1
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Drake KA, Talantov D, Tong GJ, Lin JT, Verheijden S, Katz S, Leung JM, Yuen B, Krishna V, Wu MJ, Sutherland AM, Short SA, Kheradpour P, Mumbach MR, Franz KM, Trifonov V, Lucas MV, Merson J, Kim CC. Multi-omic profiling reveals early immunological indicators for identifying COVID-19 Progressors. Clin Immunol 2023; 256:109808. [PMID: 37852344 DOI: 10.1016/j.clim.2023.109808] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/25/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
We sought to better understand the immune response during the immediate post-diagnosis phase of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by identifying molecular associations with longitudinal disease outcomes. Multi-omic analyses identified differences in immune cell composition, cytokine levels, and cell subset-specific transcriptomic and epigenomic signatures between individuals on a more serious disease trajectory (Progressors) as compared to those on a milder course (Non-progressors). Higher levels of multiple cytokines were observed in Progressors, with IL-6 showing the largest difference. Blood monocyte cell subsets were also skewed, showing a comparative decrease in non-classical CD14-CD16+ and intermediate CD14+CD16+ monocytes. In lymphocytes, the CD8+ T effector memory cells displayed a gene expression signature consistent with stronger T cell activation in Progressors. These early stage observations could serve as the basis for the development of prognostic biomarkers of disease risk and interventional strategies to improve the management of severe COVID-19. BACKGROUND: Much of the literature on immune response post-SARS-CoV-2 infection has been in the acute and post-acute phases of infection. TRANSLATIONAL SIGNIFICANCE: We found differences at early time points of infection in approximately 160 participants. We compared multi-omic signatures in immune cells between individuals progressing to needing more significant medical intervention and non-progressors. We observed widespread evidence of a state of increased inflammation associated with progression, supported by a range of epigenomic, transcriptomic, and proteomic signatures. The signatures we identified support other findings at later time points and serve as the basis for prognostic biomarker development or to inform interventional strategies.
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Affiliation(s)
- Katherine A Drake
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Dimitri Talantov
- Janssen Research & Development, LLC, San Diego, CA, United States of America
| | - Gary J Tong
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Jack T Lin
- Verily Life Sciences, South San Francisco, CA, United States of America
| | | | - Samuel Katz
- Verily Life Sciences, South San Francisco, CA, United States of America
| | | | - Benjamin Yuen
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Vinod Krishna
- Janssen Research & Development, LLC, San Diego, CA, United States of America
| | - Michelle J Wu
- Verily Life Sciences, South San Francisco, CA, United States of America
| | | | - Sarah A Short
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Pouya Kheradpour
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Maxwell R Mumbach
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Kate M Franz
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Vladimir Trifonov
- Janssen Research & Development, LLC, San Diego, CA, United States of America
| | - Molly V Lucas
- Janssen Research & Development, LLC, NJ, United States of America
| | - James Merson
- Janssen Research & Development, LLC, San Francisco, CA, United States of America
| | - Charles C Kim
- Verily Life Sciences, South San Francisco, CA, United States of America.
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2
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Moonen JR, Chappell J, Shi M, Shinohara T, Li D, Mumbach MR, Zhang F, Nair RV, Nasser J, Mai DH, Taylor S, Wang L, Metzger RJ, Chang HY, Engreitz JM, Snyder MP, Rabinovitch M. KLF4 recruits SWI/SNF to increase chromatin accessibility and reprogram the endothelial enhancer landscape under laminar shear stress. Nat Commun 2022; 13:4941. [PMID: 35999210 PMCID: PMC9399231 DOI: 10.1038/s41467-022-32566-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [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: 07/07/2020] [Accepted: 08/05/2022] [Indexed: 12/14/2022] Open
Abstract
Physiologic laminar shear stress (LSS) induces an endothelial gene expression profile that is vasculo-protective. In this report, we delineate how LSS mediates changes in the epigenetic landscape to promote this beneficial response. We show that under LSS, KLF4 interacts with the SWI/SNF nucleosome remodeling complex to increase accessibility at enhancer sites that promote the expression of homeostatic endothelial genes. By combining molecular and computational approaches we discover enhancers that loop to promoters of KLF4- and LSS-responsive genes that stabilize endothelial cells and suppress inflammation, such as BMPR2, SMAD5, and DUSP5. By linking enhancers to genes that they regulate under physiologic LSS, our work establishes a foundation for interpreting how non-coding DNA variants in these regions might disrupt protective gene expression to influence vascular disease.
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Affiliation(s)
- Jan-Renier Moonen
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- BASE Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - James Chappell
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Minyi Shi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Tsutomu Shinohara
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- BASE Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Dan Li
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Maxwell R Mumbach
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Fan Zhang
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ramesh V Nair
- Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Joseph Nasser
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Daniel H Mai
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Shalina Taylor
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Lingli Wang
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- BASE Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ross J Metzger
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Howard Y Chang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Jesse M Engreitz
- BASE Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Michael P Snyder
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Marlene Rabinovitch
- Vera Moulton Wall Center for Pulmonary Vascular Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- BASE Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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3
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Maciag K, Raychowdhury R, Smith K, Schneider AM, Coers J, Mumbach MR, Schwartz S, Hacohen N. IRF3 inhibits IFN-γ-mediated restriction of intracellular pathogens in macrophages independently of IFNAR. J Leukoc Biol 2022; 112:257-271. [PMID: 34826345 PMCID: PMC9550582 DOI: 10.1002/jlb.3a0218-069rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 10/25/2021] [Accepted: 10/30/2021] [Indexed: 01/14/2023] Open
Abstract
Macrophages use an array of innate immune sensors to detect intracellular pathogens and to tailor effective antimicrobial responses. In addition, extrinsic activation with the cytokine IFN-γ is often required as well to tip the scales of the host-pathogen balance toward pathogen restriction. However, little is known about how host-pathogen sensing impacts the antimicrobial IFN-γ-activated state. It was observed that in the absence of IRF3, a key downstream component of pathogen sensing pathways, IFN-γ-primed macrophages more efficiently restricted the intracellular bacterium Legionella pneumophila and the intracellular protozoan parasite Trypanosoma cruzi. This effect did not require IFNAR, the receptor for Type I IFNs known to be induced by IRF3, nor the sensing adaptors MyD88/TRIF, MAVS, or STING. This effect also did not involve differential activation of STAT1, the major signaling protein downstream of both Type 1 and Type 2 IFN receptors. IRF3-deficient macrophages displayed a significantly altered IFN-γ-induced gene expression program, with up-regulation of microbial restriction factors such as Nos2. Finally, we found that IFN-γ-primed but not unprimed macrophages largely excluded the activated form of IRF3 from the nucleus following bacterial infection. These data are consistent with a relationship of mutual inhibition between IRF3 and IFN-γ-activated programs, possibly as a component of a partially reversible mechanism for modulating the activity of potent innate immune effectors (such as Nos2) in the context of intracellular infection.
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Affiliation(s)
- Karolina Maciag
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Program in Immunology, Harvard Medical School, Boston, MA 02115, USA,Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | | | - Karen Smith
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexis M. Schneider
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jörn Coers
- Departments of Molecular Genetics and Microbiology and Immunology, Duke University Medical Center, Durham, NC 27710, USA
| | | | | | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Program in Immunology, Harvard Medical School, Boston, MA 02115, USA,Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA 02129, USA
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4
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Flynn RA, Belk JA, Qi Y, Yasumoto Y, Wei J, Alfajaro MM, Shi Q, Mumbach MR, Limaye A, DeWeirdt PC, Schmitz CO, Parker KR, Woo E, Chang HY, Horvath TL, Carette JE, Bertozzi CR, Wilen CB, Satpathy AT. Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions. Cell 2021; 184:2394-2411.e16. [PMID: 33743211 PMCID: PMC7951565 DOI: 10.1016/j.cell.2021.03.012] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 02/03/2021] [Accepted: 03/04/2021] [Indexed: 12/22/2022]
Abstract
SARS-CoV-2 is the cause of a pandemic with growing global mortality. Using comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS), we identified 309 host proteins that bind the SARS-CoV-2 RNA during active infection. Integration of this data with ChIRP-MS data from three other RNA viruses defined viral specificity of RNA-host protein interactions. Targeted CRISPR screens revealed that the majority of functional RNA-binding proteins protect the host from virus-induced cell death, and comparative CRISPR screens across seven RNA viruses revealed shared and SARS-specific antiviral factors. Finally, by combining the RNA-centric approach and functional CRISPR screens, we demonstrated a physical and functional connection between SARS-CoV-2 and mitochondria, highlighting this organelle as a general platform for antiviral activity. Altogether, these data provide a comprehensive catalog of functional SARS-CoV-2 RNA-host protein interactions, which may inform studies to understand the host-virus interface and nominate host pathways that could be targeted for therapeutic benefit.
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Affiliation(s)
- Ryan A Flynn
- Stanford ChEM-H and Department of Chemistry, Stanford University, Stanford, CA, USA.
| | - Julia A Belk
- Department of Computer Science, Stanford University, Stanford, CA, USA; Department of Pathology, Stanford University, Stanford, CA, USA
| | - Yanyan Qi
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Yuki Yasumoto
- Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, Yale University, New Haven, CT, USA
| | - Jin Wei
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Mia Madel Alfajaro
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Quanming Shi
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Aditi Limaye
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Peter C DeWeirdt
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Cameron O Schmitz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Kevin R Parker
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Elizabeth Woo
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Tamas L Horvath
- Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, Yale University, New Haven, CT, USA
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Carolyn R Bertozzi
- Stanford ChEM-H and Department of Chemistry, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Craig B Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
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5
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Corces MR, Shcherbina A, Kundu S, Gloudemans MJ, Frésard L, Granja JM, Louie BH, Eulalio T, Shams S, Bagdatli ST, Mumbach MR, Liu B, Montine KS, Greenleaf WJ, Kundaje A, Montgomery SB, Chang HY, Montine TJ. Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer's and Parkinson's diseases. Nat Genet 2020; 52:1158-1168. [PMID: 33106633 PMCID: PMC7606627 DOI: 10.1038/s41588-020-00721-x] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [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: 12/27/2019] [Accepted: 09/18/2020] [Indexed: 02/06/2023]
Abstract
Genome-wide association studies of neurological diseases have identified thousands of variants associated with disease phenotypes. However, most of these variants do not alter coding sequences, making it difficult to assign their function. Here, we present a multi-omic epigenetic atlas of the adult human brain through profiling of single-cell chromatin accessibility landscapes and three-dimensional chromatin interactions of diverse adult brain regions across a cohort of cognitively healthy individuals. We developed a machine-learning classifier to integrate this multi-omic framework and predict dozens of functional SNPs for Alzheimer's and Parkinson's diseases, nominating target genes and cell types for previously orphaned loci from genome-wide association studies. Moreover, we dissected the complex inverted haplotype of the MAPT (encoding tau) Parkinson's disease risk locus, identifying putative ectopic regulatory interactions in neurons that may mediate this disease association. This work expands understanding of inherited variation and provides a roadmap for the epigenomic dissection of causal regulatory variation in disease.
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Affiliation(s)
- M Ryan Corces
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Anna Shcherbina
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Soumya Kundu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Michael J Gloudemans
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Laure Frésard
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Program in Biophysics, Stanford University, Stanford, CA, USA
| | - Bryan H Louie
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Tiffany Eulalio
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Shadi Shams
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - S Tansu Bagdatli
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Boxiang Liu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
- Baidu Research, Sunnyvale, CA, USA
| | - Kathleen S Montine
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Stephen B Montgomery
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Program in Epithelial Biology, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
| | - Thomas J Montine
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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6
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Flynn RA, Belk JA, Qi Y, Yasumoto Y, Schmitz CO, Mumbach MR, Limaye A, Wei J, Alfajaro MM, Parker KR, Chang HY, Horvath TL, Carette JE, Bertozzi C, Wilen CB, Satpathy AT. Systematic discovery and functional interrogation of SARS-CoV-2 viral RNA-host protein interactions during infection. bioRxiv 2020:2020.10.06.327445. [PMID: 33052334 PMCID: PMC7553159 DOI: 10.1101/2020.10.06.327445] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of a pandemic with growing global mortality. There is an urgent need to understand the molecular pathways required for host infection and anti-viral immunity. Using comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS), we identified 309 host proteins that bind the SARS-CoV-2 RNA during active infection. Integration of this data with viral ChIRP-MS data from three other positive-sense RNA viruses defined pan-viral and SARS-CoV-2-specific host interactions. Functional interrogation of these factors with a genome-wide CRISPR screen revealed that the vast majority of viral RNA-binding proteins protect the host from virus-induced cell death, and we identified known and novel anti-viral proteins that regulate SARS-CoV-2 pathogenicity. Finally, our RNA-centric approach demonstrated a physical connection between SARS-CoV-2 RNA and host mitochondria, which we validated with functional and electron microscopy data, providing new insights into a more general virus-specific protein logic for mitochondrial interactions. Altogether, these data provide a comprehensive catalogue of SARS-CoV-2 RNA-host protein interactions, which may inform future studies to understand the mechanisms of viral pathogenesis, as well as nominate host pathways that could be targeted for therapeutic benefit. HIGHLIGHTS · ChIRP-MS of SARS-CoV-2 RNA identifies a comprehensive viral RNA-host protein interaction network during infection across two species· Comparison to RNA-protein interaction networks with Zika virus, dengue virus, and rhinovirus identify SARS-CoV-2-specific and pan-viral RNA protein complexes and highlights distinct intracellular trafficking pathways· Intersection of ChIRP-MS and genome-wide CRISPR screens identify novel SARS-CoV-2-binding proteins with pro- and anti-viral function· Viral RNA-RNA and RNA-protein interactions reveal specific SARS-CoV-2-mediated mitochondrial dysfunction during infection.
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Affiliation(s)
- Ryan A. Flynn
- Stanford ChEM-H and Department of Chemistry, Stanford University, Stanford, CA
- These authors contributed equally
| | - Julia A. Belk
- Department of Computer Science, Stanford University, Stanford, CA
- Department of Pathology, Stanford University, Stanford, CA
- These authors contributed equally
| | - Yanyan Qi
- Department of Pathology, Stanford University, Stanford, CA
| | - Yuki Yasumoto
- Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, Yale University, New Haven, CT
| | - Cameron O. Schmitz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Maxwell R. Mumbach
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA
| | - Aditi Limaye
- Department of Pathology, Stanford University, Stanford, CA
| | - Jin Wei
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Mia Madel Alfajaro
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Kevin R. Parker
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA
| | - Howard Y. Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA
| | - Tamas L. Horvath
- Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, Yale University, New Haven, CT
| | - Jan E. Carette
- Department of Microbiology and Immunology, Stanford University, Stanford, CA
| | - Carolyn Bertozzi
- Stanford ChEM-H and Department of Chemistry, Stanford University, Stanford, CA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA
| | - Craig B. Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
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7
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Wilson KD, Ameen M, Guo H, Abilez OJ, Tian L, Mumbach MR, Diecke S, Qin X, Liu Y, Yang H, Ma N, Gaddam S, Cunningham NJ, Gu M, Neofytou E, Prado M, Hildebrandt TB, Karakikes I, Chang HY, Wu JC. Endogenous Retrovirus-Derived lncRNA BANCR Promotes Cardiomyocyte Migration in Humans and Non-human Primates. Dev Cell 2020; 54:694-709.e9. [PMID: 32763147 DOI: 10.1016/j.devcel.2020.07.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 06/03/2020] [Accepted: 07/11/2020] [Indexed: 01/04/2023]
Abstract
Transposable elements (TEs) comprise nearly half of the human genome and are often transcribed or exhibit cis-regulatory properties with unknown function in specific processes such as heart development. In the case of endogenous retroviruses (ERVs), a TE subclass, experimental interrogation is constrained as many are primate-specific or human-specific. Here, we use primate pluripotent stem-cell-derived cardiomyocytes that mimic fetal cardiomyocytes in vitro to discover hundreds of ERV transcripts from the primate-specific MER41 family, some of which are regulated by the cardiogenic transcription factor TBX5. The most significant of these are located within BANCR, a long non-coding RNA (lncRNA) exclusively expressed in primate fetal cardiomyocytes. Functional studies reveal that BANCR promotes cardiomyocyte migration in vitro and ventricular enlargement in vivo. We conclude that recently evolved TE loci such as BANCR may represent potent de novo developmental regulatory elements that can be interrogated with species-matching pluripotent stem cell models.
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Affiliation(s)
- Kitchener D Wilson
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA.
| | - Mohamed Ameen
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA; Department of Cancer Biology, Stanford University, Stanford, CA 94305, USA
| | - Hongchao Guo
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Oscar J Abilez
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Lei Tian
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Maxwell R Mumbach
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | - Sebastian Diecke
- Berlin Institute of Health, Max Delbrück Center, and DZHK (German Center for Cardiovascular Research), Berlin, Germany
| | - Xulei Qin
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Yonggang Liu
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Huaxiao Yang
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Ning Ma
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Sadhana Gaddam
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Mingxia Gu
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Evgenios Neofytou
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Maricela Prado
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Thomas B Hildebrandt
- Wildlife Reproduction Medicine, Freie University and Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Ioannis Karakikes
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA; Department of Cardiothoracic Surgery, Stanford University, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University, Stanford, CA 94305, USA
| | - Joseph C Wu
- Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA; Departments of Medicine and Radiology, Stanford University, Stanford, CA 94305, USA.
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8
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Nasrallah R, Imianowski CJ, Bossini-Castillo L, Grant FM, Dogan M, Placek L, Kozhaya L, Kuo P, Sadiyah F, Whiteside SK, Mumbach MR, Glinos D, Vardaka P, Whyte CE, Lozano T, Fujita T, Fujii H, Liston A, Andrews S, Cozzani A, Yang J, Mitra S, Lugli E, Chang HY, Unutmaz D, Trynka G, Roychoudhuri R. A distal enhancer at risk locus 11q13.5 promotes suppression of colitis by T reg cells. Nature 2020; 583:447-452. [PMID: 32499651 PMCID: PMC7116706 DOI: 10.1038/s41586-020-2296-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [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] [Received: 03/27/2019] [Accepted: 03/10/2020] [Indexed: 02/02/2023]
Abstract
Genetic variations underlying susceptibility to complex autoimmune and allergic diseases are concentrated within noncoding regulatory elements termed enhancers1. The functions of a large majority of disease-associated enhancers are unknown, in part owing to their distance from the genes they regulate, a lack of understanding of the cell types in which they operate, and our inability to recapitulate the biology of immune diseases in vitro. Here, using shared synteny to guide loss-of-function analysis of homologues of human enhancers in mice, we show that the prominent autoimmune and allergic disease risk locus at chromosome 11q13.52-7 contains a distal enhancer that is functional in CD4+ regulatory T (Treg) cells and required for Treg-mediated suppression of colitis. The enhancer recruits the transcription factors STAT5 and NF-κB to mediate signal-driven expression of Lrrc32, which encodes the protein glycoprotein A repetitions predominant (GARP). Whereas disruption of the Lrrc32 gene results in early lethality, mice lacking the enhancer are viable but lack GARP expression in Foxp3+ Treg cells, which are unable to control colitis in a cell-transfer model of the disease. In human Treg cells, the enhancer forms conformational interactions with the promoter of LRRC32 and enhancer risk variants are associated with reduced histone acetylation and GARP expression. Finally, functional fine-mapping of 11q13.5 using CRISPR-activation (CRISPRa) identifies a CRISPRa-responsive element in the vicinity of risk variant rs11236797 capable of driving GARP expression. These findings provide a mechanistic basis for association of the 11q13.5 risk locus with immune-mediated diseases and identify GARP as a potential target in their therapy.
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Affiliation(s)
- Rabab Nasrallah
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
| | - Charlotte J Imianowski
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK.
- Department of Pathology, University of Cambridge, Cambridge, UK.
| | | | - Francis M Grant
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
| | | | | | | | - Paula Kuo
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Firas Sadiyah
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Sarah K Whiteside
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Maxwell R Mumbach
- Howard Hughes Medical Institute and Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Dafni Glinos
- Immune Genomics Group, Wellcome Sanger Institute, Cambridge, UK
| | - Panagiota Vardaka
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Carly E Whyte
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
| | - Teresa Lozano
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
| | - Toshitsugu Fujita
- Chromatin Biochemistry Research Group, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Hodaka Fujii
- Chromatin Biochemistry Research Group, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Adrian Liston
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
| | - Simon Andrews
- Bioinformatics Group, The Babraham Institute, Cambridge, UK
| | - Adeline Cozzani
- Inserm UMR1277/CNRS9020, Institut pour la Recherche sur le Cancer de Lille, Lille, France
| | - Jie Yang
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Suman Mitra
- Inserm UMR1277/CNRS9020, Institut pour la Recherche sur le Cancer de Lille, Lille, France
| | - Enrico Lugli
- Humanitas Clinical and Research Center, Milan, Italy
| | - Howard Y Chang
- Howard Hughes Medical Institute and Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Gosia Trynka
- Immune Genomics Group, Wellcome Sanger Institute, Cambridge, UK.
- Open Targets, Wellcome Genome Campus, Cambridge, UK.
| | - Rahul Roychoudhuri
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK.
- Department of Pathology, University of Cambridge, Cambridge, UK.
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9
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López-Isac E, Acosta-Herrera M, Kerick M, Assassi S, Satpathy AT, Granja J, Mumbach MR, Beretta L, Simeón CP, Carreira P, Ortego-Centeno N, Castellvi I, Bossini-Castillo L, Carmona FD, Orozco G, Hunzelmann N, Distler JHW, Franke A, Lunardi C, Moroncini G, Gabrielli A, de Vries-Bouwstra J, Wijmenga C, Koeleman BPC, Nordin A, Padyukov L, Hoffmann-Vold AM, Lie B, Proudman S, Stevens W, Nikpour M, Vyse T, Herrick AL, Worthington J, Denton CP, Allanore Y, Brown MA, Radstake TRDJ, Fonseca C, Chang HY, Mayes MD, Martin J. GWAS for systemic sclerosis identifies multiple risk loci and highlights fibrotic and vasculopathy pathways. Nat Commun 2019; 10:4955. [PMID: 31672989 PMCID: PMC6823490 DOI: 10.1038/s41467-019-12760-y] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [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: 02/28/2019] [Accepted: 09/30/2019] [Indexed: 12/12/2022] Open
Abstract
Systemic sclerosis (SSc) is an autoimmune disease that shows one of the highest mortality rates among rheumatic diseases. We perform a large genome-wide association study (GWAS), and meta-analysis with previous GWASs, in 26,679 individuals and identify 27 independent genome-wide associated signals, including 13 new risk loci. The novel associations nearly double the number of genome-wide hits reported for SSc thus far. We define 95% credible sets of less than 5 likely causal variants in 12 loci. Additionally, we identify specific SSc subtype-associated signals. Functional analysis of high-priority variants shows the potential function of SSc signals, with the identification of 43 robust target genes through HiChIP. Our results point towards molecular pathways potentially involved in vasculopathy and fibrosis, two main hallmarks in SSc, and highlight the spectrum of critical cell types for the disease. This work supports a better understanding of the genetic basis of SSc and provides directions for future functional experiments.
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Affiliation(s)
- Elena López-Isac
- Institute of Parasitology and Biomedicine López-Neyra, IPBLN-CSIC, Granada, Spain.
| | | | - Martin Kerick
- Institute of Parasitology and Biomedicine López-Neyra, IPBLN-CSIC, Granada, Spain
| | - Shervin Assassi
- The University of Texas Health Science Center-Houston, Houston, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Jeffrey Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Lorenzo Beretta
- Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | - Carmen P Simeón
- Department of Internal Medicine, Valle de Hebrón Hospital, Barcelona, Spain
| | - Patricia Carreira
- Department of Rheumatology, 12 de Octubre University Hospital, Madrid, Spain
| | | | - Ivan Castellvi
- Department of Rheumatology, Santa Creu i Sant Pau University Hospital, Barcelona, Spain
| | | | - F David Carmona
- Department of Genetics and Institute of Biotechnology, University of Granada, Granada, Spain
| | - Gisela Orozco
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester, UK
| | | | - Jörg H W Distler
- Department of Internal Medicine 3, Institute for Clinical Immunology, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Claudio Lunardi
- Department of Medicine, Università degli Studi di Verona, Verona, Italy
| | - Gianluca Moroncini
- Clinica Medica, Department of Clinical and Molecular Science, Università Politecnica delle Marche and Ospedali Riuniti, Ancona, Italy
| | - Armando Gabrielli
- Clinica Medica, Department of Clinical and Molecular Science, Università Politecnica delle Marche and Ospedali Riuniti, Ancona, Italy
| | | | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | | | - Annika Nordin
- Division of Rheumatology, Department of Medicine, Karolinska University Hospital, Karolinska Institute, Stockholm, Sweden
| | - Leonid Padyukov
- Division of Rheumatology, Department of Medicine, Karolinska University Hospital, Karolinska Institute, Stockholm, Sweden
| | | | - Benedicte Lie
- Department of Medical Genetics, and the Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Susanna Proudman
- Royal Adelaide Hospital and University of Adelaide, Adelaide, SA, Australia
| | | | - Mandana Nikpour
- The University of Melbourne at St. Vincent's Hospital, Melbourne, VIC, Australia
| | - Timothy Vyse
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Ariane L Herrick
- Centre for Musculoskeletal Research, The University of Manchester, Salford Royal NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester, UK
| | - Jane Worthington
- Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester, UK
| | - Christopher P Denton
- Centre for Rheumatology, Royal Free and University College Medical School, London, United Kingdom
| | - Yannick Allanore
- Department of Rheumatology A, Cochin Hospital, INSERM U1016, Paris Descartes University, Paris, France
| | - Matthew A Brown
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Timothy R D J Radstake
- Department of Rheumatology & Clinical Immunology, Laboratory of Translational Immunology, department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Carmen Fonseca
- Centre for Rheumatology, Royal Free and University College Medical School, London, United Kingdom
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Maureen D Mayes
- The University of Texas Health Science Center-Houston, Houston, USA
| | - Javier Martin
- Institute of Parasitology and Biomedicine López-Neyra, IPBLN-CSIC, Granada, Spain.
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10
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Satpathy AT, Granja JM, Yost KE, Qi Y, Meschi F, McDermott GP, Olsen BN, Mumbach MR, Pierce SE, Corces MR, Shah P, Bell JC, Jhutty D, Nemec CM, Wang J, Wang L, Yin Y, Giresi PG, Chang ALS, Zheng GXY, Greenleaf WJ, Chang HY. Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion. Nat Biotechnol 2019; 37:925-936. [PMID: 31375813 PMCID: PMC7299161 DOI: 10.1038/s41587-019-0206-z] [Citation(s) in RCA: 457] [Impact Index Per Article: 91.4] [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] [Received: 01/21/2019] [Accepted: 07/01/2019] [Indexed: 02/08/2023]
Abstract
Understanding complex tissues requires single-cell deconstruction of gene regulation with precision and scale. Here, we assess the performance of a massively parallel droplet-based method for mapping transposase-accessible chromatin in single cells using sequencing (scATAC-seq). We apply scATAC-seq to obtain chromatin profiles of more than 200,000 single cells in human blood and basal cell carcinoma. In blood, application of scATAC-seq enables marker-free identification of cell type-specific cis- and trans-regulatory elements, mapping of disease-associated enhancer activity and reconstruction of trajectories of cellular differentiation. In basal cell carcinoma, application of scATAC-seq reveals regulatory networks in malignant, stromal and immune cells in the tumor microenvironment. Analysis of scATAC-seq profiles from serial tumor biopsies before and after programmed cell death protein 1 blockade identifies chromatin regulators of therapy-responsive T cell subsets and reveals a shared regulatory program that governs intratumoral CD8+ T cell exhaustion and CD4+ T follicular helper cell development. We anticipate that scATAC-seq will enable the unbiased discovery of gene regulatory factors across diverse biological systems.
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Affiliation(s)
- Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA
| | - Yanyan Qi
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA
| | | | | | | | - Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Sarah E Pierce
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA
| | | | | | | | | | - Jean Wang
- 10x Genomics, Inc., Pleasanton, CA, USA
| | - Li Wang
- 10x Genomics, Inc., Pleasanton, CA, USA
| | | | | | - Anne Lynn S Chang
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA
| | | | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Applied Physics, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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11
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Mumbach MR, Granja JM, Flynn RA, Roake CM, Satpathy AT, Rubin AJ, Qi Y, Jiang Z, Shams S, Louie BH, Guo JK, Gennert DG, Corces MR, Khavari PA, Atianand MK, Artandi SE, Fitzgerald KA, Greenleaf WJ, Chang HY. HiChIRP reveals RNA-associated chromosome conformation. Nat Methods 2019; 16:489-492. [PMID: 31133759 DOI: 10.1038/s41592-019-0407-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 04/05/2019] [Indexed: 12/25/2022]
Abstract
Modular domains of long non-coding RNAs can serve as scaffolds to bring distant regions of the linear genome into spatial proximity. Here, we present HiChIRP, a method leveraging bio-orthogonal chemistry and optimized chromosome conformation capture conditions, which enables interrogation of chromatin architecture focused around a specific RNA of interest down to approximately ten copies per cell. HiChIRP of three nuclear RNAs reveals insights into promoter interactions (7SK), telomere biology (telomerase RNA component) and inflammatory gene regulation (lincRNA-EPS).
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Affiliation(s)
- Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Program in Biophysics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ryan A Flynn
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Caitlin M Roake
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Adam J Rubin
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yanyan Qi
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Zhaozhao Jiang
- Program in Innate Immunity, University of Massachusetts Medical School, Worcester, MA, USA
| | - Shadi Shams
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Bryan H Louie
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Jimmy K Guo
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - David G Gennert
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Maninjay K Atianand
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Steven E Artandi
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Katherine A Fitzgerald
- Program in Innate Immunity, University of Massachusetts Medical School, Worcester, MA, USA
| | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Applied Physics, Stanford University, Stanford, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. .,Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA. .,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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12
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Jeng MY, Mumbach MR, Granja JM, Satpathy AT, Chang HY, Chang ALS. Enhancer Connectome Nominates Target Genes of Inherited Risk Variants from Inflammatory Skin Disorders. J Invest Dermatol 2019; 139:605-614. [DOI: 10.1016/j.jid.2018.09.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 08/24/2018] [Accepted: 09/18/2018] [Indexed: 12/22/2022]
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13
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Van Gool F, Nguyen MLT, Mumbach MR, Satpathy AT, Rosenthal WL, Giacometti S, Le DT, Liu W, Brusko TM, Anderson MS, Rudensky AY, Marson A, Chang HY, Bluestone JA. A Mutation in the Transcription Factor Foxp3 Drives T Helper 2 Effector Function in Regulatory T Cells. Immunity 2019; 50:362-377.e6. [PMID: 30709738 PMCID: PMC6476426 DOI: 10.1016/j.immuni.2018.12.016] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [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: 03/29/2018] [Revised: 10/25/2018] [Accepted: 12/14/2018] [Indexed: 12/30/2022]
Abstract
Regulatory T (Treg) cells maintain immune tolerance through the master transcription factor forkhead box P3 (FOXP3), which is crucial for Treg cell function and homeostasis. We identified an IPEX (immune dysregulation polyendocrinopathy enteropathy X-linked) syndrome patient with a FOXP3 mutation in the domain swap interface of the protein. Recapitulation of this Foxp3 variant in mice led to the development of an autoimmune syndrome consistent with an unrestrained T helper type 2 (Th2) immune response. Genomic analysis of Treg cells by RNA-sequencing, Foxp3 chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-sequencing), and H3K27ac-HiChIP revealed a specific de-repression of the Th2 transcriptional program leading to the generation of Th2-like Treg cells that were unable to suppress extrinsic Th2 cells. Th2-like Treg cells showed increased intra-chromosomal interactions in the Th2 locus, leading to type 2 cytokine production. These findings identify a direct role for Foxp3 in suppressing Th2-like Treg cells and implicate additional pathways that could be targeted to restrain Th2 trans-differentiated Treg cells.
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MESH Headings
- Animals
- Cell Differentiation/genetics
- Cell Differentiation/immunology
- Child
- Cytokines/genetics
- Cytokines/immunology
- Cytokines/metabolism
- Forkhead Transcription Factors/genetics
- Forkhead Transcription Factors/immunology
- Forkhead Transcription Factors/metabolism
- Gene Expression Regulation
- Genetic Diseases, X-Linked/genetics
- Genetic Diseases, X-Linked/immunology
- Genetic Diseases, X-Linked/metabolism
- Humans
- Male
- Mice, Inbred C57BL
- Mice, Knockout
- Mutation
- Polyendocrinopathies, Autoimmune/genetics
- Polyendocrinopathies, Autoimmune/immunology
- Polyendocrinopathies, Autoimmune/metabolism
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/metabolism
- Th2 Cells/immunology
- Th2 Cells/metabolism
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Affiliation(s)
- Frédéric Van Gool
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA; Sean N. Parker Autoimmune Research Laboratory, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michelle L T Nguyen
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Wendy L Rosenthal
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA; Sean N. Parker Autoimmune Research Laboratory, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Simone Giacometti
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Duy T Le
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA; Sean N. Parker Autoimmune Research Laboratory, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Weihong Liu
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA; Sean N. Parker Autoimmune Research Laboratory, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Todd M Brusko
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Mark S Anderson
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alexander Y Rudensky
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alexander Marson
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Jeffrey A Bluestone
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA; Sean N. Parker Autoimmune Research Laboratory, University of California, San Francisco, San Francisco, CA 94143, USA.
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14
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Petrovic J, Zhou Y, Fasolino M, Goldman N, Schwartz GW, Mumbach MR, Nguyen SC, Rome KS, Sela Y, Zapataro Z, Blacklow SC, Kruhlak MJ, Shi J, Aster JC, Joyce EF, Little SC, Vahedi G, Pear WS, Faryabi RB. Oncogenic Notch Promotes Long-Range Regulatory Interactions within Hyperconnected 3D Cliques. Mol Cell 2019; 73:1174-1190.e12. [PMID: 30745086 DOI: 10.1016/j.molcel.2019.01.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 11/21/2018] [Accepted: 01/03/2019] [Indexed: 01/10/2023]
Abstract
Chromatin loops enable transcription-factor-bound distal enhancers to interact with their target promoters to regulate transcriptional programs. Although developmental transcription factors such as active forms of Notch can directly stimulate transcription by activating enhancers, the effect of their oncogenic subversion on the 3D organization of cancer genomes is largely undetermined. By mapping chromatin looping genome-wide in Notch-dependent triple-negative breast cancer and B cell lymphoma, we show that beyond the well-characterized role of Notch as an activator of distal enhancers, Notch regulates its direct target genes by instructing enhancer repositioning. Moreover, a large fraction of Notch-instructed regulatory loops form highly interacting enhancer and promoter spatial clusters termed "3D cliques." Loss- and gain-of-function experiments show that Notch preferentially targets hyperconnected 3D cliques that regulate the expression of crucial proto-oncogenes. Our observations suggest that oncogenic hijacking of developmental transcription factors can dysregulate transcription through widespread effects on the spatial organization of cancer genomes.
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Affiliation(s)
- Jelena Petrovic
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yeqiao Zhou
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maria Fasolino
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Naomi Goldman
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gregory W Schwartz
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maxwell R Mumbach
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Son C Nguyen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kelly S Rome
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yogev Sela
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zachary Zapataro
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stephen C Blacklow
- Department of Biological Chemistry, Harvard Medical School, Boston, MA 02215, USA
| | | | - Junwei Shi
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jon C Aster
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Eric F Joyce
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shawn C Little
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Golnaz Vahedi
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Warren S Pear
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Robert B Faryabi
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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15
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Rubin AJ, Parker KR, Satpathy AT, Qi Y, Wu B, Ong AJ, Mumbach MR, Ji AL, Kim DS, Cho SW, Zarnegar BJ, Greenleaf WJ, Chang HY, Khavari PA. Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks. Cell 2018; 176:361-376.e17. [PMID: 30580963 DOI: 10.1016/j.cell.2018.11.022] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/12/2018] [Accepted: 11/12/2018] [Indexed: 12/31/2022]
Abstract
Here, we present Perturb-ATAC, a method that combines multiplexed CRISPR interference or knockout with genome-wide chromatin accessibility profiling in single cells based on the simultaneous detection of CRISPR guide RNAs and open chromatin sites by assay of transposase-accessible chromatin with sequencing (ATAC-seq). We applied Perturb-ATAC to transcription factors (TFs), chromatin-modifying factors, and noncoding RNAs (ncRNAs) in ∼4,300 single cells, encompassing more than 63 genotype-phenotype relationships. Perturb-ATAC in human B lymphocytes uncovered regulators of chromatin accessibility, TF occupancy, and nucleosome positioning and identified a hierarchy of TFs that govern B cell state, variation, and disease-associated cis-regulatory elements. Perturb-ATAC in primary human epidermal cells revealed three sequential modules of cis-elements that specify keratinocyte fate. Combinatorial deletion of all pairs of these TFs uncovered their epistatic relationships and highlighted genomic co-localization as a basis for synergistic interactions. Thus, Perturb-ATAC is a powerful strategy to dissect gene regulatory networks in development and disease.
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Affiliation(s)
- Adam J Rubin
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kevin R Parker
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ansuman T Satpathy
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yanyan Qi
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Beijing Wu
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alvin J Ong
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Maxwell R Mumbach
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew L Ji
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Daniel S Kim
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Seung Woo Cho
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brian J Zarnegar
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Howard Y Chang
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA 94304, USA.
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16
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Corces MR, Granja JM, Shams S, Louie BH, Seoane JA, Zhou W, Silva TC, Groeneveld C, Wong CK, Cho SW, Satpathy AT, Mumbach MR, Hoadley KA, Robertson AG, Sheffield NC, Felau I, Castro MAA, Berman BP, Staudt LM, Zenklusen JC, Laird PW, Curtis C, Greenleaf WJ, Chang HY. The chromatin accessibility landscape of primary human cancers. Science 2018; 362:362/6413/eaav1898. [PMID: 30361341 DOI: 10.1126/science.aav1898] [Citation(s) in RCA: 593] [Impact Index Per Article: 98.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 09/28/2018] [Indexed: 12/11/2022]
Abstract
We present the genome-wide chromatin accessibility profiles of 410 tumor samples spanning 23 cancer types from The Cancer Genome Atlas (TCGA). We identify 562,709 transposase-accessible DNA elements that substantially extend the compendium of known cis-regulatory elements. Integration of ATAC-seq (the assay for transposase-accessible chromatin using sequencing) with TCGA multi-omic data identifies a large number of putative distal enhancers that distinguish molecular subtypes of cancers, uncovers specific driving transcription factors via protein-DNA footprints, and nominates long-range gene-regulatory interactions in cancer. These data reveal genetic risk loci of cancer predisposition as active DNA regulatory elements in cancer, identify gene-regulatory interactions underlying cancer immune evasion, and pinpoint noncoding mutations that drive enhancer activation and may affect patient survival. These results suggest a systematic approach to understanding the noncoding genome in cancer to advance diagnosis and therapy.
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17
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Pattison JM, Melo SP, Piekos SN, Torkelson JL, Bashkirova E, Mumbach MR, Rajasingh C, Zhen HH, Li L, Liaw E, Alber D, Rubin AJ, Shankar G, Bao X, Chang HY, Khavari PA, Oro AE. Retinoic acid and BMP4 cooperate with p63 to alter chromatin dynamics during surface epithelial commitment. Nat Genet 2018; 50:1658-1665. [PMID: 30397335 PMCID: PMC6265075 DOI: 10.1038/s41588-018-0263-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [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: 12/07/2017] [Accepted: 09/21/2018] [Indexed: 01/14/2023]
Abstract
Human embryonic stem cell (hESC) differentiation promises advances in regenerative medicine1–3, yet conversion into transplantable tissues remains poorly understood. Using our keratinocyte differentiation system, we employ a multi-dimensional genomics approach to interrogate the contributions of inductive morphogens retinoic acid (RA) and bone morphogenetic protein 4 (BMP4) and the epidermal master regulator p634,5 during surface ectoderm commitment. In contrast to other master regulators6–9, p63 effects major transcriptional changes only after morphogens alter chromatin accessibility, establishing an epigenetic landscape for p63 to modify. p63 distally closes chromatin accessibility and promotes accumulation of H3K27me3 modifications. Cohesin HiChIP10 visualizations of chromosome conformation reveal that p63 and the morphogens contribute to dynamic long-range chromatin interactions, as illustrated with TFAP2C regulation11. Our study demonstrates the unexpected dependency of p63 on morphogenetic signaling and provides novel insights into how a master regulator can specify diverse transcriptional programs based on the chromatin landscape induced by specific morphogen exposure.
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Affiliation(s)
- Jillian M Pattison
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sandra P Melo
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA.,Agilent Technologies, Santa Clara, CA, USA
| | - Samantha N Piekos
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jessica L Torkelson
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Elizaveta Bashkirova
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA.,Columbia Stem Cell Initiative, Columbia University Medical Center, New York, NY, USA
| | - Maxwell R Mumbach
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA.,Center for Personal Dynamic Regulomes, Stanford, CA, USA
| | - Charlotte Rajasingh
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Hanson Hui Zhen
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lingjie Li
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Eric Liaw
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA.,David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Daniel Alber
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Adam J Rubin
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Gautam Shankar
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Xiaomin Bao
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA.,Departments of Molecular Sciences and Dermatology, Northwestern University, Evanston, IL, USA
| | - Howard Y Chang
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA.,Center for Personal Dynamic Regulomes, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Anthony E Oro
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA.
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18
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Simeonov DR, Gowen BG, Boontanrart M, Roth TL, Gagnon JD, Mumbach MR, Satpathy AT, Lee Y, Bray NL, Chan AY, Lituiev DS, Nguyen ML, Gate RE, Subramaniam M, Li Z, Woo JM, Mitros T, Ray GJ, Curie GL, Naddaf N, Chu JS, Ma H, Boyer E, Van Gool F, Huang H, Liu R, Tobin VR, Schumann K, Daly MJ, Farh KK, Ansel KM, Ye CJ, Greenleaf WJ, Anderson MS, Bluestone JA, Chang HY, Corn JE, Marson A. Author Correction: Discovery of stimulation-responsive immune enhancers with CRISPR activation. Nature 2018; 559:E13. [PMID: 29899441 DOI: 10.1038/s41586-018-0227-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this Letter, analysis of steady-state regulatory T (Treg) cell percentages from Il2ra enhancer deletion (EDEL) and wild-type (WT) mice revealed no differences between them (Extended Data Fig. 9d). This analysis included two mice whose genotypes were incorrectly assigned. Even after correction of the genotypes, no significant differences in Treg cell percentages were seen when data across experimental cohorts were averaged (as was done in Extended Data Fig. 9d). However, if we normalize the corrected data to account for variation among experimental cohorts, a subtle decrease in EDEL Treg cell percentages is revealed and, using the corrected and normalized data, we have redrawn Extended Data Fig. 9d in Supplementary Fig. 1. The Supplementary Information to this Amendment contains the corrected and reanalysed Extended Data Fig. 9d. The sentence "This enhancer deletion (EDEL) strain also had no obvious T cell phenotypes at steady state (Extended Data Fig. 9)." should read: "This enhancer deletion (EDEL) strain had a small decrease in the percentage of Treg cells (Extended Data Fig. 9).". This error does not affect any of the main figures in the Letter or the data from mice with the human autoimmune-associated single nucleotide polymorphism (SNP) knocked in or with a 12-base-pair deletion at the site (12DEL). In addition, we stated in the Methods that we observed consistent immunophenotypes of EDEL mice across three founders, but in fact, we observed consistent phenotypes in mice from two founders. This does not change any of our conclusions and the original Letter has not been corrected.
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Affiliation(s)
- Dimitre R Simeonov
- Biomedical Sciences Graduate Program, University of California, San Francisco, California, 94143, USA.,Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Diabetes Center, University of California, San Francisco, California, 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA
| | - Benjamin G Gowen
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA
| | - Mandy Boontanrart
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA
| | - Theodore L Roth
- Biomedical Sciences Graduate Program, University of California, San Francisco, California, 94143, USA.,Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Diabetes Center, University of California, San Francisco, California, 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA
| | - John D Gagnon
- Biomedical Sciences Graduate Program, University of California, San Francisco, California, 94143, USA.,Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Sandler Asthma Basic Research Center, University of California, San Francisco, California, 94143, USA
| | - Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, 94305, USA.,Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, 94305, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, 94305, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, 94305, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, 94305, USA
| | - Youjin Lee
- Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Diabetes Center, University of California, San Francisco, California, 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA
| | - Nicolas L Bray
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA
| | - Alice Y Chan
- Diabetes Center, University of California, San Francisco, California, 94143, USA.,Department of Pediatrics, University of California, San Francisco, California, 94143, USA
| | - Dmytro S Lituiev
- Department of Epidemiology and Biostatistics, Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics (IHG), University of California, San Francisco, California, 94143, USA
| | - Michelle L Nguyen
- Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Diabetes Center, University of California, San Francisco, California, 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA
| | - Rachel E Gate
- Department of Epidemiology and Biostatistics, Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics (IHG), University of California, San Francisco, California, 94143, USA.,Biological and Medical Informatics Graduate Program, University of California, San Francisco, California, 94158, USA
| | - Meena Subramaniam
- Department of Epidemiology and Biostatistics, Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics (IHG), University of California, San Francisco, California, 94143, USA.,Biological and Medical Informatics Graduate Program, University of California, San Francisco, California, 94158, USA
| | - Zhongmei Li
- Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Diabetes Center, University of California, San Francisco, California, 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA
| | - Jonathan M Woo
- Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Diabetes Center, University of California, San Francisco, California, 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA
| | - Therese Mitros
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA
| | - Graham J Ray
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA
| | - Gemma L Curie
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA
| | - Nicki Naddaf
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA
| | - Julia S Chu
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA
| | - Hong Ma
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA
| | - Eric Boyer
- Diabetes Center, University of California, San Francisco, California, 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA
| | - Frederic Van Gool
- Diabetes Center, University of California, San Francisco, California, 94143, USA
| | - Hailiang Huang
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, 02142, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, 02114, USA
| | - Ruize Liu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, 02142, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, 02114, USA
| | - Victoria R Tobin
- Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Diabetes Center, University of California, San Francisco, California, 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA
| | - Kathrin Schumann
- Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Diabetes Center, University of California, San Francisco, California, 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA
| | - Mark J Daly
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, 02142, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, 02114, USA
| | - Kyle K Farh
- Illumina Inc., 5200 Illumina Way, San Diego, California, 92122, USA
| | - K Mark Ansel
- Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Sandler Asthma Basic Research Center, University of California, San Francisco, California, 94143, USA
| | - Chun J Ye
- Department of Epidemiology and Biostatistics, Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics (IHG), University of California, San Francisco, California, 94143, USA
| | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, 94305, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, 94305, USA.,Department of Applied Physics, Stanford University, Stanford, California, 94025, USA.,Chan Zuckerberg Biohub, San Francisco, California, 94158, USA
| | - Mark S Anderson
- Diabetes Center, University of California, San Francisco, California, 94143, USA.,Department of Medicine, University of California, San Francisco, California, 94143, USA
| | - Jeffrey A Bluestone
- Diabetes Center, University of California, San Francisco, California, 94143, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, 94305, USA.,Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, 94305, USA
| | - Jacob E Corn
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA. .,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA.
| | - Alexander Marson
- Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA. .,Diabetes Center, University of California, San Francisco, California, 94143, USA. .,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA. .,Chan Zuckerberg Biohub, San Francisco, California, 94158, USA. .,Department of Medicine, University of California, San Francisco, California, 94143, USA. .,UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, 94158, USA.
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19
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Cho SW, Xu J, Sun R, Mumbach MR, Carter AC, Chen YG, Yost KE, Kim J, He J, Nevins SA, Chin SF, Caldas C, Liu SJ, Horlbeck MA, Lim DA, Weissman JS, Curtis C, Chang HY. Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element. Cell 2018; 173:1398-1412.e22. [PMID: 29731168 PMCID: PMC5984165 DOI: 10.1016/j.cell.2018.03.068] [Citation(s) in RCA: 299] [Impact Index Per Article: 49.8] [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: 10/17/2017] [Revised: 02/08/2018] [Accepted: 03/26/2018] [Indexed: 12/31/2022]
Abstract
Noncoding mutations in cancer genomes are frequent but challenging to interpret. PVT1 encodes an oncogenic lncRNA, but recurrent translocations and deletions in human cancers suggest alternative mechanisms. Here, we show that the PVT1 promoter has a tumor-suppressor function that is independent of PVT1 lncRNA. CRISPR interference of PVT1 promoter enhances breast cancer cell competition and growth in vivo. The promoters of the PVT1 and the MYC oncogenes, located 55 kb apart on chromosome 8q24, compete for engagement with four intragenic enhancers in the PVT1 locus, thereby allowing the PVT1 promoter to regulate pause release of MYC transcription. PVT1 undergoes developmentally regulated monoallelic expression, and the PVT1 promoter inhibits MYC expression only from the same chromosome via promoter competition. Cancer genome sequencing identifies recurrent mutations encompassing the human PVT1 promoter, and genome editing verified that PVT1 promoter mutation promotes cancer cell growth. These results highlight regulatory sequences of lncRNA genes as potential disease-associated DNA elements.
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MESH Headings
- Animals
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- CRISPR-Cas Systems
- Carcinogenesis/genetics
- Cell Line, Tumor
- Cell Proliferation
- Cell Transformation, Neoplastic
- Chromatin
- DNA, Neoplasm/genetics
- Enhancer Elements, Genetic
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Genes, myc
- Humans
- Mice
- Mice, Inbred NOD
- Mutation
- Neoplasm Transplantation
- Promoter Regions, Genetic
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- Transcription, Genetic
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Affiliation(s)
- Seung Woo Cho
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Jin Xu
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Ruping Sun
- Departments of Medicine and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Ava C Carter
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Y Grace Chen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Jeewon Kim
- Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Jing He
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Stephanie A Nevins
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Suet-Feung Chin
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - Carlos Caldas
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK; Breast Cancer Program, CRUK Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 2QQ, UK
| | - S John Liu
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Max A Horlbeck
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Daniel A Lim
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; San Francisco Veterans Affairs Medical Center, San Francisco, San Francisco, CA 94121, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Christina Curtis
- Departments of Medicine and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA.
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20
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Cortez JT, Shifrut E, Lee Y, Mumbach MR, Satpathy AT, Granja J, Subramaniam M, Roth T, Simeonov D, Ye CJ, Chang HY, Van Gool F, Marson A. Dissecting the genetic networks that control regulatory T cell stability using pooled CRISPR screens. The Journal of Immunology 2018. [DOI: 10.4049/jimmunol.200.supp.101.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Regulatory T cells (Tregs) are a specialized subset of CD4+ T cells that suppress inflammation to maintain homeostasis and prevent autoimmunity. Treg development and function depend on expression of the master transcription factor Foxp3. While Tregs have been thought to be irreversibly committed to suppressive functions, lineage tracing studies have challenged this by revealing that Tregs can exhibit plasticity. Tregs that lose Foxp3 expression, termed ‘exTregs’, have been shown to acquire cytokine production capabilities of pro-inflammatory effector T cells and exacerbate autoimmunity. However, the gene regulatory programs that promote or disrupt Foxp3 stability in Tregs under various physiological conditions are not well understood. Here we have leveraged improved functional genetic tools, including pooled CRISPR screens, to identify nuclear factors that regulate Treg plasticity. A Foxp3 lineage-tracing reporter mouse model was used to confidently distinguish Foxp3− exTregs from contaminating Foxp3−T effectors. Using HiChIP, we identified Treg and exTreg-specific chromatin loops and systematically assessed their contribution to Foxp3 stability. Furthermore, we investigated transcriptional signatures of distinct exTreg populations residing in the peripheral organs using single-cell RNA sequencing. Collectively, this work helps us better understand the genetic networks that control stable expression of Foxp3 in Tregs as they encounter changing inflammatory environments.
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21
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Maciag K, Raychowdhury R, Smith K, Coers J, Mumbach MR, Schwartz S, Polidoro RB, Gazzinelli R, Hacohen N. IRF3 inhibits IFNγ-mediated restriction of intracellular pathogens in macrophages independently of type I interferons. The Journal of Immunology 2018. [DOI: 10.4049/jimmunol.200.supp.117.27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Macrophages use an array of innate immune sensors to detect intracellular pathogens and to tailor effective antimicrobial responses. In addition, extrinsic activation with the cytokine interferon gamma (IFNγ) is often required as well to tip the scales of the host-pathogen balance toward pathogen restriction. However, little is known about how host pathogen sensing impacts the anti-microbial IFNγ-activated state. We observed that in the absence of IRF3, a key downstream component of pathogen sensing pathways, IFNγ-primed macrophages more efficiently restricted the intracellular bacterium Legionella pneumophila and the intracellular protozoan parasite Trypanosoma cruzi. This effect was not mediated by Type I interferons, the key cytokines known to be induced by IRF3, or by the sensing adaptors MyD88/TRIF, MAVS, and STING. However, IRF3-deficient macrophages displayed a significantly altered IFNγ-induced gene expression program, with upregulation of microbial restriction factors such as Nos2. Furthermore, Nos2 activity was required for the enhanced IFNγ-mediated restriction of T. cruzi observed in IRF3-deficient macrophages. Finally, we found that IFNγ-primed but not resting macrophages largely excluded the activated form of IRF3 from the nucleus. These data are consistent with a relationship of mutual inhibition between IRF3 and IFNγ-activated programs, possibly as a component of a partially reversible mechanism for modulating the activity of potent innate immune effectors such as Nos2 in the context of intracellular infection.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Nir Hacohen
- 1Harvard Med. Sch
- 2Broad Inst. of MIT and Harvard
- 6Massachusetts Gen. Hosp
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22
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Van Gool F, Nguyen ML, Mumbach MR, Satpathy AT, Anderson MS, Marson A, Chang HY, Bluestone JA. Foxp3 domain-swap interface is required to suppress T helper type 2 transcriptional program in Regulatory T cells. The Journal of Immunology 2018. [DOI: 10.4049/jimmunol.200.supp.101.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Regulatory T cells (Treg) play a fundamental role in maintaining immune tolerance. These cells are defined and characterized by expression of the master regulator Foxp3, a transcription factor that is crucial for Treg function and homeostasis. Natural occurring mutations in Foxp3 gene have been shown to be responsible for the immunodysregulation polyendocrinopathy enteropathy X-linked (IPEX) syndrome, which is characterized by widespread autoimmune diseases. We recently identified a Foxp3 mutation in a boy that manifested a severe IPEX syndrome. This mutation, resulting in the substitution of methionine for isoleucine at amino acid 370 was determined to be part of a class of Foxp3 mutations that disrupt the dimerization motif in the domain swap interface of the protein. We have shown that, although dimerization mutants retain DNA binding, allows Treg development and certain Treg characteristics, it inevitably led to an IPEX syndrome in humans and mice. Genomic analysis of M370I mutant Treg by RNAseq, ChIPseq and HiChIP revealed a de-repression of the T helper type 2 (Th2) transcriptional program leading to the generation of Th2-like Treg. We have shown that, dimerization mutant proteins bind to multiple locations in the Th2 locus leading to increased intrachromosomal interactions and Th2 cytokines production. As expected, M370I Tregs were unable to suppress Th2 immune responses. Transgenic mice expressing M370I Foxp3 developed autoimmune diseases characterized by systemic Th2 cytokines production and skin and lung inflammation. In conclusion, disruption of the domain swap interface of Foxp3 by M370I mutation led to the development of Th2-like Treg which are functionally unable to suppress the development/function of Th2 cells.
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23
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Satpathy AT, Saligrama N, Buenrostro JD, Wei Y, Wu B, Rubin AJ, Granja JM, Lareau CA, Li R, Qi Y, Parker KR, Mumbach MR, Serratelli WS, Gennert DG, Schep AN, Corces MR, Khodadoust MS, Kim YH, Khavari PA, Greenleaf WJ, Davis MM, Chang HY. Transcript-indexed ATAC-seq for precision immune profiling. Nat Med 2018; 24:580-590. [PMID: 29686426 PMCID: PMC5948148 DOI: 10.1038/s41591-018-0008-8] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [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: 06/08/2017] [Accepted: 02/07/2018] [Indexed: 02/04/2023]
Abstract
T cells create vast amounts of diversity in the genes that encode their T cell receptors (TCRs), which enables individual clones to recognize specific peptide-major histocompatibility complex (MHC) ligands. Here we combined sequencing of the TCR-encoding genes with assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis at the single-cell level to provide information on the TCR specificity and epigenomic state of individual T cells. By using this approach, termed transcript-indexed ATAC-seq (T-ATAC-seq), we identified epigenomic signatures in immortalized leukemic T cells, primary human T cells from healthy volunteers and primary leukemic T cells from patient samples. In peripheral blood CD4+ T cells from healthy individuals, we identified cis and trans regulators of naive and memory T cell states and found substantial heterogeneity in surface-marker-defined T cell populations. In patients with a leukemic form of cutaneous T cell lymphoma, T-ATAC-seq enabled identification of leukemic and nonleukemic regulatory pathways in T cells from the same individual by allowing separation of the signals that arose from the malignant clone from the background T cell noise. Thus, T-ATAC-seq is a new tool that enables analysis of epigenomic landscapes in clonal T cells and should be valuable for studies of T cell malignancy, immunity and immunotherapy.
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Affiliation(s)
- Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Naresha Saligrama
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jason D Buenrostro
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.,Harvard Society of Fellows, Harvard University, Cambridge, MA, USA
| | - Yuning Wei
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Beijing Wu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Adam J Rubin
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Caleb A Lareau
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yanyan Qi
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kevin R Parker
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - William S Serratelli
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - David G Gennert
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Alicia N Schep
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.,Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael S Khodadoust
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Youn H Kim
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Paul A Khavari
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Department of Applied Physics, Stanford University, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA. .,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA. .,Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA.
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
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24
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Corces MR, Trevino AE, Hamilton EG, Greenside PG, Sinnott-Armstrong NA, Vesuna S, Satpathy AT, Rubin AJ, Montine KS, Wu B, Kathiria A, Cho SW, Mumbach MR, Carter AC, Kasowski M, Orloff LA, Risca VI, Kundaje A, Khavari PA, Montine TJ, Greenleaf WJ, Chang HY. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 2017; 14:959-962. [PMID: 28846090 PMCID: PMC5623106 DOI: 10.1038/nmeth.4396] [Citation(s) in RCA: 1185] [Impact Index Per Article: 169.3] [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] [Received: 04/04/2017] [Accepted: 07/11/2017] [Indexed: 12/16/2022]
Abstract
We present Omni-ATAC, an improved ATAC-seq protocol for chromatin accessibility profiling that works across multiple applications with substantial improvement of signal-to-background ratio and information content. The Omni-ATAC protocol generates chromatin accessibility profiles from archival frozen tissue samples and 50-μm sections, revealing the activities of disease-associated DNA elements in distinct human brain structures. The Omni-ATAC protocol enables the interrogation of personal regulomes in tissue context and translational studies.
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Affiliation(s)
- M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| | - Alexandro E Trevino
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Department of Bioengineering, Stanford University School of Medicine and School of Engineering, Stanford, California, USA
| | - Emily G Hamilton
- Program in Cancer Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Peyton G Greenside
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Program in Biomedical Informatics, Stanford University School of Medicine, Stanford, California, USA
| | | | - Sam Vesuna
- Department of Bioengineering, Stanford University School of Medicine and School of Engineering, Stanford, California, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Adam J Rubin
- Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| | - Kathleen S Montine
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Beijing Wu
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Arwa Kathiria
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Seung Woo Cho
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| | - Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Ava C Carter
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| | - Maya Kasowski
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Lisa A Orloff
- Department of Otolaryngology Head and Neck Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Viviana I Risca
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Department of Computer Science, Stanford University, Stanford, California, USA
| | - Paul A Khavari
- Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| | - Thomas J Montine
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
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25
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Mumbach MR, Satpathy AT, Boyle EA, Dai C, Gowen BG, Cho SW, Nguyen ML, Rubin AJ, Granja JM, Kazane KR, Wei Y, Nguyen T, Greenside PG, Corces MR, Tycko J, Simeonov DR, Suliman N, Li R, Xu J, Flynn RA, Kundaje A, Khavari PA, Marson A, Corn JE, Quertermous T, Greenleaf WJ, Chang HY. Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements. Nat Genet 2017; 49:1602-1612. [PMID: 28945252 DOI: 10.1038/ng.3963] [Citation(s) in RCA: 305] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 09/01/2017] [Indexed: 12/14/2022]
Abstract
The challenge of linking intergenic mutations to target genes has limited molecular understanding of human diseases. Here we show that H3K27ac HiChIP generates high-resolution contact maps of active enhancers and target genes in rare primary human T cell subtypes and coronary artery smooth muscle cells. Differentiation of naive T cells into T helper 17 cells or regulatory T cells creates subtype-specific enhancer-promoter interactions, specifically at regions of shared DNA accessibility. These data provide a principled means of assigning molecular functions to autoimmune and cardiovascular disease risk variants, linking hundreds of noncoding variants to putative gene targets. Target genes identified with HiChIP are further supported by CRISPR interference and activation at linked enhancers, by the presence of expression quantitative trait loci, and by allele-specific enhancer loops in patient-derived primary cells. The majority of disease-associated enhancers contact genes beyond the nearest gene in the linear genome, leading to a fourfold increase in the number of potential target genes for autoimmune and cardiovascular diseases.
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Affiliation(s)
- Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Evan A Boyle
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Chao Dai
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Benjamin G Gowen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
| | - Seung Woo Cho
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Michelle L Nguyen
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Adam J Rubin
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Katelynn R Kazane
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
| | - Yuning Wei
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Trieu Nguyen
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Peyton G Greenside
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Josh Tycko
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Dimitre R Simeonov
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA.,Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, California, USA
| | - Nabeela Suliman
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Jin Xu
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Ryan A Flynn
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Alexander Marson
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA.,Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA.,Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Jacob E Corn
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
| | - Thomas Quertermous
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.,Chan Zuckerberg Biohub, San Francisco, California, USA.,Department of Applied Physics, Stanford University, Stanford, California, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
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26
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Rubin AJ, Barajas BC, Furlan-Magaril M, Lopez-Pajares V, Mumbach MR, Howard I, Kim DS, Boxer LD, Cairns J, Spivakov M, Wingett SW, Shi M, Zhao Z, Greenleaf WJ, Kundaje A, Snyder M, Chang HY, Fraser P, Khavari PA. Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation. Nat Genet 2017; 49:1522-1528. [PMID: 28805829 PMCID: PMC5715812 DOI: 10.1038/ng.3935] [Citation(s) in RCA: 186] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/21/2017] [Indexed: 12/16/2022]
Abstract
Chromosome conformation is an important feature of metazoan gene regulation; however, enhancer-promoter contact remodeling during cellular differentiation remains poorly understood. To address this, genome-wide promoter capture Hi-C (CHi-C) was performed during epidermal differentiation. Two classes of enhancer-promoter contacts associated with differentiation-induced genes were identified. The first class ('gained') increased in contact strength during differentiation in concert with enhancer acquisition of the H3K27ac activation mark. The second class ('stable') were pre-established in undifferentiated cells, with enhancers constitutively marked by H3K27ac. The stable class was associated with the canonical conformation regulator cohesin, whereas the gained class was not, implying distinct mechanisms of contact formation and regulation. Analysis of stable enhancers identified a new, essential role for a constitutively expressed, lineage-restricted ETS-family transcription factor, EHF, in epidermal differentiation. Furthermore, neither class of contacts was observed in pluripotent cells, suggesting that lineage-specific chromatin structure is established in tissue progenitor cells and is further remodeled in terminal differentiation.
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Affiliation(s)
- Adam J Rubin
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Brook C Barajas
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Mayra Furlan-Magaril
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK.,Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Vanessa Lopez-Pajares
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Maxwell R Mumbach
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Imani Howard
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Daniel S Kim
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Lisa D Boxer
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Jonathan Cairns
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
| | | | | | - Minyi Shi
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Zhixin Zhao
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Howard Y Chang
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Peter Fraser
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK.,Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA.,Veterans Affairs Palo Alto Healthcare System, Palo Alto, California, USA
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27
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Mumbach MR, Rubin AJ, Flynn RA, Dai C, Khavari PA, Greenleaf WJ, Chang HY. HiChIP: efficient and sensitive analysis of protein-directed genome architecture. Nat Methods 2016; 13:919-922. [PMID: 27643841 PMCID: PMC5501173 DOI: 10.1038/nmeth.3999] [Citation(s) in RCA: 646] [Impact Index Per Article: 80.8] [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] [Received: 05/02/2016] [Accepted: 08/10/2016] [Indexed: 12/19/2022]
Abstract
Genome conformation is central to gene control but challenging to interrogate. Here we present HiChIP, a protein-centric chromatin conformation method. HiChIP improves the yield of conformation-informative reads by over 10-fold and lowers the input requirement over 100-fold relative to that of ChIA-PET. HiChIP of cohesin reveals multiscale genome architecture with greater signal-to-background ratios than those of in situ Hi-C.
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Affiliation(s)
- Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Adam J Rubin
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Ryan A Flynn
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Chao Dai
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Department of Applied Physics, Stanford University, Stanford, California, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
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28
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Nozue K, Tat AV, Kumar Devisetty U, Robinson M, Mumbach MR, Ichihashi Y, Lekkala S, Maloof JN. Shade avoidance components and pathways in adult plants revealed by phenotypic profiling. PLoS Genet 2015; 11:e1004953. [PMID: 25874869 PMCID: PMC4398415 DOI: 10.1371/journal.pgen.1004953] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 12/11/2014] [Indexed: 01/01/2023] Open
Abstract
Shade from neighboring plants limits light for photosynthesis; as a consequence, plants have a variety of strategies to avoid canopy shade and compete with their neighbors for light. Collectively the response to foliar shade is called the shade avoidance syndrome (SAS). The SAS includes elongation of a variety of organs, acceleration of flowering time, and additional physiological responses, which are seen throughout the plant life cycle. However, current mechanistic knowledge is mainly limited to shade-induced elongation of seedlings. Here we use phenotypic profiling of seedling, leaf, and flowering time traits to untangle complex SAS networks. We used over-representation analysis (ORA) of shade-responsive genes, combined with previous annotation, to logically select 59 known and candidate novel mutants for phenotyping. Our analysis reveals shared and separate pathways for each shade avoidance response. In particular, auxin pathway components were required for shade avoidance responses in hypocotyl, petiole, and flowering time, whereas jasmonic acid pathway components were only required for petiole and flowering time responses. Our phenotypic profiling allowed discovery of seventeen novel shade avoidance mutants. Our results demonstrate that logical selection of mutants increased success of phenotypic profiling to dissect complex traits and discover novel components.
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Affiliation(s)
- Kazunari Nozue
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - An V. Tat
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Upendra Kumar Devisetty
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Matthew Robinson
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Maxwell R. Mumbach
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Yasunori Ichihashi
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Saradadevi Lekkala
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Julin N. Maloof
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
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Jovanovic M, Rooney MS, Mertins P, Przybylski D, Chevrier N, Satija R, Rodriguez EH, Fields AP, Schwartz S, Raychowdhury R, Mumbach MR, Eisenhaure T, Rabani M, Gennert D, Lu D, Delorey T, Weissman JS, Carr SA, Hacohen N, Regev A. Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens. Science 2015; 347:1259038. [PMID: 25745177 DOI: 10.1126/science.1259038] [Citation(s) in RCA: 327] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein expression is regulated by the production and degradation of messenger RNAs (mRNAs) and proteins, but their specific relationships remain unknown. We combine measurements of protein production and degradation and mRNA dynamics so as to build a quantitative genomic model of the differential regulation of gene expression in lipopolysaccharide-stimulated mouse dendritic cells. Changes in mRNA abundance play a dominant role in determining most dynamic fold changes in protein levels. Conversely, the preexisting proteome of proteins performing basic cellular functions is remodeled primarily through changes in protein production or degradation, accounting for more than half of the absolute change in protein molecules in the cell. Thus, the proteome is regulated by transcriptional induction for newly activated cellular functions and by protein life-cycle changes for remodeling of preexisting functions.
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Affiliation(s)
- Marko Jovanovic
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael S Rooney
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Philipp Mertins
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Nicolas Chevrier
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Harvard Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Rahul Satija
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Edwin H Rodriguez
- Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alexander P Fields
- Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Schraga Schwartz
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Thomas Eisenhaure
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Michal Rabani
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dave Gennert
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Diana Lu
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Toni Delorey
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA. Howard Hughes Medical Institute (HHMI), University of California, San Francisco, San Francisco, CA 94158, USA
| | - Steven A Carr
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nir Hacohen
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA 02114, USA. Harvard Medical School, Boston, MA 02115, USA.
| | - Aviv Regev
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA. HHMI, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA.
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Schwartz S, Bernstein DA, Mumbach MR, Jovanovic M, Herbst RH, León-Ricardo BX, Engreitz JM, Guttman M, Satija R, Lander ES, Fink G, Regev A. Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA. Cell 2014; 159:148-162. [PMID: 25219674 DOI: 10.1016/j.cell.2014.08.028] [Citation(s) in RCA: 661] [Impact Index Per Article: 66.1] [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] [Received: 07/30/2014] [Revised: 08/21/2014] [Accepted: 08/22/2014] [Indexed: 01/14/2023]
Abstract
Pseudouridine is the most abundant RNA modification, yet except for a few well-studied cases, little is known about the modified positions and their function(s). Here, we develop Ψ-seq for transcriptome-wide quantitative mapping of pseudouridine. We validate Ψ-seq with spike-ins and de novo identification of previously reported positions and discover hundreds of unique sites in human and yeast mRNAs and snoRNAs. Perturbing pseudouridine synthases (PUS) uncovers which pseudouridine synthase modifies each site and their target sequence features. mRNA pseudouridinylation depends on both site-specific and snoRNA-guided pseudouridine synthases. Upon heat shock in yeast, Pus7p-mediated pseudouridylation is induced at >200 sites, and PUS7 deletion decreases the levels of otherwise pseudouridylated mRNA, suggesting a role in enhancing transcript stability. rRNA pseudouridine stoichiometries are conserved but reduced in cells from dyskeratosis congenita patients, where the PUS DKC1 is mutated. Our work identifies an enhanced, transcriptome-wide scope for pseudouridine and methods to dissect its underlying mechanisms and function.
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Affiliation(s)
| | | | | | - Marko Jovanovic
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rebecca H Herbst
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02114, USA
| | - Brian X León-Ricardo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan 00931, Puerto Rico
| | - Jesse M Engreitz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Health Sciences and Technology, MIT, Cambridge, MA 02139, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rahul Satija
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02114, USA; Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Gerald Fink
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA.
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA.
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31
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Schwartz S, Mumbach MR, Jovanovic M, Wang T, Maciag K, Bushkin GG, Mertins P, Ter-Ovanesyan D, Habib N, Cacchiarelli D, Sanjana NE, Freinkman E, Pacold ME, Satija R, Mikkelsen TS, Hacohen N, Zhang F, Carr SA, Lander ES, Regev A. Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites. Cell Rep 2014; 8:284-96. [PMID: 24981863 DOI: 10.1016/j.celrep.2014.05.048] [Citation(s) in RCA: 856] [Impact Index Per Article: 85.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/07/2014] [Accepted: 05/27/2014] [Indexed: 12/31/2022] Open
Abstract
N6-methyladenosine (m6A) is a common modification of mRNA with potential roles in fine-tuning the RNA life cycle. Here, we identify a dense network of proteins interacting with METTL3, a component of the methyltransferase complex, and show that three of them (WTAP, METTL14, and KIAA1429) are required for methylation. Monitoring m6A levels upon WTAP depletion allowed the definition of accurate and near single-nucleotide resolution methylation maps and their classification into WTAP-dependent and -independent sites. WTAP-dependent sites are located at internal positions in transcripts, topologically static across a variety of systems we surveyed, and inversely correlated with mRNA stability, consistent with a role in establishing "basal" degradation rates. WTAP-independent sites form at the first transcribed base as part of the cap structure and are present at thousands of sites, forming a previously unappreciated layer of transcriptome complexity. Our data shed light on the proteomic and transcriptional underpinnings of this RNA modification.
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Affiliation(s)
| | | | - Marko Jovanovic
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tim Wang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Karolina Maciag
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Graduate Program in Immunology, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - G Guy Bushkin
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Philipp Mertins
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Naomi Habib
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Davide Cacchiarelli
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | | | | | - Michael E Pacold
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Radiation Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Rahul Satija
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tarjei S Mikkelsen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02114, USA.
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA.
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32
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Schwartz S, Agarwala SD, Mumbach MR, Jovanovic M, Mertins P, Shishkin A, Tabach Y, Mikkelsen TS, Satija R, Ruvkun G, Carr SA, Lander ES, Fink GR, Regev A. High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis. Cell 2013; 155:1409-21. [PMID: 24269006 DOI: 10.1016/j.cell.2013.10.047] [Citation(s) in RCA: 474] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 10/22/2013] [Accepted: 10/29/2013] [Indexed: 01/12/2023]
Abstract
N(6)-methyladenosine (m(6)A) is the most ubiquitous mRNA base modification, but little is known about its precise location, temporal dynamics, and regulation. Here, we generated genomic maps of m(6)A sites in meiotic yeast transcripts at nearly single-nucleotide resolution, identifying 1,308 putatively methylated sites within 1,183 transcripts. We validated eight out of eight methylation sites in different genes with direct genetic analysis, demonstrated that methylated sites are significantly conserved in a related species, and built a model that predicts methylated sites directly from sequence. Sites vary in their methylation profiles along a dense meiotic time course and are regulated both locally, via predictable methylatability of each site, and globally, through the core meiotic circuitry. The methyltransferase complex components localize to the yeast nucleolus, and this localization is essential for mRNA methylation. Our data illuminate a conserved, dynamically regulated methylation program in yeast meiosis and provide an important resource for studying the function of this epitranscriptomic modification.
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Abstract
High throughput phenotyping (phenomics) is a powerful tool for linking genes to their functions (see review and recent examples). Leaves are the primary photosynthetic organ, and their size and shape vary developmentally and environmentally within a plant. For these reasons studies on leaf morphology require measurement of multiple parameters from numerous leaves, which is best done by semi-automated phenomics tools. Canopy shade is an important environmental cue that affects plant architecture and life history; the suite of responses is collectively called the shade avoidance syndrome (SAS). Among SAS responses, shade induced leaf petiole elongation and changes in blade area are particularly useful as indices. To date, leaf shape programs (e.g. SHAPE, LAMINA, LeafAnalyzer, LEAFPROCESSOR) can measure leaf outlines and categorize leaf shapes, but can not output petiole length. Lack of large-scale measurement systems of leaf petioles has inhibited phenomics approaches to SAS research. In this paper, we describe a newly developed ImageJ plugin, called LeafJ, which can rapidly measure petiole length and leaf blade parameters of the model plant Arabidopsis thaliana. For the occasional leaf that required manual correction of the petiole/leaf blade boundary we used a touch-screen tablet. Further, leaf cell shape and leaf cell numbers are important determinants of leaf size. Separate from LeafJ we also present a protocol for using a touch-screen tablet for measuring cell shape, area, and size. Our leaf trait measurement system is not limited to shade-avoidance research and will accelerate leaf phenotyping of many mutants and screening plants by leaf phenotyping.
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Affiliation(s)
- Julin N Maloof
- Department of Plant Biology, University of California Davis, USA.
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