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Ocampo D, Damon LJ, Sanford L, Holtzen SE, Jones T, Allen MA, Dowell RD, Palmer AE. Cellular zinc status alters chromatin accessibility and binding of p53 to DNA. Life Sci Alliance 2024; 7:e202402638. [PMID: 38969365 PMCID: PMC11231577 DOI: 10.26508/lsa.202402638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 07/07/2024] Open
Abstract
Zn2+ is an essential metal required by approximately 850 human transcription factors. How these proteins acquire their essential Zn2+ cofactor and whether they are sensitive to changes in the labile Zn2+ pool in cells remain open questions. Using ATAC-seq to profile regions of accessible chromatin coupled with transcription factor enrichment analysis, we examined how increases and decreases in the labile zinc pool affect chromatin accessibility and transcription factor enrichment. We found 685 transcription factor motifs were differentially enriched, corresponding to 507 unique transcription factors. The pattern of perturbation and the types of transcription factors were notably different at promoters versus intergenic regions, with zinc-finger transcription factors strongly enriched in intergenic regions in elevated Zn2+ To test whether ATAC-seq and transcription factor enrichment analysis predictions correlate with changes in transcription factor binding, we used ChIP-qPCR to profile six p53 binding sites. We found that for five of the six targets, p53 binding correlates with the local accessibility determined by ATAC-seq. These results demonstrate that changes in labile zinc alter chromatin accessibility and transcription factor binding to DNA.
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Affiliation(s)
- Daniel Ocampo
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Leah J Damon
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Lynn Sanford
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Samuel E Holtzen
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Taylor Jones
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Mary A Allen
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Robin D Dowell
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Amy E Palmer
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
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Korenfeld N, Gorbonos T, Romero Florian MC, Rotaro D, Goldberg D, Radushkevitz-Frishman T, Charni-Natan M, Bar-Shimon M, Cummins CL, Goldstein I. LXR-dependent enhancer activation regulates the temporal organization of the liver's response to refeeding leading to lipogenic gene overshoot. PLoS Biol 2024; 22:e3002735. [PMID: 39241209 PMCID: PMC11379474 DOI: 10.1371/journal.pbio.3002735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 07/04/2024] [Indexed: 09/08/2024] Open
Abstract
Transitions between the fed and fasted state are common in mammals. The liver orchestrates adaptive responses to feeding/fasting by transcriptionally regulating metabolic pathways of energy usage and storage. Transcriptional and enhancer dynamics following cessation of fasting (refeeding) have not been explored. We examined the transcriptional and chromatin events occurring upon refeeding in mice, including kinetic behavior and molecular drivers. We found that the refeeding response is temporally organized with the early response focused on ramping up protein translation while the later stages of refeeding drive a bifurcated lipid synthesis program. While both the cholesterol biosynthesis and lipogenesis pathways were inhibited during fasting, most cholesterol biosynthesis genes returned to their basal levels upon refeeding while most lipogenesis genes markedly overshoot above pre-fasting levels. Gene knockout, enhancer dynamics, and ChIP-seq analyses revealed that lipogenic gene overshoot is dictated by LXRα. These findings from unbiased analyses unravel the mechanism behind the long-known phenomenon of refeeding fat overshoot.
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Affiliation(s)
- Noga Korenfeld
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Tali Gorbonos
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Maria C Romero Florian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Dan Rotaro
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Dana Goldberg
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Talia Radushkevitz-Frishman
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Meital Charni-Natan
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Meirav Bar-Shimon
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Carolyn L Cummins
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Ido Goldstein
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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Patrick R, Naval-Sanchez M, Deshpande N, Huang Y, Zhang J, Chen X, Yang Y, Tiwari K, Esmaeili M, Tran M, Mohamed AR, Wang B, Xia D, Ma J, Bayliss J, Wong K, Hun ML, Sun X, Cao B, Cottle DL, Catterall T, Barzilai-Tutsch H, Troskie RL, Chen Z, Wise AF, Saini S, Soe YM, Kumari S, Sweet MJ, Thomas HE, Smyth IM, Fletcher AL, Knoblich K, Watt MJ, Alhomrani M, Alsanie W, Quinn KM, Merson TD, Chidgey AP, Ricardo SD, Yu D, Jardé T, Cheetham SW, Marcelle C, Nilsson SK, Nguyen Q, White MD, Nefzger CM. The activity of early-life gene regulatory elements is hijacked in aging through pervasive AP-1-linked chromatin opening. Cell Metab 2024; 36:1858-1881.e23. [PMID: 38959897 DOI: 10.1016/j.cmet.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 03/28/2024] [Accepted: 06/06/2024] [Indexed: 07/05/2024]
Abstract
A mechanistic connection between aging and development is largely unexplored. Through profiling age-related chromatin and transcriptional changes across 22 murine cell types, analyzed alongside previous mouse and human organismal maturation datasets, we uncovered a transcription factor binding site (TFBS) signature common to both processes. Early-life candidate cis-regulatory elements (cCREs), progressively losing accessibility during maturation and aging, are enriched for cell-type identity TFBSs. Conversely, cCREs gaining accessibility throughout life have a lower abundance of cell identity TFBSs but elevated activator protein 1 (AP-1) levels. We implicate TF redistribution toward these AP-1 TFBS-rich cCREs, in synergy with mild downregulation of cell identity TFs, as driving early-life cCRE accessibility loss and altering developmental and metabolic gene expression. Such remodeling can be triggered by elevating AP-1 or depleting repressive H3K27me3. We propose that AP-1-linked chromatin opening drives organismal maturation by disrupting cell identity TFBS-rich cCREs, thereby reprogramming transcriptome and cell function, a mechanism hijacked in aging through ongoing chromatin opening.
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Affiliation(s)
- Ralph Patrick
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Marina Naval-Sanchez
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Nikita Deshpande
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Yifei Huang
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Jingyu Zhang
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Xiaoli Chen
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Ying Yang
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Kanupriya Tiwari
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Mohammadhossein Esmaeili
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Minh Tran
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Amin R Mohamed
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Binxu Wang
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Di Xia
- Genome Innovation Hub, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Jun Ma
- Genome Innovation Hub, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Jacqueline Bayliss
- Department of Anatomy and Physiology, Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Kahlia Wong
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Michael L Hun
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Xuan Sun
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organization, Melbourne, VIC, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Benjamin Cao
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organization, Melbourne, VIC, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Denny L Cottle
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Tara Catterall
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Hila Barzilai-Tutsch
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; Institut NeuroMyoGène, University Claude Bernard Lyon 1, 69008 Lyon, France
| | - Robin-Lee Troskie
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Zhian Chen
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Andrea F Wise
- Department of Pharmacology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Sheetal Saini
- Department of Pharmacology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Ye Mon Soe
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Snehlata Kumari
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Matthew J Sweet
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Helen E Thomas
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Ian M Smyth
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Anne L Fletcher
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Konstantin Knoblich
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Matthew J Watt
- Department of Anatomy and Physiology, Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Majid Alhomrani
- Department of Clinical Laboratories Sciences, Faculty of Applied Medical Sciences, Taif University, Taif, Saudi Arabia; Research Centre for Health Sciences, Taif University, Taif, Saudi Arabia
| | - Walaa Alsanie
- Department of Clinical Laboratories Sciences, Faculty of Applied Medical Sciences, Taif University, Taif, Saudi Arabia; Research Centre for Health Sciences, Taif University, Taif, Saudi Arabia
| | - Kylie M Quinn
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC 3083, Australia
| | - Tobias D Merson
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ann P Chidgey
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Sharon D Ricardo
- Department of Pharmacology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Di Yu
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia; Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Thierry Jardé
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Cancer Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Department of Surgery, Cabrini Monash University, Malvern, VIC 3144, Australia
| | - Seth W Cheetham
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Christophe Marcelle
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; Institut NeuroMyoGène, University Claude Bernard Lyon 1, 69008 Lyon, France
| | - Susan K Nilsson
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organization, Melbourne, VIC, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Quan Nguyen
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; School of Biomedical Sciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Melanie D White
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; School of Biomedical Sciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Christian M Nefzger
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia.
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Shukla V, Wang H, Varticovski L, Baek S, Wang R, Wu X, Echtenkamp F, Villa-Hernandez F, Prothro KP, Gara SK, Zhang MR, Shiffka S, Raziuddin R, Neckers LM, Linehan WM, Chen H, Hager GL, Schrump DS. Genome-Wide Analysis Identifies Nuclear Factor 1C as a Novel Transcription Factor and Potential Therapeutic Target in SCLC. J Thorac Oncol 2024; 19:1201-1217. [PMID: 38583771 DOI: 10.1016/j.jtho.2024.03.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/14/2024] [Accepted: 03/30/2024] [Indexed: 04/09/2024]
Abstract
INTRODUCTION Recent insights regarding mechanisms mediating stemness, heterogeneity, and metastatic potential of lung cancers have yet to be fully translated to effective regimens for the treatment of these malignancies. This study sought to identify novel targets for lung cancer therapy. METHODS Transcriptomes and DNA methylomes of 14 SCLC and 10 NSCLC lines were compared with normal human small airway epithelial cells (SAECs) and induced pluripotent stem cell (iPSC) clones derived from SAEC. SCLC lines, lung iPSC (Lu-iPSC), and SAEC were further evaluated by DNase I hypersensitive site sequencing (DHS-seq). Changes in chromatin accessibility and depths of transcription factor (TF) footprints were quantified using Bivariate analysis of Genomic Footprint. Standard techniques were used to evaluate growth, tumorigenicity, and changes in transcriptomes and glucose metabolism of SCLC cells after NFIC knockdown and to evaluate NFIC expression in SCLC cells after exposure to BET inhibitors. RESULTS Considerable commonality of transcriptomes and DNA methylomes was observed between Lu-iPSC and SCLC; however, this analysis was uninformative regarding pathways unique to lung cancer. Linking results of DHS-seq to RNA sequencing enabled identification of networks not previously associated with SCLC. When combined with footprint depth, NFIC, a transcription factor not previously associated with SCLC, had the highest score of occupancy at open chromatin sites. Knockdown of NFIC impaired glucose metabolism, decreased stemness, and inhibited growth of SCLC cells in vitro and in vivo. ChIP-seq analysis identified numerous sites occupied by BRD4 in the NFIC promoter region. Knockdown of BRD4 or treatment with Bromodomain and extra-terminal domain (BET) inhibitors (BETis) markedly reduced NFIC expression in SCLC cells and SCLC PDX models. Approximately 8% of genes down-regulated by BETi treatment were repressed by NFIC knockdown in SCLC, whereas 34% of genes repressed after NFIC knockdown were also down-regulated in SCLC cells after BETi treatment. CONCLUSIONS NFIC is a key TF and possible mediator of transcriptional regulation by BET family proteins in SCLC. Our findings highlight the potential of genome-wide chromatin accessibility analysis for elucidating mechanisms of pulmonary carcinogenesis and identifying novel targets for lung cancer therapy.
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Affiliation(s)
- Vivek Shukla
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland; Present Address: Division of Nonclinical Sciences (DNCS), FDA, Silver Spring, Maryland
| | - Haitao Wang
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Lyuba Varticovski
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Ruihong Wang
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Xinwei Wu
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Frank Echtenkamp
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Frank Villa-Hernandez
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Katherine P Prothro
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Sudheer K Gara
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Mary R Zhang
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Stephanie Shiffka
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Razi Raziuddin
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Leonard M Neckers
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Haobin Chen
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland; Present Address: Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - David S Schrump
- Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
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Trauernicht M, Filipovska T, Rastogi C, van Steensel B. Optimized reporters for multiplexed detection of transcription factor activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.26.605239. [PMID: 39091757 PMCID: PMC11291157 DOI: 10.1101/2024.07.26.605239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
In any given cell type, dozens of transcription factors (TFs) act in concert to control the activity of the genome by binding to specific DNA sequences in regulatory elements. Despite their considerable importance in determining cell identity and their pivotal role in numerous disorders, we currently lack simple tools to directly measure the activity of many TFs in parallel. Massively parallel reporter assays (MPRAs) allow the detection of TF activities in a multiplexed fashion; however, we lack basic understanding to rationally design sensitive reporters for many TFs. Here, we use an MPRA to systematically optimize transcriptional reporters for 86 TFs and evaluate the specificity of all reporters across a wide array of TF perturbation conditions. We thus identified critical TF reporter design features and obtained highly sensitive and specific reporters for 60 TFs, many of which outperform available reporters. The resulting collection of "prime" TF reporters can be used to uncover TF regulatory networks and to illuminate signaling pathways. HIGHLIGHTS Systematic design and optimization of transcriptional reporters for 86 TFsCharacterization of TF-specific reporter design optimization rulesEvaluation of reporter TF-specificity across a wide array of TF perturbationsIdentification of a collection of 60 "prime" TF reporters with optimized performance.
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6
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Lu Z, Xiao X, Zheng Q, Wang X, Xu L. Assessing next-generation sequencing-based computational methods for predicting transcriptional regulators with query gene sets. Brief Bioinform 2024; 25:bbae366. [PMID: 39082650 PMCID: PMC11289684 DOI: 10.1093/bib/bbae366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/21/2024] [Accepted: 07/18/2024] [Indexed: 08/03/2024] Open
Abstract
This article provides an in-depth review of computational methods for predicting transcriptional regulators (TRs) with query gene sets. Identification of TRs is of utmost importance in many biological applications, including but not limited to elucidating biological development mechanisms, identifying key disease genes, and predicting therapeutic targets. Various computational methods based on next-generation sequencing (NGS) data have been developed in the past decade, yet no systematic evaluation of NGS-based methods has been offered. We classified these methods into two categories based on shared characteristics, namely library-based and region-based methods. We further conducted benchmark studies to evaluate the accuracy, sensitivity, coverage, and usability of NGS-based methods with molecular experimental datasets. Results show that BART, ChIP-Atlas, and Lisa have relatively better performance. Besides, we point out the limitations of NGS-based methods and explore potential directions for further improvement.
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Affiliation(s)
- Zeyu Lu
- Department of Statistics and Data Science, Moody School of Graduate and Advanced Studies, Southern Methodist University, 3225 Daniel Ave., P.O. Box 750332, Dallas, TX, United States
| | - Xue Xiao
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, United States
| | - Qiang Zheng
- Division of Data Science, College of Science, University of Texas at Arlington, 501 S. Nedderman Dr., Arlington, TX 76019, United States
| | - Xinlei Wang
- Division of Data Science, College of Science, University of Texas at Arlington, 501 S. Nedderman Dr., Arlington, TX 76019, United States
- Department of Mathematics, University of Texas at Arlington, 411 S. Nedderman Dr., Arlington, TX 76019, United States
| | - Lin Xu
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, United States
- Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, United States
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7
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Xiang K, Wang E, Mantyh J, Rupprecht G, Negrete M, Sanati G, Hsu C, Randon P, Dohlman A, Kretzschmar K, Bose S, Giroux N, Ding S, Wang L, Balcazar JP, Huang Q, Sundaramoorthy P, Xi R, McCall SJ, Wang Z, Jiang C, Kang Y, Kopetz S, Crawford GE, Lipkin SM, Wang XF, Clevers H, Hsu D, Shen X. Chromatin Remodeling in Patient-Derived Colorectal Cancer Models. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2303379. [PMID: 38380561 DOI: 10.1002/advs.202303379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 11/22/2023] [Indexed: 02/22/2024]
Abstract
Patient-Derived Organoids (PDO) and Xenografts (PDX) are the current gold standards for patient-derived models of cancer (PDMC). Nevertheless, how patient tumor cells evolve in these models and the impact on drug response remains unclear. Herein, the transcriptomic and chromatin accessibility landscapes of matched colorectal cancer (CRC) PDO, PDX, PDO-derived PDX (PDOX), and original patient tumors (PT) are compared. Two major remodeling axes are discovered. The first axis delineates PDMC from PT, and the second axis distinguishes PDX and PDO. PDOX are more similar to PDX than PDO, indicating the growth environment is a driving force for chromatin adaptation. Transcription factors (TF) that differentially bind to open chromatins between matched PDO and PDOX are identified. Among them, KLF14 and EGR2 footprints are enriched in PDOX relative to matched PDO, and silencing of KLF14 or EGR2 promoted tumor growth. Furthermore, EPHA4, a shared downstream target gene of KLF14 and EGR2, altered tumor sensitivity to MEK inhibitor treatment. Altogether, patient-derived CRC cells undergo both common and distinct chromatin remodeling in PDO and PDX/PDOX, driven largely by their respective microenvironments, which results in differences in growth and drug sensitivity and needs to be taken into consideration when interpreting their ability to predict clinical outcome.
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Affiliation(s)
- Kun Xiang
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, 27708, USA
| | - Ergang Wang
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, 27708, USA
| | - John Mantyh
- Department of Medicine, School of Medicine, Duke University, Durham, NC, 27710, USA
| | - Gabrielle Rupprecht
- Department of Medicine, School of Medicine, Duke University, Durham, NC, 27710, USA
| | - Marcos Negrete
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, 27708, USA
| | - Golshid Sanati
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, 27708, USA
| | - Carolyn Hsu
- Department of Medicine, School of Medicine, Duke University, Durham, NC, 27710, USA
| | - Peggy Randon
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, 27709, USA
| | - Anders Dohlman
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, 27708, USA
| | - Kai Kretzschmar
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Uppsalalaan 8, Utrecht, CT, 3584, The Netherlands
- Mildred Scheel Early Career Centre (MSNZ) for Cancer Research Würzburg, University Hospital Würzburg, 97080, Würzburg, Germany
| | - Shree Bose
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, 27708, USA
| | - Nicholas Giroux
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, 27708, USA
| | - Shengli Ding
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, 27708, USA
| | - Lihua Wang
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, 27708, USA
| | - Jorge Prado Balcazar
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, 27708, USA
| | - Qiang Huang
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, 27708, USA
- Terasaki Institute, Los Angeles, CA, 90024, USA
| | | | - Rui Xi
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, 27708, USA
| | - Shannon Jones McCall
- Department of Pathology, School of Medicine, Duke University, Durham, NC, 27710, USA
| | - Zhaohui Wang
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, 27708, USA
| | | | - Yubin Kang
- Department of Medicine, School of Medicine, Duke University, Durham, NC, 27710, USA
| | - Scott Kopetz
- Department of Gastrointestinal (GI) Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Gregory E Crawford
- Department of Pediatrics, Division of Medical Genetics, School of Medicine, Duke University, Durham, NC, 27710, USA
| | - Steven M Lipkin
- Department of Medicine and Program in Mendelian Genetics, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Xiao-Fan Wang
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Hans Clevers
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center (UMC) Utrecht, Uppsalalaan 8, Utrecht, CT, 3584, The Netherlands
| | - David Hsu
- Department of Medicine, School of Medicine, Duke University, Durham, NC, 27710, USA
| | - Xiling Shen
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, 27708, USA
- Terasaki Institute, Los Angeles, CA, 90024, USA
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8
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Lu Z, Xiao X, Zheng Q, Wang X, Xu L. Assessing NGS-based computational methods for predicting transcriptional regulators with query gene sets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578316. [PMID: 38562775 PMCID: PMC10983863 DOI: 10.1101/2024.02.01.578316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
This article provides an in-depth review of computational methods for predicting transcriptional regulators with query gene sets. Identification of transcriptional regulators is of utmost importance in many biological applications, including but not limited to elucidating biological development mechanisms, identifying key disease genes, and predicting therapeutic targets. Various computational methods based on next-generation sequencing (NGS) data have been developed in the past decade, yet no systematic evaluation of NGS-based methods has been offered. We classified these methods into two categories based on shared characteristics, namely library-based and region-based methods. We further conducted benchmark studies to evaluate the accuracy, sensitivity, coverage, and usability of NGS-based methods with molecular experimental datasets. Results show that BART, ChIP-Atlas, and Lisa have relatively better performance. Besides, we point out the limitations of NGS-based methods and explore potential directions for further improvement. Key points An introduction to available computational methods for predicting functional TRs from a query gene set.A detailed walk-through along with practical concerns and limitations.A systematic benchmark of NGS-based methods in terms of accuracy, sensitivity, coverage, and usability, using 570 TR perturbation-derived gene sets.NGS-based methods outperform motif-based methods. Among NGS methods, those utilizing larger databases and adopting region-centric approaches demonstrate favorable performance. BART, ChIP-Atlas, and Lisa are recommended as these methods have overall better performance in evaluated scenarios.
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9
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Gerbaldo F, Sonder E, Fischer V, Frei S, Wang J, Gapp K, Robinson MD, Germain PL. On the identification of differentially-active transcription factors from ATAC-seq data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583825. [PMID: 38496482 PMCID: PMC10942475 DOI: 10.1101/2024.03.06.583825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
ATAC-seq has emerged as a rich epigenome profiling technique, and is commonly used to identify Transcription Factors (TFs) underlying given phenomena. A number of methods can be used to identify differentially-active TFs through the accessibility of their DNA-binding motif, however little is known on the best approaches for doing so. Here we benchmark several such methods using a combination of curated datasets with various forms of short-term perturbations on known TFs, as well as semi-simulations. We include both methods specifically designed for this type of data as well as some that can be repurposed for it. We also investigate variations to these methods, and identify three particularly promising approaches (chromVAR-limma with critical adjustments, monaLisa and a combination of GC smooth quantile normalization and multivariate modeling). We further investigate the specific use of nucleosome-free fragments, the combination of top methods, and the impact of technical variation. Finally, we illustrate the use of the top methods on a novel dataset to characterize the impact on DNA accessibility of TRAnscription Factor TArgeting Chimeras (TRAFTAC), which can deplete TFs - in our case NFkB - at the protein level.
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Affiliation(s)
- Felix Gerbaldo
- Computational Neurogenomics, D-HEST Institute for Neurosciences, Zürich, Switzerland
- Systems Neuroscience, D-HEST Institute for Neurosciences, Zürich, Switzerland
| | - Emanuel Sonder
- Computational Neurogenomics, D-HEST Institute for Neurosciences, Zürich, Switzerland
- Systems Neuroscience, D-HEST Institute for Neurosciences, Zürich, Switzerland
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Switzerland
| | - Vincent Fischer
- Epigenetics and Neuroendocrinology, D-HEST Institute for Neurosciences, Zürich, Switzerland
| | - Selina Frei
- Epigenetics and Neuroendocrinology, D-HEST Institute for Neurosciences, Zürich, Switzerland
| | - Jiayi Wang
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
| | - Katharina Gapp
- Epigenetics and Neuroendocrinology, D-HEST Institute for Neurosciences, Zürich, Switzerland
| | - Mark D Robinson
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Switzerland
| | - Pierre-Luc Germain
- Computational Neurogenomics, D-HEST Institute for Neurosciences, Zürich, Switzerland
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Switzerland
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10
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Watson NB, Patel RK, Kean C, Veazey J, Oyesola OO, Laniewski N, Grenier JK, Wang J, Tabilas C, Yee Mon KJ, McNairn AJ, Peng SA, Wesnak SP, Nzingha K, Davenport MP, Tait Wojno ED, Scheible KM, Smith NL, Grimson A, Rudd BD. The gene regulatory basis of bystander activation in CD8 + T cells. Sci Immunol 2024; 9:eadf8776. [PMID: 38394230 DOI: 10.1126/sciimmunol.adf8776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/26/2024] [Indexed: 02/25/2024]
Abstract
CD8+ T cells are classically recognized as adaptive lymphocytes based on their ability to recognize specific foreign antigens and mount memory responses. However, recent studies indicate that some antigen-inexperienced CD8+ T cells can respond to innate cytokines alone in the absence of cognate T cell receptor stimulation, a phenomenon referred to as bystander activation. Here, we demonstrate that neonatal CD8+ T cells undergo a robust and diverse program of bystander activation, which corresponds to enhanced innate-like protection against unrelated pathogens. Using a multi-omics approach, we found that the ability of neonatal CD8+ T cells to respond to innate cytokines derives from their capacity to undergo rapid chromatin remodeling, resulting in the usage of a distinct set of enhancers and transcription factors typically found in innate-like T cells. We observed that the switch between innate and adaptive functions in the CD8+ T cell compartment is mediated by changes in the abundance of distinct subsets of cells. The innate CD8+ T cell subset that predominates in early life was also present in adult mice and humans. Our findings provide support for the layered immune hypothesis and indicate that the CD8+ T cell compartment is more functionally diverse than previously thought.
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Affiliation(s)
- Neva B Watson
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Ravi K Patel
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Connor Kean
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Janelle Veazey
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Oyebola O Oyesola
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Nathan Laniewski
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jennifer K Grenier
- Genomics Innovation Hub and TREx Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Jocelyn Wang
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Cybelle Tabilas
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Kristel J Yee Mon
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Adrian J McNairn
- Genomics Innovation Hub and TREx Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Seth A Peng
- Department of Clinical Science, Cornell University, Ithaca, NY 14853, USA
| | - Samantha P Wesnak
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Kito Nzingha
- Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Miles P Davenport
- Kirby Institute for Infection and Immunity, UNSW Australia, Sydney, NSW 2052, Australia
| | - Elia D Tait Wojno
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Kristin M Scheible
- Department of Pediatrics, University of Rochester, Rochester, NY 14642, USA
| | - Norah L Smith
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Andrew Grimson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Brian D Rudd
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
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11
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Long T, Bhattacharyya T, Repele A, Naylor M, Nooti S, Krueger S, Manu. The contributions of DNA accessibility and transcription factor occupancy to enhancer activity during cellular differentiation. G3 (BETHESDA, MD.) 2024; 14:jkad269. [PMID: 38124496 PMCID: PMC11090500 DOI: 10.1093/g3journal/jkad269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/01/2023] [Indexed: 12/23/2023]
Abstract
During gene regulation, DNA accessibility is thought to limit the availability of transcription factor (TF) binding sites, while TFs can increase DNA accessibility to recruit additional factors that upregulate gene expression. Given this interplay, the causative regulatory events in the modulation of gene expression remain unknown for the vast majority of genes. We utilized deeply sequenced ATAC-Seq data and site-specific knock-in reporter genes to investigate the relationship between the binding-site resolution dynamics of DNA accessibility and the expression dynamics of the enhancers of Cebpa during macrophage-neutrophil differentiation. While the enhancers upregulate reporter expression during the earliest stages of differentiation, there is little corresponding increase in their total accessibility. Conversely, total accessibility peaks during the last stages of differentiation without any increase in enhancer activity. The accessibility of positions neighboring C/EBP-family TF binding sites, which indicates TF occupancy, does increase significantly during early differentiation, showing that the early upregulation of enhancer activity is driven by TF binding. These results imply that a generalized increase in DNA accessibility is not sufficient, and binding by enhancer-specific TFs is necessary, for the upregulation of gene expression. Additionally, high-coverage ATAC-Seq combined with time-series expression data can infer the sequence of regulatory events at binding-site resolution.
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Affiliation(s)
- Trevor Long
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Tapas Bhattacharyya
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Andrea Repele
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Madison Naylor
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Sunil Nooti
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Shawn Krueger
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Manu
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
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12
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Hecker D, Lauber M, Behjati Ardakani F, Ashrafiyan S, Manz Q, Kersting J, Hoffmann M, Schulz MH, List M. Computational tools for inferring transcription factor activity. Proteomics 2023; 23:e2200462. [PMID: 37706624 DOI: 10.1002/pmic.202200462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/11/2023] [Accepted: 08/22/2023] [Indexed: 09/15/2023]
Abstract
Transcription factors (TFs) are essential players in orchestrating the regulatory landscape in cells. Still, their exact modes of action and dependencies on other regulatory aspects remain elusive. Since TFs act cell type-specific and each TF has its own characteristics, untangling their regulatory interactions from an experimental point of view is laborious and convoluted. Thus, there is an ongoing development of computational tools that estimate transcription factor activity (TFA) from a variety of data modalities, either based on a mapping of TFs to their putative target genes or in a genome-wide, gene-unspecific fashion. These tools can help to gain insights into TF regulation and to prioritize candidates for experimental validation. We want to give an overview of available computational tools that estimate TFA, illustrate examples of their application, debate common result validation strategies, and discuss assumptions and concomitant limitations.
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Affiliation(s)
- Dennis Hecker
- Goethe University Frankfurt, Frankfurt am Main, Germany
- German Center for Cardiovascular Research, Partner site Rhein-Main, Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, Frankfurt am Main, Germany
| | - Michael Lauber
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Fatemeh Behjati Ardakani
- Goethe University Frankfurt, Frankfurt am Main, Germany
- German Center for Cardiovascular Research, Partner site Rhein-Main, Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, Frankfurt am Main, Germany
| | - Shamim Ashrafiyan
- Goethe University Frankfurt, Frankfurt am Main, Germany
- German Center for Cardiovascular Research, Partner site Rhein-Main, Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, Frankfurt am Main, Germany
| | - Quirin Manz
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Johannes Kersting
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- GeneSurge GmbH, München, Germany
| | - Markus Hoffmann
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Institute for Advanced Study, Technical University of Munich, Garching, Germany
- National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Marcel H Schulz
- Goethe University Frankfurt, Frankfurt am Main, Germany
- German Center for Cardiovascular Research, Partner site Rhein-Main, Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, Frankfurt am Main, Germany
| | - Markus List
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
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13
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Cox LS, Alvarez-Martinez M, Wu X, Gabryšová L, Luisier R, Briscoe J, Luscombe NM, O'Garra A. Blimp-1 and c-Maf regulate Il10 and negatively regulate common and unique proinflammatory gene networks in IL-12 plus IL-27-driven T helper-1 cells. Wellcome Open Res 2023; 8:403. [PMID: 38074197 PMCID: PMC10709690 DOI: 10.12688/wellcomeopenres.19680.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2023] [Indexed: 02/12/2024] Open
Abstract
Background CD4 + Th1 cells producing IFN-γ are required to eradicate intracellular pathogens, however if uncontrolled these cells can cause immunopathology. The cytokine IL-10 is produced by multiple immune cells including Th1 cells during infection and regulates the immune response to minimise collateral host damage. In this study we aimed to elucidate the transcriptional network of genes controlling the expression of Il10 and proinflammatory cytokines, including Ifng in Th1 cells differentiated from mouse naive CD4 + T cells. Methods We applied computational analysis of gene regulation derived from temporal profiling of gene expression clusters obtained from bulk RNA sequencing (RNA-seq) of flow cytometry sorted naïve CD4 + T cells from mouse spleens differentiated in vitro into Th1 effector cells with IL-12 and IL-27 to produce Ifng and Il10, compared to IL-27 alone which express Il10 only , or IL-12 alone which express Ifng and no Il10, or medium control driven-CD4 + T cells which do not express effector cytokines . Data were integrated with analysis of active genomic regions from these T cells using an assay for transposase-accessible chromatin with sequencing (ATAC)-seq, integrated with literature derived-Chromatin-immunoprecipitation (ChIP)-seq data and the RNA-seq data, to elucidate the transcriptional network of genes controlling expression of Il10 and pro-inflammatory effector genes in Th1 cells. The co-dominant role for the transcription factors, Prdm1 (encoding Blimp-1) and Maf (encoding c-Maf) , in cytokine gene regulation in Th1 cells, was confirmed using T cells obtained from mice with T-cell specific deletion of these transcription factors. Results We show that the transcription factors Blimp-1 and c-Maf each have unique and common effects on cytokine gene regulation and not only co-operate to induce Il10 gene expression in IL-12 plus IL-27 differentiated mouse Th1 cells, but additionally directly negatively regulate key proinflammatory cytokines including Ifng, thus providing mechanisms for reinforcement of regulated Th1 cell responses. Conclusions These data show that Blimp-1 and c-Maf positively and negatively regulate a network of both unique and common anti-inflammatory and pro-inflammatory genes to reinforce a Th1 response in mice that will eradicate pathogens with minimum immunopathology.
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Affiliation(s)
- Luke S. Cox
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, England, NW1 1AT, UK
| | - Marisol Alvarez-Martinez
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, England, NW1 1AT, UK
| | - Xuemei Wu
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, England, NW1 1AT, UK
| | - Leona Gabryšová
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, England, NW1 1AT, UK
| | - Raphaëlle Luisier
- Computational Biology Laboratory, The Francis Crick Institute, London, England, NW1 1AT, UK
| | - James Briscoe
- Developmental Dynamics Laboratory, The Francis Crick Institute, London, England, NW1 1AT, UK
| | - Nicholas M. Luscombe
- Computational Biology Laboratory, The Francis Crick Institute, London, England, NW1 1AT, UK
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, England, UK
| | - Anne O'Garra
- Immunoregulation and Infection Laboratory, The Francis Crick Institute, London, England, NW1 1AT, UK
- National Heart and Lung Institute, Imperial College London, London, England, UK
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14
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Damon LJ, Ocampo D, Sanford L, Jones T, Allen MA, Dowell RD, Palmer AE. Cellular zinc status alters chromatin accessibility and binding of transcription factor p53 to genomic sites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.20.567954. [PMID: 38045276 PMCID: PMC10690171 DOI: 10.1101/2023.11.20.567954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Zinc (Zn2+) is an essential metal required by approximately 2500 proteins. Nearly half of these proteins act on DNA, including > 850 human transcription factors, polymerases, DNA damage response factors, and proteins involved in chromatin architecture. How these proteins acquire their essential Zn2+ cofactor and whether they are sensitive to changes in the labile Zn2+ pool in cells remain open questions. Here, we examine how changes in the labile Zn2+ pool affect chromatin accessibility and transcription factor binding to DNA. We observed both increases and decreases in accessibility in different chromatin regions via ATAC-seq upon treating MCF10A cells with elevated Zn2+ or the Zn2+-specific chelator tris(2-pyridylmethyl)amine (TPA). Transcription factor enrichment analysis was used to correlate changes in chromatin accessibility with transcription factor motifs, revealing 477 transcription factor motifs that were differentially enriched upon Zn2+ perturbation. 186 of these transcription factor motifs were enriched in Zn2+ and depleted in TPA, and the majority correspond to Zn2+ finger transcription factors. We selected TP53 as a candidate to examine how changes in motif enrichment correlate with changes in transcription factor occupancy by ChIP-qPCR. Using publicly available ChIP-seq and nascent transcription datasets, we narrowed the 50,000+ ATAC-seq peaks to 2164 TP53 targets and subsequently selected 6 high-probability TP53 binding sites for testing. ChIP-qPCR revealed that for 5 of the 6 targets, TP53 binding correlates with the local accessibility determined by ATAC-seq. These results demonstrate that changes in labile zinc directly alter chromatin accessibility and transcription factor binding to DNA.
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Affiliation(s)
- Leah J. Damon
- Department of Biochemistry, University of Colorado, Boulder, CO 80303
| | - Daniel Ocampo
- Department of Biochemistry, University of Colorado, Boulder, CO 80303
| | - Lynn Sanford
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, 80309
| | - Taylor Jones
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, 80309
| | - Mary A. Allen
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, 80309
- BioFrontiers Institute, University of Colorado, Boulder, CO 80303
| | - Robin D. Dowell
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, 80309
- BioFrontiers Institute, University of Colorado, Boulder, CO 80303
| | - Amy E. Palmer
- Department of Biochemistry, University of Colorado, Boulder, CO 80303
- BioFrontiers Institute, University of Colorado, Boulder, CO 80303
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15
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Owen LJ, Rainger J, Bengani H, Kilanowski F, FitzPatrick DR, Papanastasiou AS. Characterization of an eye field-like state during optic vesicle organoid development. Development 2023; 150:dev201432. [PMID: 37306293 PMCID: PMC10445745 DOI: 10.1242/dev.201432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 06/02/2023] [Indexed: 06/13/2023]
Abstract
Specification of the eye field (EF) within the neural plate marks the earliest detectable stage of eye development. Experimental evidence, primarily from non-mammalian model systems, indicates that the stable formation of this group of cells requires the activation of a set of key transcription factors. This crucial event is challenging to probe in mammals and, quantitatively, little is known regarding the regulation of the transition of cells to this ocular fate. Using optic vesicle organoids to model the onset of the EF, we generate time-course transcriptomic data allowing us to identify dynamic gene expression programmes that characterize this cellular-state transition. Integrating this with chromatin accessibility data suggests a direct role of canonical EF transcription factors in regulating these gene expression changes, and highlights candidate cis-regulatory elements through which these transcription factors act. Finally, we begin to test a subset of these candidate enhancer elements, within the organoid system, by perturbing the underlying DNA sequence and measuring transcriptomic changes during EF activation.
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Affiliation(s)
- Liusaidh J. Owen
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Jacqueline Rainger
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Hemant Bengani
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Fiona Kilanowski
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - David R. FitzPatrick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Andrew S. Papanastasiou
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
- School of Informatics, University of Edinburgh, Edinburgh EH8 9AB, UK
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16
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Radushkevitz-Frishman T, Charni-Natan M, Goldstein I. Dynamic chromatin accessibility during nutritional iron overload reveals a BMP6-independent induction of cell cycle genes. J Nutr Biochem 2023:109407. [PMID: 37336330 DOI: 10.1016/j.jnutbio.2023.109407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/28/2023] [Accepted: 06/14/2023] [Indexed: 06/21/2023]
Abstract
Iron is essential to organism physiology as it participates in numerous biological processes including oxygen transport, respiration and erythropoiesis. Although iron is critical to physiology, excess iron is toxic to cells and tissues due to generation of reactive oxygen species. Therefore, well-kept iron homeostasis is a mainstay of proper cell and organ function. Iron overload disorders, caused by nutritional or genetic factors, contribute to many pathologies such as diabetes, non-alcoholic steatohepatitis and hepatocellular carcinoma. The liver is not only vulnerable to the effects of iron overload, it is also the major organ controlling iron homeostasis. During iron overload, Bone Morphogenic Protein (BMP) levels increase and initiate a hepatic response aimed at lowering iron levels. The transcriptional effects of iron overload are not well-characterized and the underlining enhancer regulation is uncharted. Here, we profiled the liver's transcriptome and chromatin accessibility following nutritional iron overload. We found marked changes in gene expression and enhancer accessibility following iron overload. Surprisingly, 16% of genes induced following iron overload participate in propagating the cell cycle. Induction of cell cycle genes was independent of BMP. Genome-wide enhancer landscape profiling revealed hundreds of enhancers with altered activity following iron overload. Characterization of transcription factor motifs and footprints in iron-regulated enhancers showed a role for the Activator Protein 1 (AP-1) transcription factor in promoting cell cycle-related transcription. In summary, we found that the transcriptional program at play during iron overload is bifurcated in which BMP signaling controls iron homeostasis genes while an AP-1-driven program controls cell cycle genes.
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Affiliation(s)
- Talia Radushkevitz-Frishman
- Institute of Biochemistry, Food Science and Nutrition. The Robert H. Smith Faculty of Agriculture, Food and Environment. The Hebrew University of Jerusalem. 229 Herzl St., Rehovot 7610001, Israel
| | - Meital Charni-Natan
- Institute of Biochemistry, Food Science and Nutrition. The Robert H. Smith Faculty of Agriculture, Food and Environment. The Hebrew University of Jerusalem. 229 Herzl St., Rehovot 7610001, Israel
| | - Ido Goldstein
- Institute of Biochemistry, Food Science and Nutrition. The Robert H. Smith Faculty of Agriculture, Food and Environment. The Hebrew University of Jerusalem. 229 Herzl St., Rehovot 7610001, Israel.
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17
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Chaand M, Fiore C, Johnston B, D'Ippolito A, Moon DH, Carulli JP, Shearstone JR. Erythroid lineage chromatin accessibility maps facilitate identification and validation of NFIX as a fetal hemoglobin repressor. Commun Biol 2023; 6:640. [PMID: 37316562 DOI: 10.1038/s42003-023-05025-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/07/2023] [Indexed: 06/16/2023] Open
Abstract
Human genetics has validated de-repression of fetal gamma globin (HBG) in adult erythroblasts as a powerful therapeutic paradigm in diseases involving defective adult beta globin (HBB)1. To identify factors involved in the switch from HBG to HBB expression, we performed Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq)2 on sorted erythroid lineage cells derived from bone marrow (BM) or cord blood (CB), representing adult and fetal states, respectively. BM to CB cell ATAC-seq profile comparisons revealed genome-wide enrichment of NFI DNA binding motifs and increased NFIX promoter chromatin accessibility, suggesting that NFIX may repress HBG. NFIX knockdown in BM cells increased HBG mRNA and fetal hemoglobin (HbF) protein levels, coincident with increased chromatin accessibility and decreased DNA methylation at the HBG promoter. Conversely, overexpression of NFIX in CB cells reduced HbF levels. Identification and validation of NFIX as a new target for HbF activation has implications in the development of therapeutics for hemoglobinopathies.
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Affiliation(s)
| | | | | | | | | | | | - Jeffrey R Shearstone
- Syros Pharmaceuticals, Cambridge, MA, USA
- Scientific and Medical Writing Partners, Cambridge, MA, USA
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18
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Long T, Bhattacharyya T, Repele A, Naylor M, Nooti S, Krueger S, Manu. The contributions of DNA accessibility and transcription factor occupancy to enhancer activity during cellular differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.22.529579. [PMID: 37090616 PMCID: PMC10120690 DOI: 10.1101/2023.02.22.529579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
The upregulation of gene expression by enhancers depends upon the interplay between the binding of sequence-specific transcription factors (TFs) and DNA accessibility. DNA accessibility is thought to limit the ability of TFs to bind to their sites, while TFs can increase accessibility to recruit additional factors that upregulate gene expression. Given this interplay, the causative regulatory events underlying the modulation of gene expression during cellular differentiation remain unknown for the vast majority of genes. We investigated the binding-site resolution dynamics of DNA accessibility and the expression dynamics of the enhancers of an important neutrophil gene, Cebpa, during macrophage-neutrophil differentiation. Reporter genes were integrated in a site-specific manner in PUER cells, which are progenitors that can be differentiated into neutrophils or macrophages in vitro by activating the pan-leukocyte TF PU.1. Time series data show that two enhancers upregulate reporter expression during the first 48 hours of neutrophil differentiation. Surprisingly, there is little or no increase in the total accessibility, measured by ATAC-Seq, of the enhancers during the same time period. Conversely, total accessibility peaks 96 hrs after PU.1 activation-consistent with its role as a pioneer-but the enhancers do not upregulate gene expression. Combining deeply sequenced ATAC-Seq data with a new bias-correction method allowed the profiling of accessibility at single-nucleotide resolution and revealed protected regions in the enhancers that match all previously characterized TF binding sites and ChIP-Seq data. Although the accessibility of most positions does not change during early differentiation, that of positions neighboring TF binding sites, an indicator of TF occupancy, did increase significantly. The localized accessibility changes are limited to nucleotides neighboring C/EBP-family TF binding sites, showing that the upregulation of enhancer activity during early differentiation is driven by C/EBP-family TF binding. These results show that increasing the total accessibility of enhancers is not sufficient for upregulating their activity and other events such as TF binding are necessary for upregulation. Also, TF binding can cause upregulation without a perceptible increase in total accessibility. Finally, this study demonstrates the feasibility of comprehensively mapping individual TF binding sites as footprints using high coverage ATAC-Seq and inferring the sequence of events in gene regulation by combining with time-series gene expression data.
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Affiliation(s)
- Trevor Long
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Tapas Bhattacharyya
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Andrea Repele
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Madison Naylor
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Sunil Nooti
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Shawn Krueger
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Manu
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
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19
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Madrigal P, Deng S, Feng Y, Militi S, Goh KJ, Nibhani R, Grandy R, Osnato A, Ortmann D, Brown S, Pauklin S. Epigenetic and transcriptional regulations prime cell fate before division during human pluripotent stem cell differentiation. Nat Commun 2023; 14:405. [PMID: 36697417 PMCID: PMC9876972 DOI: 10.1038/s41467-023-36116-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
Stem cells undergo cellular division during their differentiation to produce daughter cells with a new cellular identity. However, the epigenetic events and molecular mechanisms occurring between consecutive cell divisions have been insufficiently studied due to technical limitations. Here, using the FUCCI reporter we developed a cell-cycle synchronised human pluripotent stem cell (hPSC) differentiation system for uncovering epigenome and transcriptome dynamics during the first two divisions leading to definitive endoderm. We observed that transcription of key differentiation markers occurs before cell division, while chromatin accessibility analyses revealed the early inhibition of alternative cell fates. We found that Activator protein-1 members controlled by p38/MAPK signalling are necessary for inducing endoderm while blocking cell fate shifting toward mesoderm, and that enhancers are rapidly established and decommissioned between different cell divisions. Our study has practical biomedical utility for producing hPSC-derived patient-specific cell types since p38/MAPK induction increased the differentiation efficiency of insulin-producing pancreatic beta-cells.
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Affiliation(s)
- Pedro Madrigal
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0SZ, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Siwei Deng
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK
| | - Yuliang Feng
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK
| | - Stefania Militi
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK
| | - Kim Jee Goh
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
- The Francis Crick Institute, London, NW1 1AT, UK
| | - Reshma Nibhani
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK
| | - Rodrigo Grandy
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Anna Osnato
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Daniel Ortmann
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Stephanie Brown
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Siim Pauklin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK.
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20
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Müller F, Chadwick JS, Di Giovanni S, Palmisano I. Epigenomic Profiling of Dorsal Root Ganglia upon Regenerative and Non-regenerative Axonal Injury. Methods Mol Biol 2023; 2636:101-144. [PMID: 36881298 DOI: 10.1007/978-1-0716-3012-9_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
RNA sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), and assay for transposase-accessible chromatin sequencing (ATAC-seq) are genome-wide techniques that provide information relative to gene expression, chromatin binding sites, and chromatin accessibility, respectively. Here we describe RNA-seq, H3K9ac, H3K27ac and H3K27me3 ChIP-seq, and ATAC-seq in dorsal root ganglia (DRG) after sciatic nerve or dorsal column axotomy, to characterize the transcriptional and epigenetic signatures of DRG upon regenerative vs non-regenerative axonal lesion.
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Affiliation(s)
- Franziska Müller
- Division of Neuroscience, Department of Brain Sciences, Imperial College London, London, UK
| | - Jessica S Chadwick
- Division of Neuroscience, Department of Brain Sciences, Imperial College London, London, UK
| | - Simone Di Giovanni
- Division of Neuroscience, Department of Brain Sciences, Imperial College London, London, UK
| | - Ilaria Palmisano
- Division of Neuroscience, Department of Brain Sciences, Imperial College London, London, UK.
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21
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Intrinsic bias estimation for improved analysis of bulk and single-cell chromatin accessibility profiles using SELMA. Nat Commun 2022; 13:5533. [PMID: 36130957 PMCID: PMC9492688 DOI: 10.1038/s41467-022-33194-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 09/08/2022] [Indexed: 11/25/2022] Open
Abstract
Genome-wide profiling of chromatin accessibility by DNase-seq or ATAC-seq has been widely used to identify regulatory DNA elements and transcription factor binding sites. However, enzymatic DNA cleavage exhibits intrinsic sequence biases that confound chromatin accessibility profiling data analysis. Existing computational tools are limited in their ability to account for such intrinsic biases and not designed for analyzing single-cell data. Here, we present Simplex Encoded Linear Model for Accessible Chromatin (SELMA), a computational method for systematic estimation of intrinsic cleavage biases from genomic chromatin accessibility profiling data. We demonstrate that SELMA yields accurate and robust bias estimation from both bulk and single-cell DNase-seq and ATAC-seq data. SELMA can utilize internal mitochondrial DNA data to improve bias estimation. We show that transcription factor binding inference from DNase footprints can be improved by incorporating estimated biases using SELMA. Furthermore, we show strong effects of intrinsic biases in single-cell ATAC-seq data, and develop the first single-cell ATAC-seq intrinsic bias correction model to improve cell clustering. SELMA can enhance the performance of existing bioinformatics tools and improve the analysis of both bulk and single-cell chromatin accessibility sequencing data. Genome-wide profiling of chromatin accessibility by DNase-seq or ATAC-seq has been widely used to identify regulatory DNA elements and transcription factor binding sites. Here the authors develop a computational model, SELMA, to estimate and correct enzymatic cleavage biases in chromatin accessibility profiling data.
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22
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Ren G, Lai B, Harly C, Baek S, Ding Y, Zheng M, Cao Y, Cui K, Yang Y, Zhu J, Hager GL, Bhandoola A, Zhao K. Transcription factors TCF-1 and GATA3 are key factors for the epigenetic priming of early innate lymphoid progenitors toward distinct cell fates. Immunity 2022; 55:1402-1413.e4. [PMID: 35882235 PMCID: PMC9393082 DOI: 10.1016/j.immuni.2022.06.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/15/2022] [Accepted: 06/23/2022] [Indexed: 11/17/2022]
Abstract
The differentiation of innate lymphoid cells (ILCs) from hematopoietic stem cells needs to go through several multipotent progenitor stages. However, it remains unclear whether the fates of multipotent progenitors are predefined by epigenetic states. Here, we report the identification of distinct accessible chromatin regions in all lymphoid progenitors (ALPs), EILPs, and ILC precursors (ILCPs). Single-cell MNase-seq analyses revealed that EILPs contained distinct subpopulations epigenetically primed toward either dendritic cell lineages or ILC lineages. We found that TCF-1 and GATA3 co-bound to the lineage-defining sites for ILCs (LDS-Is), whereas PU.1 binding was enriched in the LDSs for alternative dendritic cells (LDS-As). TCF-1 and GATA3 were indispensable for the epigenetic priming of LDSs at the EILP stage. Our results suggest that the multipotency of progenitor cells is defined by the existence of a heterogeneous population of cells epigenetically primed for distinct downstream lineages, which are regulated by key transcription factors.
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Affiliation(s)
- Gang Ren
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA; Northwest Agriculture and Forest University, College of Animal Science and Technology, Yangling, Shaanxi 712100, China
| | - Binbin Lai
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA; Biomedical Engineering Department, Peking University, Beijing 100191, China; Department of Dermatology and Venereology, Peking University First Hospital, Beijing 100034, China
| | - Christelle Harly
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yi Ding
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mingzhu Zheng
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; Department of Microbiology and Immunology, School of Medicine, Jiangsu Provincial Key Laboratory of Critical Care Medicine, Southeast University, Nanjing, Jiangsu 210009, China
| | - Yaqiang Cao
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Kairong Cui
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Yu Yang
- Biomedical Engineering Department, Peking University, Beijing 100191, China; Department of Dermatology and Venereology, Peking University First Hospital, Beijing 100034, China
| | - Jinfang Zhu
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Avinash Bhandoola
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA.
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23
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Duvall E, Benitez CM, Tellez K, Enge M, Pauerstein PT, Li L, Baek S, Quake SR, Smith JP, Sheffield NC, Kim SK, Arda HE. Single-cell transcriptome and accessible chromatin dynamics during endocrine pancreas development. Proc Natl Acad Sci U S A 2022; 119:e2201267119. [PMID: 35733248 PMCID: PMC9245718 DOI: 10.1073/pnas.2201267119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 05/10/2022] [Indexed: 12/24/2022] Open
Abstract
Delineating gene regulatory networks that orchestrate cell-type specification is a continuing challenge for developmental biologists. Single-cell analyses offer opportunities to address these challenges and accelerate discovery of rare cell lineage relationships and mechanisms underlying hierarchical lineage decisions. Here, we describe the molecular analysis of mouse pancreatic endocrine cell differentiation using single-cell transcriptomics, chromatin accessibility assays coupled to genetic labeling, and cytometry-based cell purification. We uncover transcription factor networks that delineate β-, α-, and δ-cell lineages. Through genomic footprint analysis, we identify transcription factor-regulatory DNA interactions governing pancreatic cell development at unprecedented resolution. Our analysis suggests that the transcription factor Neurog3 may act as a pioneer transcription factor to specify the pancreatic endocrine lineage. These findings could improve protocols to generate replacement endocrine cells from renewable sources, like stem cells, for diabetes therapy.
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Affiliation(s)
- Eliza Duvall
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Cecil M. Benitez
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Krissie Tellez
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Martin Enge
- Department of Bioengineering and Applied Physics, Stanford University, Stanford, CA 94305
| | - Philip T. Pauerstein
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Lingyu Li
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Stephen R. Quake
- Department of Bioengineering and Applied Physics, Stanford University, Stanford, CA 94305
- Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Jason P. Smith
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908
| | - Nathan C. Sheffield
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908
| | - Seung K. Kim
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA 94305
| | - H. Efsun Arda
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
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24
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Grandi FC, Modi H, Kampman L, Corces MR. Chromatin accessibility profiling by ATAC-seq. Nat Protoc 2022; 17:1518-1552. [PMID: 35478247 PMCID: PMC9189070 DOI: 10.1038/s41596-022-00692-9] [Citation(s) in RCA: 112] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 02/22/2022] [Indexed: 12/13/2022]
Abstract
The assay for transposase-accessible chromatin using sequencing (ATAC-seq) provides a simple and scalable way to detect the unique chromatin landscape associated with a cell type and how it may be altered by perturbation or disease. ATAC-seq requires a relatively small number of input cells and does not require a priori knowledge of the epigenetic marks or transcription factors governing the dynamics of the system. Here we describe an updated and optimized protocol for ATAC-seq, called Omni-ATAC, that is applicable across a broad range of cell and tissue types. The ATAC-seq workflow has five main steps: sample preparation, transposition, library preparation, sequencing and data analysis. This protocol details the steps to generate and sequence ATAC-seq libraries, with recommendations for sample preparation and downstream bioinformatic analysis. ATAC-seq libraries for roughly 12 samples can be generated in 10 h by someone familiar with basic molecular biology, and downstream sequencing analysis can be implemented using benchmarked pipelines by someone with basic bioinformatics skills and with access to a high-performance computing environment.
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Affiliation(s)
- Fiorella C Grandi
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Hailey Modi
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Lucas Kampman
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - M Ryan Corces
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA.
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA.
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25
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Panara V, Monteiro R, Koltowska K. Epigenetic Regulation of Endothelial Cell Lineages During Zebrafish Development-New Insights From Technical Advances. Front Cell Dev Biol 2022; 10:891538. [PMID: 35615697 PMCID: PMC9125237 DOI: 10.3389/fcell.2022.891538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/10/2022] [Indexed: 01/09/2023] Open
Abstract
Epigenetic regulation is integral in orchestrating the spatiotemporal regulation of gene expression which underlies tissue development. The emergence of new tools to assess genome-wide epigenetic modifications has enabled significant advances in the field of vascular biology in zebrafish. Zebrafish represents a powerful model to investigate the activity of cis-regulatory elements in vivo by combining technologies such as ATAC-seq, ChIP-seq and CUT&Tag with the generation of transgenic lines and live imaging to validate the activity of these regulatory elements. Recently, this approach led to the identification and characterization of key enhancers of important vascular genes, such as gata2a, notch1b and dll4. In this review we will discuss how the latest technologies in epigenetics are being used in the zebrafish to determine chromatin states and assess the function of the cis-regulatory sequences that shape the zebrafish vascular network.
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Affiliation(s)
- Virginia Panara
- Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Rui Monteiro
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
- Birmingham Centre of Genome Biology, University of Birmingham, Birmingham, United Kingdom
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26
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Lemma RB, Fleischer T, Martinsen E, Ledsaak M, Kristensen V, Eskeland R, Gabrielsen OS, Mathelier A. Pioneer transcription factors are associated with the modulation of DNA methylation patterns across cancers. Epigenetics Chromatin 2022; 15:13. [PMID: 35440061 PMCID: PMC9016969 DOI: 10.1186/s13072-022-00444-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/14/2022] [Indexed: 12/15/2022] Open
Abstract
Methylation of cytosines on DNA is a prominent modification associated with gene expression regulation. Aberrant DNA methylation patterns have recurrently been linked to dysregulation of the regulatory program in cancer cells. To shed light on the underlying molecular mechanism driving this process, we hypothesised that aberrant methylation patterns could be controlled by the binding of specific transcription factors (TFs) across cancer types. By combining DNA methylation arrays and gene expression data with TF binding sites (TFBSs), we explored the interplay between TF binding and DNA methylation in 19 cancer types. We performed emQTL (expression-methylation quantitative trait loci) analyses independently in each cancer type and identified 13 TFs whose expression levels are correlated with local DNA methylation patterns around their binding sites in at least 2 cancer types. The 13 TFs are mainly associated with local demethylation and are enriched for pioneer function, suggesting a specific role for these TFs in modulating chromatin structure and transcription in cancer patients. Furthermore, we confirmed that de novo methylation is precluded across cancers at CpGs lying in genomic regions enriched for TF binding signatures associated with SP1, CTCF, NRF1, GABPA, KLF9, and/or YY1. The modulation of DNA methylation associated with TF binding was observed at cis-regulatory regions controlling immune- and cancer-associated pathways, corroborating that the emQTL signals were derived from both cancer and tumor-infiltrating cells. As a case example, we experimentally confirmed that FOXA1 knock-down is associated with higher methylation in regions bound by FOXA1 in breast cancer MCF-7 cells. Finally, we reported physical interactions between FOXA1 with TET1 and TET2 both in an in vitro setup and in vivo at physiological levels in MCF-7 cells, adding further support for FOXA1 attracting TET1 and TET2 to induce local demethylation in cancer cells.
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Affiliation(s)
- Roza Berhanu Lemma
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
| | - Thomas Fleischer
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Emily Martinsen
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
- Institute of Basic Medical Sciences, Department of Molecular Medicine, and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Marit Ledsaak
- Institute of Basic Medical Sciences, Department of Molecular Medicine, and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Vessela Kristensen
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ragnhild Eskeland
- Institute of Basic Medical Sciences, Department of Molecular Medicine, and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | - Anthony Mathelier
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway.
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
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27
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Coda DM, Patel H, Gori I, Gaarenstroom TE, Song OR, Howell M, Hill CS. A network of transcription factors governs the dynamics of NODAL/Activin transcriptional responses. J Cell Sci 2022; 135:jcs259972. [PMID: 35302162 PMCID: PMC9080556 DOI: 10.1242/jcs.259972] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/08/2022] [Indexed: 11/20/2022] Open
Abstract
SMAD2, an effector of the NODAL/Activin signalling pathway, regulates developmental processes by sensing distinct chromatin states and interacting with different transcriptional partners. However, the network of factors that controls SMAD2 chromatin binding and shapes its transcriptional programme over time is poorly characterised. Here, we combine ATAC-seq with computational footprinting to identify temporal changes in chromatin accessibility and transcription factor activity upon NODAL/Activin signalling. We show that SMAD2 binding induces chromatin opening genome wide. We discover footprints for FOXI3, FOXO3 and ZIC3 at the SMAD2-bound enhancers of the early response genes, Pmepa1 and Wnt3, respectively, and demonstrate their functionality. Finally, we determine a mechanism by which NODAL/Activin signalling induces delayed gene expression, by uncovering a self-enabling transcriptional cascade whereby activated SMADs, together with ZIC3, induce the expression of Wnt3. The resultant activated WNT pathway then acts together with the NODAL/Activin pathway to regulate expression of delayed target genes in prolonged NODAL/Activin signalling conditions. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Davide M. Coda
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Harshil Patel
- Bioinformatics and Biostatistics Facility, The Francis Crick Institute, London, NW1 1AT, UK
| | - Ilaria Gori
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Tessa E. Gaarenstroom
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Ok-Ryul Song
- High Throughput Screening Facility, The Francis Crick Institute, London, NW1 1AT, UK
| | - Michael Howell
- High Throughput Screening Facility, The Francis Crick Institute, London, NW1 1AT, UK
| | - Caroline S. Hill
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
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28
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Brown MR, Laouteouet D, Delobel M, Villard O, Broca C, Bertrand G, Wojtusciszyn A, Dalle S, Ravier MA, Matveyenko AV, Costes S. The nuclear receptor REV-ERBα is implicated in the alteration of β-cell autophagy and survival under diabetogenic conditions. Cell Death Dis 2022; 13:353. [PMID: 35428762 PMCID: PMC9012816 DOI: 10.1038/s41419-022-04767-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 03/16/2022] [Accepted: 03/25/2022] [Indexed: 01/07/2023]
Abstract
Pancreatic β-cell failure in type 2 diabetes mellitus (T2DM) is associated with impaired regulation of autophagy which controls β-cell development, function, and survival through clearance of misfolded proteins and damaged organelles. However, the mechanisms responsible for defective autophagy in T2DM β-cells remain unknown. Since recent studies identified circadian clock transcriptional repressor REV-ERBα as a novel regulator of autophagy in cancer, in this study we set out to test whether REV-ERBα-mediated inhibition of autophagy contributes to the β-cell failure in T2DM. Our study provides evidence that common diabetogenic stressors (e.g., glucotoxicity and cytokine-mediated inflammation) augment β-cell REV-ERBα expression and impair β-cell autophagy and survival. Notably, pharmacological activation of REV-ERBα was shown to phenocopy effects of diabetogenic stressors on the β-cell through inhibition of autophagic flux, survival, and insulin secretion. In contrast, negative modulation of REV-ERBα was shown to provide partial protection from inflammation and glucotoxicity-induced β-cell failure. Finally, using bioinformatic approaches, we provide further supporting evidence for augmented REV-ERBα activity in T2DM human islets associated with impaired transcriptional regulation of autophagy and protein degradation pathways. In conclusion, our study reveals a previously unexplored causative relationship between REV-ERBα expression, inhibition of autophagy, and β-cell failure in T2DM.
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Affiliation(s)
- Matthew R. Brown
- grid.66875.3a0000 0004 0459 167XDepartment of Physiology and Biomedical Engineering, Mayo Clinic School of Medicine, Mayo Clinic, Rochester, MN USA
| | - Damien Laouteouet
- grid.121334.60000 0001 2097 0141Institute of Functional Genomics, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Morgane Delobel
- grid.121334.60000 0001 2097 0141Institute of Functional Genomics, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Orianne Villard
- grid.157868.50000 0000 9961 060XLaboratory of Cell Therapy for Diabetes (LTCD), PRIMS facility, Institute for Regenerative Medicine and Biotherapy (IRMB), University hospital of Montpellier, Montpellier, France ,grid.157868.50000 0000 9961 060XDepartment of Endocrinology, Diabetes, and Nutrition, University Hospital of Montpellier, Montpellier, France
| | - Christophe Broca
- grid.157868.50000 0000 9961 060XLaboratory of Cell Therapy for Diabetes (LTCD), PRIMS facility, Institute for Regenerative Medicine and Biotherapy (IRMB), University hospital of Montpellier, Montpellier, France
| | - Gyslaine Bertrand
- grid.121334.60000 0001 2097 0141Institute of Functional Genomics, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Anne Wojtusciszyn
- grid.121334.60000 0001 2097 0141Institute of Functional Genomics, University of Montpellier, CNRS, INSERM, Montpellier, France ,grid.157868.50000 0000 9961 060XLaboratory of Cell Therapy for Diabetes (LTCD), PRIMS facility, Institute for Regenerative Medicine and Biotherapy (IRMB), University hospital of Montpellier, Montpellier, France ,grid.157868.50000 0000 9961 060XDepartment of Endocrinology, Diabetes, and Nutrition, University Hospital of Montpellier, Montpellier, France
| | - Stéphane Dalle
- grid.121334.60000 0001 2097 0141Institute of Functional Genomics, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Magalie A. Ravier
- grid.121334.60000 0001 2097 0141Institute of Functional Genomics, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Aleksey V. Matveyenko
- grid.66875.3a0000 0004 0459 167XDepartment of Physiology and Biomedical Engineering, Mayo Clinic School of Medicine, Mayo Clinic, Rochester, MN USA ,grid.66875.3a0000 0004 0459 167XDivision of Endocrinology, Metabolism, Diabetes, and Nutrition, Department of Medicine, Mayo Clinic, Rochester, MN USA
| | - Safia Costes
- grid.121334.60000 0001 2097 0141Institute of Functional Genomics, University of Montpellier, CNRS, INSERM, Montpellier, France
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29
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Müller M, Schaefer M, Fäh T, Spies D, Hermes V, Ngondo RP, Peña-Hernández R, Santoro R, Ciaudo C. Argonaute proteins regulate a specific network of genes through KLF4 in mouse embryonic stem cells. Stem Cell Reports 2022; 17:1070-1080. [PMID: 35452597 PMCID: PMC9133645 DOI: 10.1016/j.stemcr.2022.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/22/2022] [Accepted: 03/22/2022] [Indexed: 12/04/2022] Open
Abstract
The Argonaute proteins (AGOs) are well known for their role in post-transcriptional gene silencing in the microRNA (miRNA) pathway. Here we show that in mouse embryonic stem cells, AGO1&2 serve additional functions that go beyond the miRNA pathway. Through the combined deletion of both Agos, we identified a specific set of genes that are uniquely regulated by AGOs but not by the other miRNA biogenesis factors. Deletion of Ago2&1 caused a global reduction of the repressive histone mark H3K27me3 due to downregulation at protein levels of Polycomb repressive complex 2 components. By integrating chromatin accessibility, prediction of transcription factor binding sites, and chromatin immunoprecipitation sequencing data, we identified the pluripotency factor KLF4 as a key modulator of AGO1&2-regulated genes. Our findings revealed a novel axis of gene regulation that is mediated by noncanonical functions of AGO proteins that affect chromatin states and gene expression using mechanisms outside the miRNA pathway. AGO1&2 regulate a specific set of genes in mESCs, independently of the miRNA pathway PRC2 proteins are downregulated in Ago2&1_KO mESCs, leading to H3K27me3 global loss AGO1&2 regulate gene expression through the pluripotency factor KLF4
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Affiliation(s)
- Madlen Müller
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences, Chair of RNAi and Genome Integrity, Zurich, Switzerland; Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Moritz Schaefer
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences, Chair of RNAi and Genome Integrity, Zurich, Switzerland; Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Tara Fäh
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences, Chair of RNAi and Genome Integrity, Zurich, Switzerland
| | - Daniel Spies
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences, Chair of RNAi and Genome Integrity, Zurich, Switzerland
| | - Victoria Hermes
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences, Chair of RNAi and Genome Integrity, Zurich, Switzerland
| | - Richard Patryk Ngondo
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences, Chair of RNAi and Genome Integrity, Zurich, Switzerland
| | - Rodrigo Peña-Hernández
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, Zurich, Switzerland
| | - Raffaella Santoro
- Department of Molecular Mechanisms of Disease, DMMD, University of Zurich, Zurich, Switzerland
| | - Constance Ciaudo
- Swiss Federal Institute of Technology Zurich, Institute of Molecular Health Sciences, Chair of RNAi and Genome Integrity, Zurich, Switzerland.
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30
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Kadur Lakshminarasimha Murthy P, Xi R, Arguijo D, Everitt JI, Kocak DD, Kobayashi Y, Bozec A, Vicent S, Ding S, Crawford GE, Hsu D, Tata PR, Reddy T, Shen X. Epigenetic basis of oncogenic-Kras-mediated epithelial-cellular proliferation and plasticity. Dev Cell 2022; 57:310-328.e9. [PMID: 35134344 PMCID: PMC8938988 DOI: 10.1016/j.devcel.2022.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 09/15/2021] [Accepted: 01/06/2022] [Indexed: 12/13/2022]
Abstract
Oncogenic Kras induces a hyper-proliferative state that permits cells to progress to neoplasms in diverse epithelial tissues. Depending on the cell of origin, this also involves lineage transformation. Although a multitude of downstream factors have been implicated in these processes, the precise chronology of molecular events controlling them remains elusive. Using mouse models, primary human tissues, and cell lines, we show that, in Kras-mutant alveolar type II cells (AEC2), FOSL1-based AP-1 factor guides the mSWI/SNF complex to increase chromatin accessibility at genomic loci controlling the expression of genes necessary for neoplastic transformation. We identified two orthogonal processes in Kras-mutant distal airway club cells. The first promoted their transdifferentiation into an AEC2-like state through NKX2.1, and the second controlled oncogenic transformation through the AP-1 complex. Our results suggest that neoplasms retain an epigenetic memory of their cell of origin through cell-type-specific transcription factors. Our analysis showed that a cross-tissue-conserved AP-1-dependent chromatin remodeling program regulates carcinogenesis.
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Affiliation(s)
- Preetish Kadur Lakshminarasimha Murthy
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY 14853, USA; Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA. :
| | - Rui Xi
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA
| | - Diana Arguijo
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Jeffrey I Everitt
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Dewran D Kocak
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA
| | - Yoshihiko Kobayashi
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Aline Bozec
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Internal Medicine 3 - Rheumatology and Immunology, Universitätsklinikum Erlangen, Erlangen, Germany
| | - Silvestre Vicent
- University of Navarra, Center for Applied Medical Research, Program in Solid Tumors, Pamplona, Spain; University of Navarra, Department of Pathology, Anatomy and Physiology, Pamplona, Spain; IdiSNA, Navarra Institute for Health Research, Pamplona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Shengli Ding
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Gregory E Crawford
- Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27710, USA
| | - David Hsu
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Purushothama Rao Tata
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Timothy Reddy
- Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA
| | - Xiling Shen
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Terasaki Institute for Biomedical Innovation, Los Angeles, CA 90024, USA.
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31
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Singh H, Seruggia D, Madha S, Saxena M, Nagaraja AK, Wu Z, Zhou J, Huebner AJ, Maglieri A, Wezenbeek J, Hochedlinger K, Orkin SH, Bass AJ, Hornick JL, Shivdasani RA. Transcription factor-mediated intestinal metaplasia and the role of a shadow enhancer. Genes Dev 2021; 36:38-52. [PMID: 34969824 PMCID: PMC8763054 DOI: 10.1101/gad.348983.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/13/2021] [Indexed: 12/02/2022]
Abstract
Here, Singh et al. show extensive but selective recruitment of intestinal enhancers by CDX2 in gastric cells and that HNF4A-mediated ectopic CDX2 expression in the stomach occurs through a conserved shadow cis-element. These findings identify mechanisms for TF-driven intestinal metaplasia and a likely pathogenic TF hierarchy. Barrett's esophagus (BE) and gastric intestinal metaplasia are related premalignant conditions in which areas of human stomach epithelium express mixed gastric and intestinal features. Intestinal transcription factors (TFs) are expressed in both conditions, with unclear causal roles and cis-regulatory mechanisms. Ectopic CDX2 reprogrammed isogenic mouse stomach organoid lines to a hybrid stomach–intestinal state transcriptionally similar to clinical metaplasia; squamous esophageal organoids resisted this CDX2-mediated effect. Reprogramming was associated with induced activity at thousands of previously inaccessible intestine-restricted enhancers, where CDX2 occupied DNA directly. HNF4A, a TF recently implicated in BE pathogenesis, induced weaker intestinalization by binding a novel shadow Cdx2 enhancer and hence activating Cdx2 expression. CRISPR/Cas9-mediated germline deletion of that cis-element demonstrated its requirement in Cdx2 induction and in the resulting activation of intestinal genes in stomach cells. dCas9-conjugated KRAB repression mapped this activity to the shadow enhancer's HNF4A binding site. Altogether, we show extensive but selective recruitment of intestinal enhancers by CDX2 in gastric cells and that HNF4A-mediated ectopic CDX2 expression in the stomach occurs through a conserved shadow cis-element. These findings identify mechanisms for TF-driven intestinal metaplasia and a likely pathogenic TF hierarchy.
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Affiliation(s)
- Harshabad Singh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Davide Seruggia
- Division of Hematology Oncology, Boston Children's Hospital, Boston, Massachusetts 02215, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Shariq Madha
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Madhurima Saxena
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ankur K Nagaraja
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Zhong Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Jin Zhou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Aaron J Huebner
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts, 02114, USA
| | - Adrianna Maglieri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Juliette Wezenbeek
- Hubretch Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Center Utrecht, Utrecht 3584 CT, Netherlands
| | - Konrad Hochedlinger
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts, 02114, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
| | - Stuart H Orkin
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.,Division of Hematology Oncology, Boston Children's Hospital, Boston, Massachusetts 02215, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Boston, Massachusetts 02215, USA
| | - Adam J Bass
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jason L Hornick
- Departments of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ramesh A Shivdasani
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
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32
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Brown MR, Sen SK, Mazzone A, Her TK, Xiong Y, Lee JH, Javeed N, Colwell CS, Rakshit K, LeBrasseur NK, Gaspar-Maia A, Ordog T, Matveyenko AV. Time-restricted feeding prevents deleterious metabolic effects of circadian disruption through epigenetic control of β cell function. SCIENCE ADVANCES 2021; 7:eabg6856. [PMID: 34910509 PMCID: PMC8673777 DOI: 10.1126/sciadv.abg6856] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 10/28/2021] [Indexed: 05/30/2023]
Abstract
Circadian rhythm disruption (CD) is associated with impaired glucose homeostasis and type 2 diabetes mellitus (T2DM). While the link between CD and T2DM remains unclear, there is accumulating evidence that disruption of fasting/feeding cycles mediates metabolic dysfunction. Here, we used an approach encompassing analysis of behavioral, physiological, transcriptomic, and epigenomic effects of CD and consequences of restoring fasting/feeding cycles through time-restricted feeding (tRF) in mice. Results show that CD perturbs glucose homeostasis through disruption of pancreatic β cell function and loss of circadian transcriptional and epigenetic identity. In contrast, restoration of fasting/feeding cycle prevented CD-mediated dysfunction by reestablishing circadian regulation of glucose tolerance, β cell function, transcriptional profile, and reestablishment of proline and acidic amino acid–rich basic leucine zipper (PAR bZIP) transcription factor DBP expression/activity. This study provides mechanistic insights into circadian regulation of β cell function and corresponding beneficial effects of tRF in prevention of T2DM.
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Affiliation(s)
- Matthew R. Brown
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Satish K. Sen
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Amelia Mazzone
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Tracy K. Her
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Yuning Xiong
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Jeong-Heon Lee
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Naureen Javeed
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Christopher S. Colwell
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kuntol Rakshit
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Nathan K. LeBrasseur
- Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, USA
| | - Alexandre Gaspar-Maia
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Tamas Ordog
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
| | - Aleksey V. Matveyenko
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
- Division of Endocrinology, Metabolism, Diabetes, and Nutrition, Department of Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN, USA
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33
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Yee Mon KJ, Zhu H, Daly CWP, Vu LT, Smith NL, Patel R, Topham DJ, Scheible K, Jambo K, Le MTN, Rudd BD, Grimson A. MicroRNA-29 specifies age-related differences in the CD8+ T cell immune response. Cell Rep 2021; 37:109969. [PMID: 34758312 DOI: 10.1016/j.celrep.2021.109969] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 08/09/2021] [Accepted: 10/19/2021] [Indexed: 11/27/2022] Open
Abstract
MicroRNAs (miRNAs) have emerged as critical regulators of cell fate in the CD8+ T cell response to infection. Although there are several examples of miRNAs acting on effector CD8+ T cells after infection, it is unclear whether differential expression of one or more miRNAs in the naive state is consequential in altering their long-term trajectory. To answer this question, we examine the role of miR-29 in neonatal and adult CD8+ T cells, which express different amounts of miR-29 only prior to infection and adopt profoundly different fates after immune challenge. We find that manipulation of miR-29 expression in the naive state is sufficient for age-adjusting the phenotype and function of CD8+ T cells, including their regulatory landscapes and long-term differentiation trajectories after infection. Thus, miR-29 acts as a developmental switch by controlling the balance between a rapid effector response in neonates and the generation of long-lived memory in adults.
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Affiliation(s)
- Kristel J Yee Mon
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Hongya Zhu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Ciarán W P Daly
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Luyen T Vu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Pharmacology and Institute for Digital Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Norah L Smith
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Ravi Patel
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - David J Topham
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA
| | - Kristin Scheible
- Department of Pediatrics, Division of Neonatology, University of Rochester, Rochester, NY 14642, USA
| | - Kondwani Jambo
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Minh T N Le
- Department of Pharmacology and Institute for Digital Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Brian D Rudd
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA.
| | - Andrew Grimson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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34
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Yun H, Narayan N, Vohra S, Giotopoulos G, Mupo A, Madrigal P, Sasca D, Lara-Astiaso D, Horton SJ, Agrawal-Singh S, Meduri E, Basheer F, Marando L, Gozdecka M, Dovey OM, Castillo-Venzor A, Wang X, Gallipoli P, Müller-Tidow C, Osborne CS, Vassiliou GS, Huntly BJP. Mutational synergy during leukemia induction remodels chromatin accessibility, histone modifications and three-dimensional DNA topology to alter gene expression. Nat Genet 2021; 53:1443-1455. [PMID: 34556857 PMCID: PMC7611829 DOI: 10.1038/s41588-021-00925-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 07/28/2021] [Indexed: 02/08/2023]
Abstract
Altered transcription is a cardinal feature of acute myeloid leukemia (AML); however, exactly how mutations synergize to remodel the epigenetic landscape and rewire three-dimensional DNA topology is unknown. Here, we apply an integrated genomic approach to a murine allelic series that models the two most common mutations in AML: Flt3-ITD and Npm1c. We then deconvolute the contribution of each mutation to alterations of the epigenetic landscape and genome organization, and infer how mutations synergize in the induction of AML. Our studies demonstrate that Flt3-ITD signals to chromatin to alter the epigenetic environment and synergizes with mutations in Npm1c to alter gene expression and drive leukemia induction. These analyses also allow the identification of long-range cis-regulatory circuits, including a previously unknown superenhancer of Hoxa locus, as well as larger and more detailed gene-regulatory networks, driven by transcription factors including PU.1 and IRF8, whose importance we demonstrate through perturbation of network members.
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MESH Headings
- Animals
- Base Sequence
- Chromatin Assembly and Disassembly/genetics
- DNA, Neoplasm/chemistry
- Disease Models, Animal
- Enhancer Elements, Genetic/genetics
- Gene Expression Regulation, Leukemic
- Gene Regulatory Networks
- Genetic Loci
- Histones/metabolism
- Humans
- Leukemia, Myeloid, Acute/genetics
- Mice, Inbred C57BL
- Mutation/genetics
- Nuclear Proteins/metabolism
- Nucleophosmin
- Principal Component Analysis
- Protein Processing, Post-Translational
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Transcription, Genetic
- fms-Like Tyrosine Kinase 3/metabolism
- Mice
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Affiliation(s)
- Haiyang Yun
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Nisha Narayan
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Shabana Vohra
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - George Giotopoulos
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Annalisa Mupo
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Pedro Madrigal
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Daniel Sasca
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Hematology, Oncology and Pneumology, University Medical Center Mainz, Mainz, Germany
| | - David Lara-Astiaso
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Sarah J Horton
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Shuchi Agrawal-Singh
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Eshwar Meduri
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Faisal Basheer
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Ludovica Marando
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Malgorzata Gozdecka
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Oliver M Dovey
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | | | - Xiaonan Wang
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Paolo Gallipoli
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Carsten Müller-Tidow
- Department of Medicine V, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Cameron S Osborne
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - George S Vassiliou
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Brian J P Huntly
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
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35
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Dong C, Simonett SP, Shin S, Stapleton DS, Schueler KL, Churchill GA, Lu L, Liu X, Jin F, Li Y, Attie AD, Keller MP, Keleş S. INFIMA leverages multi-omics model organism data to identify effector genes of human GWAS variants. Genome Biol 2021; 22:241. [PMID: 34425882 PMCID: PMC8381555 DOI: 10.1186/s13059-021-02450-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 08/02/2021] [Indexed: 11/24/2022] Open
Abstract
Genome-wide association studies reveal many non-coding variants associated with complex traits. However, model organism studies largely remain as an untapped resource for unveiling the effector genes of non-coding variants. We develop INFIMA, Integrative Fine-Mapping, to pinpoint causal SNPs for diversity outbred (DO) mice eQTL by integrating founder mice multi-omics data including ATAC-seq, RNA-seq, footprinting, and in silico mutation analysis. We demonstrate INFIMA's superior performance compared to alternatives with human and mouse chromatin conformation capture datasets. We apply INFIMA to identify novel effector genes for GWAS variants associated with diabetes. The results of the application are available at http://www.statlab.wisc.edu/shiny/INFIMA/ .
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Affiliation(s)
- Chenyang Dong
- Department of Statistics, University of Wisconsin-Madison, Madison, WI USA
| | - Shane P. Simonett
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Sunyoung Shin
- Department of Mathematical Sciences, University of Texas at Dallas, Richardson, TX USA
| | - Donnie S. Stapleton
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Kathryn L. Schueler
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
| | | | - Leina Lu
- Case Western University, Cleveland, OH USA
| | | | - Fulai Jin
- Case Western University, Cleveland, OH USA
| | - Yan Li
- Case Western University, Cleveland, OH USA
| | - Alan D. Attie
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Mark P. Keller
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Sündüz Keleş
- Department of Statistics, University of Wisconsin-Madison, Madison, WI USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI USA
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36
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Wilk AJ, Lee MJ, Wei B, Parks B, Pi R, Martínez-Colón GJ, Ranganath T, Zhao NQ, Taylor S, Becker W, Jimenez-Morales D, Blomkalns AL, O’Hara R, Ashley EA, Nadeau KC, Yang S, Holmes S, Rabinovitch M, Rogers AJ, Greenleaf WJ, Blish CA. Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19. J Exp Med 2021; 218:e20210582. [PMID: 34128959 PMCID: PMC8210586 DOI: 10.1084/jem.20210582] [Citation(s) in RCA: 122] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/13/2021] [Accepted: 05/13/2021] [Indexed: 12/20/2022] Open
Abstract
Our understanding of protective versus pathological immune responses to SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), is limited by inadequate profiling of patients at the extremes of the disease severity spectrum. Here, we performed multi-omic single-cell immune profiling of 64 COVID-19 patients across the full range of disease severity, from outpatients with mild disease to fatal cases. Our transcriptomic, epigenomic, and proteomic analyses revealed widespread dysfunction of peripheral innate immunity in severe and fatal COVID-19, including prominent hyperactivation signatures in neutrophils and NK cells. We also identified chromatin accessibility changes at NF-κB binding sites within cytokine gene loci as a potential mechanism for the striking lack of pro-inflammatory cytokine production observed in monocytes in severe and fatal COVID-19. We further demonstrated that emergency myelopoiesis is a prominent feature of fatal COVID-19. Collectively, our results reveal disease severity-associated immune phenotypes in COVID-19 and identify pathogenesis-associated pathways that are potential targets for therapeutic intervention.
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Affiliation(s)
- Aaron J. Wilk
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Madeline J. Lee
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Bei Wei
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Benjamin Parks
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
- Graduate Program in Computer Science, Stanford University School of Medicine, Stanford, CA
| | - Ruoxi Pi
- Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | | | - Thanmayi Ranganath
- Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Nancy Q. Zhao
- Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Shalina Taylor
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA
| | - Winston Becker
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | | | | | - Andra L. Blomkalns
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, CA
| | - Ruth O’Hara
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA
| | - Euan A. Ashley
- Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Kari C. Nadeau
- Department of Medicine, Stanford University School of Medicine, Stanford, CA
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA
| | - Samuel Yang
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, CA
| | - Susan Holmes
- Department of Statistics, Stanford University, Stanford, CA
| | - Marlene Rabinovitch
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA
| | - Angela J. Rogers
- Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - William J. Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
- Department of Applied Physics, Stanford University, Stanford, CA
| | - Catherine A. Blish
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA
- Chan Zuckerberg Biohub, San Francisco, CA
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37
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Kukkonen K, Taavitsainen S, Huhtala L, Uusi-Makela J, Granberg KJ, Nykter M, Urbanucci A. Chromatin and Epigenetic Dysregulation of Prostate Cancer Development, Progression, and Therapeutic Response. Cancers (Basel) 2021; 13:3325. [PMID: 34283056 PMCID: PMC8268970 DOI: 10.3390/cancers13133325] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 02/07/2023] Open
Abstract
The dysregulation of chromatin and epigenetics has been defined as the overarching cancer hallmark. By disrupting transcriptional regulation in normal cells and mediating tumor progression by promoting cancer cell plasticity, this process has the ability to mediate all defined hallmarks of cancer. In this review, we collect and assess evidence on the contribution of chromatin and epigenetic dysregulation in prostate cancer. We highlight important mechanisms leading to prostate carcinogenesis, the emergence of castration-resistance upon treatment with androgen deprivation therapy, and resistance to antiandrogens. We examine in particular the contribution of chromatin structure and epigenetics to cell lineage commitment, which is dysregulated during tumorigenesis, and cell plasticity, which is altered during tumor progression.
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Affiliation(s)
- Konsta Kukkonen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Sinja Taavitsainen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Laura Huhtala
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Joonas Uusi-Makela
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Kirsi J. Granberg
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Alfonso Urbanucci
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway
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38
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Dual DNA and protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia. Nat Methods 2021; 18:293-302. [PMID: 33649590 PMCID: PMC8272231 DOI: 10.1038/s41592-021-01077-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 01/20/2021] [Indexed: 02/08/2023]
Abstract
The architecture of chromatin regulates eukaryotic cell states by controlling transcription factor access to sites of gene regulation. Here we describe a dual transposase-peroxidase approach, integrative DNA and protein tagging (iDAPT), which detects both DNA (iDAPT-seq) and protein (iDAPT-MS) associated with accessible regions of chromatin. In addition to direct identification of bound transcription factors, iDAPT enables the inference of their gene regulatory networks, protein interactors and regulation of chromatin accessibility. We applied iDAPT to profile the epigenomic consequences of granulocytic differentiation of acute promyelocytic leukemia, yielding previously undescribed mechanistic insights. Our findings demonstrate the power of iDAPT as a platform for studying the dynamic epigenomic landscapes and their transcription factor components associated with biological phenomena and disease.
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39
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Braun SMG, Petrova R, Tang J, Krokhotin A, Miller EL, Tang Y, Panagiotakos G, Crabtree GR. BAF subunit switching regulates chromatin accessibility to control cell cycle exit in the developing mammalian cortex. Genes Dev 2021; 35:335-353. [PMID: 33602870 PMCID: PMC7919417 DOI: 10.1101/gad.342345.120] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 01/08/2021] [Indexed: 12/28/2022]
Abstract
mSWI/SNF or BAF chromatin regulatory complexes are dosage-sensitive regulators of human neural development frequently mutated in autism spectrum disorders and intellectual disability. Cell cycle exit and differentiation of neural stem/progenitor cells is accompanied by BAF subunit switching to generate neuron-specific nBAF complexes. We manipulated the timing of BAF subunit exchange in vivo and found that early loss of the npBAF subunit BAF53a stalls the cell cycle to disrupt neurogenesis. Loss of BAF53a results in decreased chromatin accessibility at specific neural transcription factor binding sites, including the pioneer factors SOX2 and ASCL1, due to Polycomb accumulation. This results in repression of cell cycle genes, thereby blocking cell cycle progression and differentiation. Cell cycle block upon Baf53a deletion could be rescued by premature expression of the nBAF subunit BAF53b but not by other major drivers of proliferation or differentiation. WNT, EGF, bFGF, SOX2, c-MYC, or PAX6 all fail to maintain proliferation in the absence of BAF53a, highlighting a novel mechanism underlying neural progenitor cell cycle exit in the continued presence of extrinsic proliferative cues.
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Affiliation(s)
- Simon M G Braun
- Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Department of Developmental Biology, Stanford University, California 94305, USA
- Department of Pathology, Stanford University, California 94305, USA
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Ralitsa Petrova
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94143, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California at San Francisco, San Francisco, California 94143, USA
- Kavli Institute for Fundamental Neuroscience, University of California at San Francisco, San Francisco, California 94143, USA
| | - Jiong Tang
- Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Department of Developmental Biology, Stanford University, California 94305, USA
- Department of Pathology, Stanford University, California 94305, USA
- Singapore Bioimaging Consortium, Agency for Science Technology and Research (A*STAR), Singapore 138667, Singapore
| | - Andrey Krokhotin
- Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Department of Developmental Biology, Stanford University, California 94305, USA
- Department of Pathology, Stanford University, California 94305, USA
| | - Erik L Miller
- Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Department of Developmental Biology, Stanford University, California 94305, USA
- Department of Pathology, Stanford University, California 94305, USA
| | - Yitai Tang
- Department of Pathology, Stanford University, California 94305, USA
| | - Georgia Panagiotakos
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94143, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California at San Francisco, San Francisco, California 94143, USA
- Kavli Institute for Fundamental Neuroscience, University of California at San Francisco, San Francisco, California 94143, USA
| | - Gerald R Crabtree
- Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
- Department of Developmental Biology, Stanford University, California 94305, USA
- Department of Pathology, Stanford University, California 94305, USA
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40
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D'Oliveira Albanus R, Kyono Y, Hensley J, Varshney A, Orchard P, Kitzman JO, Parker SCJ. Chromatin information content landscapes inform transcription factor and DNA interactions. Nat Commun 2021; 12:1307. [PMID: 33637709 PMCID: PMC7910283 DOI: 10.1038/s41467-021-21534-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 01/29/2021] [Indexed: 01/31/2023] Open
Abstract
Interactions between transcription factors and chromatin are fundamental to genome organization and regulation and, ultimately, cell state. Here, we use information theory to measure signatures of organized chromatin resulting from transcription factor-chromatin interactions encoded in the patterns of the accessible genome, which we term chromatin information enrichment (CIE). We calculate CIE for hundreds of transcription factor motifs across human samples and identify two classes: low and high CIE. The 10-20% of common and tissue-specific high CIE transcription factor motifs, associate with higher protein-DNA residence time, including different binding site subclasses of the same transcription factor, increased nucleosome phasing, specific protein domains, and the genetic control of both chromatin accessibility and gene expression. These results show that variations in the information encoded in chromatin architecture reflect functional biological variation, with implications for cell state dynamics and memory.
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Affiliation(s)
| | - Yasuhiro Kyono
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, USA
- Tempus Labs, Inc. Chicago, IL, Chicago, USA
| | - John Hensley
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, USA
| | - Arushi Varshney
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, USA
| | - Peter Orchard
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, USA
| | - Jacob O Kitzman
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, USA
| | - Stephen C J Parker
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, USA.
- Department of Human Genetics, University of Michigan, Ann Arbor, USA.
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41
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Abstract
The ATAC-seq assay has emerged as the most useful, versatile, and widely adaptable method for profiling accessible chromatin regions and tracking the activity of cis-regulatory elements (cREs) in eukaryotes. Thanks to its great utility, it is now being applied to map active chromatin in the context of a very wide diversity of biological systems and questions. In the course of these studies, considerable experience working with ATAC-seq data has accumulated and a standard set of computational tasks that need to be carried for most ATAC-seq analyses has emerged. Here, we review and provide examples of common such analytical procedures (including data processing, quality control, peak calling, identifying differentially accessible open chromatin regions, and variable transcription factor (TF) motif accessibility) and discuss recommended optimal practices.
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42
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Giroux NS, Ding S, McClain MT, Burke TW, Petzold E, Chung HA, Palomino GR, Wang E, Xi R, Bose S, Rotstein T, Nicholson BP, Chen T, Henao R, Sempowski GD, Denny TN, Ko ER, Ginsburg GS, Kraft BD, Tsalik EL, Woods CW, Shen X. Chromatin remodeling in peripheral blood cells reflects COVID-19 symptom severity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.12.04.412155. [PMID: 33300002 PMCID: PMC7724678 DOI: 10.1101/2020.12.04.412155] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
SARS-CoV-2 infection triggers highly variable host responses and causes varying degrees of illness in humans. We sought to harness the peripheral blood mononuclear cell (PBMC) response over the course of illness to provide insight into COVID-19 physiology. We analyzed PBMCs from subjects with variable symptom severity at different stages of clinical illness before and after IgG seroconversion to SARS-CoV-2. Prior to seroconversion, PBMC transcriptomes did not distinguish symptom severity. In contrast, changes in chromatin accessibility were associated with symptom severity. Furthermore, single-cell analyses revealed evolution of the chromatin accessibility landscape and transcription factor motif occupancy for individual PBMC cell types. The most extensive remodeling occurred in CD14+ monocytes where sub-populations with distinct chromatin accessibility profiles were associated with disease severity. Our findings indicate that pre-seroconversion chromatin remodeling in certain innate immune populations is associated with divergence in symptom severity, and the identified transcription factors, regulatory elements, and downstream pathways provide potential prognostic markers for COVID-19 subjects.
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Affiliation(s)
- Nicholas S. Giroux
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Shengli Ding
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Micah T. McClain
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC, USA
- Durham Veterans Affairs Health Care System, Durham, NC, USA
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - Thomas W. Burke
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC, USA
| | - Elizabeth Petzold
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC, USA
| | - Hong A. Chung
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Grecia R. Palomino
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Ergang Wang
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Rui Xi
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Shree Bose
- Department of Pharmacology and Cancer Biology, School of Medicine, Duke University, Durham, NC, USA
| | - Tomer Rotstein
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | | | - Tianyi Chen
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA
| | - Ricardo Henao
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC, USA
| | - Gregory D. Sempowski
- Duke Human Vaccine Institute and Department of Medicine, School of Medicine, Duke University, Durham, NC, USA
| | - Thomas N. Denny
- Duke Human Vaccine Institute and Department of Medicine, School of Medicine, Duke University, Durham, NC, USA
| | - Emily R. Ko
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC, USA
| | - Geoffrey S. Ginsburg
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC, USA
| | - Bryan D. Kraft
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC, USA
- Durham Veterans Affairs Health Care System, Durham, NC, USA
| | - Ephraim L. Tsalik
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC, USA
- Durham Veterans Affairs Health Care System, Durham, NC, USA
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - Christopher W. Woods
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC, USA
- Durham Veterans Affairs Health Care System, Durham, NC, USA
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - Xiling Shen
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
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43
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ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation. Nat Commun 2020; 11:4267. [PMID: 32848148 PMCID: PMC7449963 DOI: 10.1038/s41467-020-18035-1] [Citation(s) in RCA: 262] [Impact Index Per Article: 65.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/23/2020] [Indexed: 12/22/2022] Open
Abstract
While footprinting analysis of ATAC-seq data can theoretically enable investigation of transcription factor (TF) binding, the lack of a computational tool able to conduct different levels of footprinting analysis has so-far hindered the widespread application of this method. Here we present TOBIAS, a comprehensive, accurate, and fast footprinting framework enabling genome-wide investigation of TF binding dynamics for hundreds of TFs simultaneously. We validate TOBIAS using paired ATAC-seq and ChIP-seq data, and find that TOBIAS outperforms existing methods for bias correction and footprinting. As a proof-of-concept, we illustrate how TOBIAS can unveil complex TF dynamics during zygotic genome activation in both humans and mice, and propose how zygotic Dux activates cascades of TFs, binds to repeat elements and induces expression of novel genetic elements.
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44
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CHD8 dosage regulates transcription in pluripotency and early murine neural differentiation. Proc Natl Acad Sci U S A 2020; 117:22331-22340. [PMID: 32839322 DOI: 10.1073/pnas.1921963117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The chromatin remodeler CHD8 is among the most frequently mutated genes in autism spectrum disorder (ASD). CHD8 has a dosage-sensitive role in ASD, but when and how it becomes critical to human social function is unclear. Here, we conducted genomic analyses of heterozygous and homozygous Chd8 mouse embryonic stem cells and differentiated neural progenitors. We identify dosage-sensitive CHD8 transcriptional targets, sites of regulated accessibility, and an unexpected cooperation with SOX transcription factors. Collectively, our findings reveal that CHD8 negatively regulates expression of neuronal genes to maintain pluripotency and also during differentiation. Thus, CHD8 is essential for both the maintenance of pluripotency and neural differentiation, providing mechanistic insight into its function with potential implications for ASD.
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45
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Funk CC, Casella AM, Jung S, Richards MA, Rodriguez A, Shannon P, Donovan-Maiye R, Heavner B, Chard K, Xiao Y, Glusman G, Ertekin-Taner N, Golde TE, Toga A, Hood L, Van Horn JD, Kesselman C, Foster I, Madduri R, Price ND, Ament SA. Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types. Cell Rep 2020; 32:108029. [PMID: 32814038 PMCID: PMC7462736 DOI: 10.1016/j.celrep.2020.108029] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 05/07/2020] [Accepted: 07/22/2020] [Indexed: 12/27/2022] Open
Abstract
Characterizing the tissue-specific binding sites of transcription factors (TFs) is essential to reconstruct gene regulatory networks and predict functions for non-coding genetic variation. DNase-seq footprinting enables the prediction of genome-wide binding sites for hundreds of TFs simultaneously. Despite the public availability of high-quality DNase-seq data from hundreds of samples, a comprehensive, up-to-date resource for the locations of genomic footprints is lacking. Here, we develop a scalable footprinting workflow using two state-of-the-art algorithms: Wellington and HINT. We apply our workflow to detect footprints in 192 ENCODE DNase-seq experiments and predict the genomic occupancy of 1,515 human TFs in 27 human tissues. We validate that these footprints overlap true-positive TF binding sites from ChIP-seq. We demonstrate that the locations, depth, and tissue specificity of footprints predict effects of genetic variants on gene expression and capture a substantial proportion of genetic risk for complex traits.
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Affiliation(s)
- Cory C Funk
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Alex M Casella
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Medical Scientist Training Program, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Segun Jung
- Globus, University of Chicago, Chicago, IL 60637, USA
| | | | | | - Paul Shannon
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | - Ben Heavner
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Kyle Chard
- Globus, University of Chicago, Chicago, IL 60637, USA
| | - Yukai Xiao
- Globus, University of Chicago, Chicago, IL 60637, USA
| | | | | | - Todd E Golde
- Mayo Clinic, Department of Neuroscience, Jacksonville, FL 32224, USA
| | - Arthur Toga
- Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, Los Angeles, CA 90033, USA
| | - Leroy Hood
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - John D Van Horn
- Department of Psychology, University of Southern California, Los Angeles, CA 90007, USA
| | - Carl Kesselman
- Information Sciences Institute, University of Southern California, Los Angeles, CA 90292, USA
| | - Ian Foster
- Globus, University of Chicago, Chicago, IL 60637, USA; Data Science and Learning Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Ravi Madduri
- Globus, University of Chicago, Chicago, IL 60637, USA; Data Science and Learning Division, Argonne National Laboratory, Argonne, IL 60439, USA.
| | | | - Seth A Ament
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
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46
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ZIC3 Controls the Transition from Naive to Primed Pluripotency. Cell Rep 2020; 27:3215-3227.e6. [PMID: 31189106 PMCID: PMC6581693 DOI: 10.1016/j.celrep.2019.05.026] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 03/14/2019] [Accepted: 05/06/2019] [Indexed: 01/06/2023] Open
Abstract
Embryonic stem cells (ESCs) must transition through a series of intermediate cell states before becoming terminally differentiated. Here, we investigated the early events in this transition by determining the changes in the open chromatin landscape as naive mouse ESCs transition to epiblast-like cells (EpiLCs). Motif enrichment analysis of the newly opening regions coupled with expression analysis identified ZIC3 as a potential regulator of this cell fate transition. Chromatin binding and genome-wide transcriptional profiling following Zic3 depletion confirmed ZIC3 as an important regulatory transcription factor, and among its targets are genes encoding a number of transcription factors. Among these is GRHL2, which acts through enhancer switching to maintain the expression of a subset of genes from the ESC state. Our data therefore place ZIC3 upstream of a set of pro-differentiation transcriptional regulators and provide an important advance in our understanding of the regulatory factors governing the early steps in ESC differentiation. Transcription factor ZIC3 regulates gene expression during the ESC to EpiLC transition Extensive changes occur in the open chromatin landscape as ESCs progress to EpiLCs ZIC3 activates the expression of a network of transcription factors ZIC3-activated genes in EpiLCs are upregulated in the post-implantation epiblast
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47
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Pongor LS, Gross JM, Vera Alvarez R, Murai J, Jang SM, Zhang H, Redon C, Fu H, Huang SY, Thakur B, Baris A, Marino-Ramirez L, Landsman D, Aladjem MI, Pommier Y. BAMscale: quantification of next-generation sequencing peaks and generation of scaled coverage tracks. Epigenetics Chromatin 2020; 13:21. [PMID: 32321568 PMCID: PMC7175505 DOI: 10.1186/s13072-020-00343-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/11/2020] [Indexed: 12/12/2022] Open
Abstract
Background Next-generation sequencing allows genome-wide analysis of changes in chromatin states and gene expression. Data analysis of these increasingly used methods either requires multiple analysis steps, or extensive computational time. We sought to develop a tool for rapid quantification of sequencing peaks from diverse experimental sources and an efficient method to produce coverage tracks for accurate visualization that can be intuitively displayed and interpreted by experimentalists with minimal bioinformatics background. We demonstrate its strength and usability by integrating data from several types of sequencing approaches. Results We have developed BAMscale, a one-step tool that processes a wide set of sequencing datasets. To demonstrate the usefulness of BAMscale, we analyzed multiple sequencing datasets from chromatin immunoprecipitation sequencing data (ChIP-seq), chromatin state change data (assay for transposase-accessible chromatin using sequencing: ATAC-seq, DNA double-strand break mapping sequencing: END-seq), DNA replication data (Okazaki fragments sequencing: OK-seq, nascent-strand sequencing: NS-seq, single-cell replication timing sequencing: scRepli-seq) and RNA-seq data. The outputs consist of raw and normalized peak scores (multiple normalizations) in text format and scaled bigWig coverage tracks that are directly accessible to data visualization programs. BAMScale also includes a visualization module facilitating direct, on-demand quantitative peak comparisons that can be used by experimentalists. Our tool can effectively analyze large sequencing datasets (~ 100 Gb size) in minutes, outperforming currently available tools. Conclusions BAMscale accurately quantifies and normalizes identified peaks directly from BAM files, and creates coverage tracks for visualization in genome browsers. BAMScale can be implemented for a wide set of methods for calculating coverage tracks, including ChIP-seq and ATAC-seq, as well as methods that currently require specialized, separate tools for analyses, such as splice-aware RNA-seq, END-seq and OK-seq for which no dedicated software is available. BAMscale is freely available on github (https://github.com/ncbi/BAMscale).
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Affiliation(s)
- Lorinc S Pongor
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, 37 Convent Dr, Bethesda, MD, 20892, USA.
| | - Jacob M Gross
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, 37 Convent Dr, Bethesda, MD, 20892, USA
| | - Roberto Vera Alvarez
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, NIH, 8600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Junko Murai
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, 37 Convent Dr, Bethesda, MD, 20892, USA
| | - Sang-Min Jang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, 37 Convent Dr, Bethesda, MD, 20892, USA
| | - Hongliang Zhang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, 37 Convent Dr, Bethesda, MD, 20892, USA
| | - Christophe Redon
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, 37 Convent Dr, Bethesda, MD, 20892, USA
| | - Haiqing Fu
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, 37 Convent Dr, Bethesda, MD, 20892, USA
| | - Shar-Yin Huang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, 37 Convent Dr, Bethesda, MD, 20892, USA
| | - Bhushan Thakur
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, 37 Convent Dr, Bethesda, MD, 20892, USA
| | - Adrian Baris
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, 37 Convent Dr, Bethesda, MD, 20892, USA
| | - Leonardo Marino-Ramirez
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, NIH, 8600 Rockville Pike, Bethesda, MD, 20892, USA
| | - David Landsman
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, NIH, 8600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, 37 Convent Dr, Bethesda, MD, 20892, USA.
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, 37 Convent Dr, Bethesda, MD, 20892, USA.
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48
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Beisaw A, Kuenne C, Guenther S, Dallmann J, Wu CC, Bentsen M, Looso M, Stainier DYR. AP-1 Contributes to Chromatin Accessibility to Promote Sarcomere Disassembly and Cardiomyocyte Protrusion During Zebrafish Heart Regeneration. Circ Res 2020; 126:1760-1778. [PMID: 32312172 DOI: 10.1161/circresaha.119.316167] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
RATIONALE The adult human heart is an organ with low regenerative potential. Heart failure following acute myocardial infarction is a leading cause of death due to the inability of cardiomyocytes to proliferate and replenish lost cardiac muscle. While the zebrafish has emerged as a powerful model to study endogenous cardiac regeneration, the molecular mechanisms by which cardiomyocytes respond to damage by disassembling sarcomeres, proliferating, and repopulating the injured area remain unclear. Furthermore, we are far from understanding the regulation of the chromatin landscape and epigenetic barriers that must be overcome for cardiac regeneration to occur. OBJECTIVE To identify transcription factor regulators of the chromatin landscape, which promote cardiomyocyte regeneration in zebrafish, and investigate their function. METHODS AND RESULTS Using the Assay for Transposase-Accessible Chromatin coupled to high-throughput sequencing (ATAC-Seq), we first find that the regenerating cardiomyocyte chromatin accessibility landscape undergoes extensive changes following cryoinjury, and that activator protein-1 (AP-1) binding sites are the most highly enriched motifs in regions that gain accessibility during cardiac regeneration. Furthermore, using bioinformatic and gene expression analyses, we find that the AP-1 response in regenerating adult zebrafish cardiomyocytes is largely different from the response in adult mammalian cardiomyocytes. Using a cardiomyocyte-specific dominant negative approach, we show that blocking AP-1 function leads to defects in cardiomyocyte proliferation as well as decreased chromatin accessibility at the fbxl22 and ilk loci, which regulate sarcomere disassembly and cardiomyocyte protrusion into the injured area, respectively. We further show that overexpression of the AP-1 family members Junb and Fosl1 can promote changes in mammalian cardiomyocyte behavior in vitro. CONCLUSIONS AP-1 transcription factors play an essential role in the cardiomyocyte response to injury by regulating chromatin accessibility changes, thereby allowing the activation of gene expression programs that promote cardiomyocyte dedifferentiation, proliferation, and protrusion into the injured area.
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Affiliation(s)
- Arica Beisaw
- From the Department of Developmental Genetics (A.B., J.D., C.-C.W., D.Y.R.S.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,German Centre for Cardiovascular Research (DZHK) Partner Site Rhine-Main (A.B., S.G., D.Y.R.S.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Carsten Kuenne
- ECCPS Bioinformatics and Deep Sequencing Platform (C.K., S.G., M.B., M.L.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Stefan Guenther
- ECCPS Bioinformatics and Deep Sequencing Platform (C.K., S.G., M.B., M.L.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,German Centre for Cardiovascular Research (DZHK) Partner Site Rhine-Main (A.B., S.G., D.Y.R.S.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Julia Dallmann
- From the Department of Developmental Genetics (A.B., J.D., C.-C.W., D.Y.R.S.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Chi-Chung Wu
- From the Department of Developmental Genetics (A.B., J.D., C.-C.W., D.Y.R.S.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mette Bentsen
- ECCPS Bioinformatics and Deep Sequencing Platform (C.K., S.G., M.B., M.L.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mario Looso
- ECCPS Bioinformatics and Deep Sequencing Platform (C.K., S.G., M.B., M.L.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Didier Y R Stainier
- From the Department of Developmental Genetics (A.B., J.D., C.-C.W., D.Y.R.S.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,German Centre for Cardiovascular Research (DZHK) Partner Site Rhine-Main (A.B., S.G., D.Y.R.S.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
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49
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Yu W, Uzun Y, Zhu Q, Chen C, Tan K. scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data. Genome Biol 2020; 21:94. [PMID: 32312293 PMCID: PMC7169039 DOI: 10.1186/s13059-020-02008-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 04/02/2020] [Indexed: 02/08/2023] Open
Abstract
Single-cell chromatin accessibility sequencing has become a powerful technology for understanding epigenetic heterogeneity of complex tissues. However, there is a lack of open-source software for comprehensive processing, analysis, and visualization of such data generated using all existing experimental protocols. Here, we present scATAC-pro for quality assessment, analysis, and visualization of single-cell chromatin accessibility sequencing data. scATAC-pro computes a range of quality control metrics for several key steps of experimental protocols, with a flexible choice of methods. It generates summary reports for both quality assessment and downstream analysis. scATAC-pro is available at https://github.com/tanlabcode/scATAC-pro.
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Affiliation(s)
- Wenbao Yu
- Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Yasin Uzun
- Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Qin Zhu
- Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Changya Chen
- Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Kai Tan
- Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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50
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Yan F, Powell DR, Curtis DJ, Wong NC. From reads to insight: a hitchhiker's guide to ATAC-seq data analysis. Genome Biol 2020; 21:22. [PMID: 32014034 PMCID: PMC6996192 DOI: 10.1186/s13059-020-1929-3] [Citation(s) in RCA: 204] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 01/08/2020] [Indexed: 12/16/2022] Open
Abstract
Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) is widely used in studying chromatin biology, but a comprehensive review of the analysis tools has not been completed yet. Here, we discuss the major steps in ATAC-seq data analysis, including pre-analysis (quality check and alignment), core analysis (peak calling), and advanced analysis (peak differential analysis and annotation, motif enrichment, footprinting, and nucleosome position analysis). We also review the reconstruction of transcriptional regulatory networks with multiomics data and highlight the current challenges of each step. Finally, we describe the potential of single-cell ATAC-seq and highlight the necessity of developing ATAC-seq specific analysis tools to obtain biologically meaningful insights.
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Affiliation(s)
- Feng Yan
- Australian Centre for Blood Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - David R Powell
- Monash Bioinformatics Platform, Monash University, Melbourne, VIC, Australia
| | - David J Curtis
- Australian Centre for Blood Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia.,Department of Clinical Haematology, Alfred Health, Melbourne, VIC, Australia
| | - Nicholas C Wong
- Australian Centre for Blood Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia. .,Monash Bioinformatics Platform, Monash University, Melbourne, VIC, Australia.
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