaz Y, Nguyen D, Bochkov I, Shamim MS, Mahajan R, Aiden E, Gingeras T, Heath S, Hirst M, Kent WJ, Kundaje A, Mortazavi A, Wold B, Cherry JM. The ENCODE Uniform Analysis Pipelines. bioRxiv 2023:2023.04.04.535623. [PMID: 37066421 PMCID: PMC10104020 DOI: 10.1101/2023.04.04.535623] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across more than 1000 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the Homo sapiens and Mus musculus genomes. All experimental data, metadata, and associated computational analyses created by the ENCODE consortium are submitted to the Data Coordination Center (DCC) for validation, tracking, storage, and distribution to community resources and the scientific community. The ENCODE project has engineered and distributed uniform processing pipelines in order to promote data provenance and reproducibility as well as allow interoperability between genomic resources and other consortia. All data files, reference genome versions, software versions, and parameters used by the pipelines are captured and available via the ENCODE Portal. The pipeline code, developed using Docker and Workflow Description Language (WDL; https://openwdl.org/) is publicly available in GitHub, with images available on Dockerhub (https://hub.docker.com), enabling access to a diverse range of biomedical researchers. ENCODE pipelines maintained and used by the DCC can be installed to run on personal computers, local HPC clusters, or in cloud computing environments via Cromwell. Access to the pipelines and data via the cloud allows small labs the ability to use the data or software without access to institutional compute clusters. Standardization of the computational methodologies for analysis and quality control leads to comparable results from different ENCODE collections - a prerequisite for successful integrative analyses.
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Affiliation(s)
- Benjamin C Hitz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lee Jin-Wook
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Otto Jolanki
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Meenakshi S Kagda
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Keenan Graham
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Paul Sud
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Idan Gabdank
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - J Seth Strattan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Cricket A Sloan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Timothy Dreszer
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laurence D Rowe
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nikhil R Podduturi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Venkat S Malladi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Esther T Chan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jean M Davidson
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marcus Ho
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stuart Miyasato
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matt Simison
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Forrest Tanaka
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yunhai Luo
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ian Whaling
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Eurie L Hong
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brian T Lee
- Genomics Institute, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Richard Sandstrom
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Eric Rynes
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Jemma Nelson
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Andrew Nishida
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Alyssa Ingersoll
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Michael Buckley
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Mark Frerker
- Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA
| | - Daniel S Kim
- Dept. of Genetics, Dept. of Computer Science, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94304, USA
| | - Nathan Boley
- Dept. of Genetics, Dept. of Computer Science, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94304, USA
| | - Diane Trout
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125 USA
| | - Alex Dobin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sorena Rahmanian
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Dana Wyman
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | | | - Fairlie Reese
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Neva C Durand
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
- Department of Computer Science, Rice University, Houston, TX 77030, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Suhas S P Rao
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Alyssa Blackburn
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Dimos Gkountaroulis
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Mahdi Sadr
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Moshe Olshansky
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yossi Eliaz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dat Nguyen
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ivan Bochkov
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muhammad Saad Shamim
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ragini Mahajan
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Erez Aiden
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Tom Gingeras
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Simon Heath
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain
| | - Martin Hirst
- Micheal Smith Laboratories, University of British Columbia, British Columbia, Canada
| | - W James Kent
- Genomics Institute, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Anshul Kundaje
- Dept. of Genetics, Dept. of Computer Science, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94304, USA
| | - Ali Mortazavi
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Barbara Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125 USA
| | - J Michael Cherry
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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11
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Moore JE, Zhang XO, Elhajjajy SI, Fan K, Pratt HE, Reese F, Mortazavi A, Weng Z. Integration of high-resolution promoter profiling assays reveals novel, cell type-specific transcription start sites across 115 human cell and tissue types. Genome Res 2021; 32:389-402. [PMID: 34949670 PMCID: PMC8805725 DOI: 10.1101/gr.275723.121] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 05/12/2021] [Accepted: 12/19/2021] [Indexed: 12/02/2022]
Abstract
Accurate transcription start site (TSS) annotations are essential for understanding transcriptional regulation and its role in human disease. Gene collections such as GENCODE contain annotations for tens of thousands of TSSs, but not all of these annotations are experimentally validated nor do they contain information on cell type–specific usage. Therefore, we sought to generate a collection of experimentally validated TSSs by integrating RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression (RAMPAGE) data from 115 cell and tissue types, which resulted in a collection of approximately 50 thousand representative RAMPAGE peaks. These peaks are primarily proximal to GENCODE-annotated TSSs and are concordant with other transcription assays. Because RAMPAGE uses paired-end reads, we were then able to connect peaks to transcripts by analyzing the genomic positions of the 3′ ends of read mates. Using this paired-end information, we classified the vast majority (37 thousand) of our RAMPAGE peaks as verified TSSs, updating TSS annotations for 20% of GENCODE genes. We also found that these updated TSS annotations are supported by epigenomic and other transcriptomic data sets. To show the utility of this RAMPAGE rPeak collection, we intersected it with the NHGRI/EBI genome-wide association study (GWAS) catalog and identified new candidate GWAS genes. Overall, our work shows the importance of integrating experimental data to further refine TSS annotations and provides a valuable resource for the biological community.
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Affiliation(s)
| | | | | | - Kaili Fan
- University of Massachusetts Chan Medical School
| | | | | | | | - Zhiping Weng
- University of Massachusetts Chan Medical School;
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12
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Rebboah E, Reese F, Williams K, Balderrama-Gutierrez G, McGill C, Trout D, Rodriguez I, Liang H, Wold BJ, Mortazavi A. Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq. Genome Biol 2021; 22:286. [PMID: 34620214 PMCID: PMC8495978 DOI: 10.1186/s13059-021-02505-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 04/28/2021] [Accepted: 09/20/2021] [Indexed: 11/24/2022] Open
Abstract
The rise in throughput and quality of long-read sequencing should allow unambiguous identification of full-length transcript isoforms. However, its application to single-cell RNA-seq has been limited by throughput and expense. Here we develop and characterize long-read Split-seq (LR-Split-seq), which uses combinatorial barcoding to sequence single cells with long reads. Applied to the C2C12 myogenic system, LR-split-seq associates isoforms to cell types with relative economy and design flexibility. We find widespread evidence of changing isoform expression during differentiation including alternative transcription start sites (TSS) and/or alternative internal exon usage. LR-Split-seq provides an affordable method for identifying cluster-specific isoforms in single cells.
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Affiliation(s)
- Elisabeth Rebboah
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, 92697, USA
| | - Fairlie Reese
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, 92697, USA
| | - Katherine Williams
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, 92697, USA
| | - Gabriela Balderrama-Gutierrez
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, 92697, USA
| | - Cassandra McGill
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, 92697, USA
| | - Diane Trout
- Division of Biology, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Isaryhia Rodriguez
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, 92697, USA
| | - Heidi Liang
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, 92697, USA
| | - Barbara J Wold
- Division of Biology, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697, USA.
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, 92697, USA.
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13
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Reese F, Mortazavi A. Swan: a library for the analysis and visualization of long-read transcriptomes. Bioinformatics 2021; 37:1322-1323. [PMID: 32991665 PMCID: PMC8189675 DOI: 10.1093/bioinformatics/btaa836] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/25/2020] [Accepted: 09/15/2020] [Indexed: 11/22/2022] Open
Abstract
Motivation Long-read RNA-sequencing technologies such as PacBio and Oxford Nanopore have discovered an explosion of new transcript isoforms that are difficult to visually analyze using currently available tools. We introduce the Swan Python library, which is designed to analyze and visualize transcript models. Results Swan finds 4909 differentially expressed transcripts between cell lines HepG2 and HFFc6, including 279 that are differentially expressed even though the parent gene is not. Additionally, Swan discovers 285 reproducible exon skipping and 47 intron retention events not recorded in the GENCODE v29 annotation. Availability and implementation The Swan library for Python 3 is available on PyPi at https://pypi.org/project/swan-vis/ and on GitHub at https://github.com/mortazavilab/swan_vis.
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Affiliation(s)
- Fairlie Reese
- Department of Developmental and Cell Biology.,Center for Complex Biological Systems, UC Irvine, Irvine, CA 92697, USA
| | - Ali Mortazavi
- Department of Developmental and Cell Biology.,Center for Complex Biological Systems, UC Irvine, Irvine, CA 92697, USA
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14
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Movassat M, Forouzmand E, Reese F, Hertel KJ. Exon size and sequence conservation improves identification of splice-altering nucleotides. RNA 2019; 25:1793-1805. [PMID: 31554659 PMCID: PMC6859846 DOI: 10.1261/rna.070987.119] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/23/2019] [Indexed: 06/10/2023]
Abstract
Pre-mRNA splicing is regulated through multiple trans-acting splicing factors. These regulators interact with the pre-mRNA at intronic and exonic positions. Given that most exons are protein coding, the evolution of exons must be modulated by a combination of selective coding and splicing pressures. It has previously been demonstrated that selective splicing pressures are more easily deconvoluted when phylogenetic comparisons are made for exons of identical size, suggesting that exon size-filtered sequence alignments may improve identification of nucleotides evolved to mediate efficient exon ligation. To test this hypothesis, an exon size database was created, filtering 76 vertebrate sequence alignments based on exon size conservation. In addition to other genomic parameters, such as splice-site strength, gene position, or flanking intron length, this database permits the identification of exons that are size- and/or sequence-conserved. Highly size-conserved exons are always sequence-conserved. However, sequence conservation does not necessitate exon size conservation. Our analysis identified evolutionarily young exons and demonstrated that length conservation is a strong predictor of alternative splicing. A published data set of approximately 5000 exonic SNPs associated with disease was analyzed to test the hypothesis that exon size-filtered sequence comparisons increase detection of splice-altering nucleotides. Improved splice predictions could be achieved when mutations occur at the third codon position, especially when a mutation decreases exon inclusion efficiency. The results demonstrate that coding pressures dominate nucleotide composition at invariable codon positions and that exon size-filtered sequence alignments permit identification of splice-altering nucleotides at wobble positions.
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Affiliation(s)
- Maliheh Movassat
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California 92697, USA
| | - Elmira Forouzmand
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California 92697, USA
| | - Fairlie Reese
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California 92697, USA
| | - Klemens J Hertel
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California 92697, USA
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Daum LT, Canas LC, Klimov AI, Shaw MW, Gibbons RV, Shrestha SK, Myint KS, Acharya RP, Rimal N, Reese F, Niemeyer DM, Arulanandam BP, Chambers JP. Molecular analysis of isolates from influenza B outbreaks in the U.S. and Nepal, 2005. Arch Virol 2006; 151:1863-74. [PMID: 16736092 DOI: 10.1007/s00705-006-0777-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2006] [Accepted: 04/06/2006] [Indexed: 10/24/2022]
Abstract
Currently circulating influenza B viruses can be divided into two antigenically and genetically distinct lineages referred to by their respective prototype strains, B/Yamagata/16/88 and B/Victoria/2/87, based on amino acid differences in the hemagglutinin surface glycoprotein. During May and July 2005, clinical specimens from two early season influenza B outbreaks in Arizona and southeastern Nepal were subjected to antigenic (hemagglutinin inhibition) and nucleotide sequence analysis of hemagglutinin (HA1), neuraminidase (NA), and NB genes. All isolates exhibited little reactivity with the B/Shanghai/361/2002 (B/Yamagata-like) vaccine strain and significantly reduced reactivity with the previous 2003/04 B/Hong Kong/330/2001 (B/Victoria-like) vaccine strain. The majority of isolates were antigenically similar to B/Hawaii/33/2004, a B/Victoria-like reference strain. Sequence analysis indicated that 33 of 34 isolates contained B/Victoria-like HA and B/Yamagata-like NA and NB proteins. Thus, these outbreak isolates are both antigenically and genetically distinct from the current Northern Hemisphere vaccine virus strain as well as the previous 2003-04 B/Hong Kong/330/2001 (B/Victoria lineage) vaccine virus strain but are genetically similar to B/Malaysia/2506/2004, the vaccine strain proposed for the coming seasons in the Northern and Southern Hemispheres. Since these influenza B outbreaks occurred in two very distant geographical locations, these viruses may continue to circulate during the 2006 season, underscoring the importance of rapid molecular monitoring of HA, NA and NB for drift and reassortment.
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Affiliation(s)
- L T Daum
- Air Force Institute for Operational Health, Brooks City Base, TX 78235, USA.
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16
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Abstract
The problem of a reduced resistance against infections in splenectomized patients is again described on the occasion of one patient who died within a very short time after the beginning of a severe infection. A retrospective study of 150 patients without spleen showed that 2.6% died in a consequence of a severe infection. From the surviving patients 20% complained of very frequent infections. Immunological laboratory data as well as the reaction against recall antigens were reduced in those patients. So not all patients without spleen bear a high risk with regard to severe infections. In spite of this fact surgeons should try to preserve the spleen even in adults.
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