1
|
Amin R, Shukla A, Zhu JJ, Kim S, Wang P, Tian SZ, Tran AD, Paul D, Cappell SD, Burkett S, Liu H, Lee MP, Kruhlak MJ, Dwyer JE, Simpson RM, Hager GL, Ruan Y, Hunter KW. Nuclear pore protein NUP210 depletion suppresses metastasis through heterochromatin-mediated disruption of tumor cell mechanical response. Nat Commun 2021; 12:7216. [PMID: 34903738 PMCID: PMC8669001 DOI: 10.1038/s41467-021-27451-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/16/2021] [Indexed: 12/26/2022] Open
Abstract
Mechanical signals from the extracellular microenvironment have been implicated in tumor and metastatic progression. Here, we identify nucleoporin NUP210 as a metastasis susceptibility gene for human estrogen receptor positive (ER+) breast cancer and a cellular mechanosensor. Nup210 depletion suppresses lung metastasis in mouse models of breast cancer. Mechanistically, NUP210 interacts with LINC complex protein SUN2 which connects the nucleus to the cytoskeleton. In addition, the NUP210/SUN2 complex interacts with chromatin via the short isoform of BRD4 and histone H3.1/H3.2 at the nuclear periphery. In Nup210 knockout cells, mechanosensitive genes accumulate H3K27me3 heterochromatin modification, mediated by the polycomb repressive complex 2 and differentially reposition within the nucleus. Transcriptional repression in Nup210 knockout cells results in defective mechanotransduction and focal adhesion necessary for their metastatic capacity. Our study provides an important role of nuclear pore protein in cellular mechanosensation and metastasis. The involvement of nuclear pore proteins in cellular mechanosensing and metastasis is unclear. Here the authors identify that nuclear pore protein NUP210 promotes metastasis through the interaction with mechanotransducer LINC complex protein and chromatin to regulate mechanosensitive genes.
Collapse
Affiliation(s)
- Ruhul Amin
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA.
| | - Anjali Shukla
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Sohyoung Kim
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Ping Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Andy D Tran
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA.,Confocal Microscopy Core Facility, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Debasish Paul
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Steven D Cappell
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Sandra Burkett
- Molecular Cytogenetics Core Facility, National Cancer Institute, NIH, Frederick, MD, USA
| | - Huaitian Liu
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA.,High-Dimension Data Analysis Group, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Maxwell P Lee
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA.,High-Dimension Data Analysis Group, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Michael J Kruhlak
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA.,Confocal Microscopy Core Facility, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Jennifer E Dwyer
- Molecular Pathology Unit, Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - R Mark Simpson
- Molecular Pathology Unit, Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Kent W Hunter
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA.
| |
Collapse
|
2
|
Liu Y, Fu L, Kaufmann K, Chen D, Chen M. A practical guide for DNase-seq data analysis: from data management to common applications. Brief Bioinform 2020; 20:1865-1877. [PMID: 30010713 DOI: 10.1093/bib/bby057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 06/06/2018] [Accepted: 06/10/2018] [Indexed: 01/01/2023] Open
Abstract
Deoxyribonuclease I (DNase I)-hypersensitive site sequencing (DNase-seq) has been widely used to determine chromatin accessibility and its underlying regulatory lexicon. However, exploring DNase-seq data requires sophisticated downstream bioinformatics analyses. In this study, we first review computational methods for all of the major steps in DNase-seq data analysis, including experimental design, quality control, read alignment, peak calling, annotation of cis-regulatory elements, genomic footprinting and visualization. The challenges associated with each step are highlighted. Next, we provide a practical guideline and a computational pipeline for DNase-seq data analysis by integrating some of these tools. We also discuss the competing techniques and the potential applications of this pipeline for the analysis of analogous experimental data. Finally, we discuss the integration of DNase-seq with other functional genomics techniques.
Collapse
Affiliation(s)
- Yongjing Liu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Liangyu Fu
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin 10115, Germany
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin 10115, Germany
| | - Dijun Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ming Chen
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin 10115, Germany
| |
Collapse
|
3
|
Fitz J, Neumann T, Steininger M, Wiedemann EM, Garcia AC, Athanasiadis A, Schoeberl UE, Pavri R. Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction. Nat Genet 2020; 52:505-515. [PMID: 32251373 DOI: 10.1038/s41588-020-0605-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 02/28/2020] [Indexed: 12/19/2022]
Abstract
Active enhancers are frequently transcribed, yet the regulatory role of enhancer transcription remains debated. Here, we depleted the RNA polymerase II pausing and elongation factor Spt5 in activated mouse B cells and found that approximately 50% of enhancer-gene pairs showed co-regulated transcription, consistent with a potential functional requirement for enhancer transcription. In particular, Spt5 depletion led to loss of super-enhancer-promoter physical interaction and gene expression at the immunoglobulin heavy-chain locus (Igh), abrogating antibody class switch recombination. This defect correlated strictly with loss of enhancer transcription but did not affect acetylation of histone H3 at lysine 27, chromatin accessibility and occupancy of Mediator and cohesin at the enhancer. Strikingly, CRISPRa-mediated rescue of enhancer transcription in Spt5-depleted cells restored Igh gene expression. Our work suggests that Spt5-mediated enhancer transcription underlies the physical and functional interaction between a subset of active enhancers and their target promoters.
Collapse
Affiliation(s)
- Johanna Fitz
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Tobias Neumann
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | | | | | | | | | | | - Rushad Pavri
- Research Institute of Molecular Pathology (IMP), Vienna, Austria.
| |
Collapse
|
4
|
Chang P, Gohain M, Yen MR, Chen PY. Computational Methods for Assessing Chromatin Hierarchy. Comput Struct Biotechnol J 2018; 16:43-53. [PMID: 29686798 PMCID: PMC5910504 DOI: 10.1016/j.csbj.2018.02.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 01/29/2018] [Accepted: 02/11/2018] [Indexed: 12/27/2022] Open
Abstract
The hierarchical organization of chromatin is known to associate with diverse cellular functions; however, the precise mechanisms and the 3D structure remain to be determined. With recent advances in high-throughput next generation sequencing (NGS) techniques, genome-wide profiling of chromatin structures is made possible. Here, we provide a comprehensive overview of NGS-based methods for profiling "higher-order" and "primary-order" chromatin structures from both experimental and computational aspects. Experimental requirements and considerations specific for each method were highlighted. For computational analysis, we summarized a common analysis strategy for both levels of chromatin assessment, focusing on the characteristic computing steps and the tools. The recently developed single-cell level techniques based on Hi-C and ATAC-seq present great potential to reveal cell-to-cell variability in chromosome architecture. A brief discussion on these methods in terms of experimental and data analysis features is included. We also touch upon the biological relevance of chromatin organization and how the combination with other techniques uncovers the underlying mechanisms. We conclude with a summary and our prospects on necessary improvements of currently available methods in order to advance understanding of chromatin hierarchy. Our review brings together the analyses of both higher- and primary-order chromatin structures, and serves as a roadmap when choosing appropriate experimental and computational methods for assessing chromatin hierarchy.
Collapse
Affiliation(s)
- Pearl Chang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Moloya Gohain
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Ming-Ren Yen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| |
Collapse
|
5
|
Portuguez AS, Schwartz M, Siersbaek R, Nielsen R, Sung MH, Mandrup S, Kaplan T, Hakim O. Hierarchical role for transcription factors and chromatin structure in genome organization along adipogenesis. FEBS J 2017; 284:3230-3244. [PMID: 28755519 PMCID: PMC5626622 DOI: 10.1111/febs.14183] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 06/24/2017] [Accepted: 07/25/2017] [Indexed: 12/24/2022]
Abstract
The three dimensional folding of mammalian genomes is cell type specific and difficult to alter suggesting that it is an important component of gene regulation. However, given the multitude of chromatin-associating factors, the mechanisms driving the colocalization of active chromosomal domains and the role of this organization in regulating the transcription program in adipocytes are not clear. Analysis of genome-wide chromosomal associations revealed cell type-specific spatial clustering of adipogenic genes in 3T3-L1 cells. Time course analysis demonstrated that the adipogenic 'hub', sampled by PPARγ and Lpin1, undergoes orchestrated reorganization during adipogenesis. Coupling the dynamics of genome architecture with multiple chromatin datasets indicated that among all the transcription factors (TFs) tested, RXR is central to genome reorganization at the beginning of adipogenesis. Interestingly, at the end of differentiation, the adipogenic hub was shifted to an H3K27me3-repressive environment in conjunction with attenuation of gene transcription. We propose a stage-specific hierarchy for the activity of TFs contributing to the establishment of an adipogenic genome architecture that brings together the adipogenic genetic program. In addition, the repositioning of this network in a H3K27me3-rich environment at the end of differentiation may contribute to the stabilization of gene transcription levels and reduce the developmental plasticity of these specialized cells. DATABASE All sequence data reported in this paper have been deposited at GEO (http://www.ncbi.nlm.nih.gov/geo/) (GSE92475).
Collapse
Affiliation(s)
- Avital Sarusi Portuguez
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Michal Schwartz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Rasmus Siersbaek
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark
| | - Ronni Nielsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark
| | - Myong-Hee Sung
- Laboratory of Molecular Biology and Immunology, NIA, National Institutes of Health, Baltimore, MD 21224, USA
| | - Susanne Mandrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Ofir Hakim
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan 5290002, Israel
| |
Collapse
|
6
|
Gibson MD, Brehove M, Luo Y, North J, Poirier MG. Methods for Investigating DNA Accessibility with Single Nucleosomes. Methods Enzymol 2017; 581:379-415. [PMID: 27793287 DOI: 10.1016/bs.mie.2016.08.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nucleosomes are the fundamental organizing unit of all eukaryotic genomes. Understanding how proteins gain access to DNA-binding sites located within nucleosomes is important for understanding DNA processing including transcription, replication, and repair. Single-molecule total internal reflection fluorescence (smTIRF) microscopy measurements can provide key insight into how proteins gain and maintain access to DNA sites within nucleosomes. Here, we describe methods for smTIRF experiments including the preparation of fluorophore-labeled nucleosomes, the smTIRF system, data acquisition, analysis, and controls. These methods are presented for investigating transcription factor binding within nucleosomes. However, they are applicable for investigating the binding of any site-specific DNA-binding protein within nucleosomes.
Collapse
Affiliation(s)
- M D Gibson
- The Ohio State University, Columbus, OH, United States
| | - M Brehove
- The Ohio State University, Columbus, OH, United States
| | - Y Luo
- The Ohio State University, Columbus, OH, United States
| | - J North
- The Ohio State University, Columbus, OH, United States
| | - M G Poirier
- The Ohio State University, Columbus, OH, United States.
| |
Collapse
|
7
|
Anti-Inflammatory Chromatinscape Suggests Alternative Mechanisms of Glucocorticoid Receptor Action. Immunity 2017; 47:298-309.e5. [PMID: 28801231 DOI: 10.1016/j.immuni.2017.07.012] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 03/14/2017] [Accepted: 07/19/2017] [Indexed: 11/21/2022]
Abstract
Despite the widespread use of glucocorticoids (GCs), their anti-inflammatory effects are not understood mechanistically. Numerous investigations have examined the effects of glucocorticoid receptor (GR) activation prior to inflammatory challenges. However, clinical situations are emulated by a GC intervention initiated in the midst of rampant inflammatory responses. To characterize the effects of a late GC treatment, we profiled macrophage transcriptional and chromatinscapes with Dexamethasone (Dex) treatment before or after stimulation by lipopolysaccharide (LPS). The late activation of GR had a similar gene-expression profile as from GR pre-activation, while ameliorating the disruption of metabolic genes. Chromatin occupancy of GR was not predictive of Dex-regulated gene expression, contradicting the "trans-repression by tethering" model. Rather, GR activation resulted in genome-wide blockade of NF-κB interaction with chromatin and directly induced inhibitors of NF-κB and AP-1. Our investigation using GC treatments with clinically relevant timing highlights mechanisms underlying GR actions for modulating the "inflamed epigenome."
Collapse
|
8
|
Pooley JR, Flynn BP, Grøntved L, Baek S, Guertin MJ, Kershaw YM, Birnie MT, Pellatt A, Rivers CA, Schiltz RL, Hager GL, Lightman SL, Conway-Campbell BL. Genome-Wide Identification of Basic Helix-Loop-Helix and NF-1 Motifs Underlying GR Binding Sites in Male Rat Hippocampus. Endocrinology 2017; 158:1486-1501. [PMID: 28200020 PMCID: PMC5460825 DOI: 10.1210/en.2016-1929] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/03/2017] [Indexed: 12/14/2022]
Abstract
Glucocorticoids regulate hippocampal function in part by modulating gene expression through the glucocorticoid receptor (GR). GR binding is highly cell type specific, directed to accessible chromatin regions established during tissue differentiation. Distinct classes of GR binding sites are dependent on the activity of additional signal-activated transcription factors that prime chromatin toward context-specific organization. We hypothesized a stress context dependency for GR binding in hippocampus as a consequence of rapidly induced stress mediators priming chromatin accessibility. Using chromatin immunoprecipitation sequencing to interrogate GR binding, we found no effect of restraint stress context on GR binding, although analysis of sequences underlying GR binding sites revealed mechanistic detail for hippocampal GR function. We note enrichment of GR binding sites proximal to genes linked to structural and organizational roles, an absence of major tethering partners for GRs, and little or no evidence for binding at negative glucocorticoid response elements. A basic helix-loop-helix motif closely resembling a NeuroD1 or Olig2 binding site was found underlying a subset of GR binding sites and is proposed as a candidate lineage-determining transcription factor directing hippocampal chromatin access for GRs. Of our GR binding sites, 54% additionally contained half-sites for nuclear factor (NF)-1 that we propose as a collaborative or general transcription factor involved in hippocampal GR function. Our findings imply a dose-dependent and context-independent action of GRs in the hippocampus. Alterations in the expression or activity of NF-1/basic helix-loop-helix factors may play an as yet undetermined role in glucocorticoid-related disease susceptibility and outcome by altering GR access to hippocampal binding sites.
Collapse
Affiliation(s)
- John R. Pooley
- Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom
| | - Ben P. Flynn
- Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom
| | - Lars Grøntved
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Songjoon Baek
- Laboratory for Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Michael J. Guertin
- University of Virginia School of Medicine, Charlottesville, Virginia 22908
| | - Yvonne M. Kershaw
- Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom
| | - Matthew T. Birnie
- Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom
| | - Annie Pellatt
- Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom
| | - Caroline A. Rivers
- Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom
| | - R. Louis Schiltz
- Laboratory for Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Gordon L. Hager
- Laboratory for Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Stafford L. Lightman
- Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom
| | - Becky L. Conway-Campbell
- Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom
| |
Collapse
|
9
|
Baskin E, Farouni R, Mathé EA. ALTRE: workflow for defining ALTered Regulatory Elements using chromatin accessibility data. Bioinformatics 2017; 33:740-742. [PMID: 28011773 PMCID: PMC5408819 DOI: 10.1093/bioinformatics/btw688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/26/2016] [Indexed: 11/13/2022] Open
Abstract
Summary Regulatory elements regulate gene transcription, and their location and accessibility is cell-type specific, particularly for enhancers. Mapping and comparing chromatin accessibility between different cell types may identify mechanisms involved in cellular development and disease progression. To streamline and simplify differential analysis of regulatory elements genome-wide using chromatin accessibility data, such as DNase-seq, ATAC-seq, we developed ALTRE ( ALT ered R egulatory E lements), an R package and associated R Shiny web app. ALTRE makes such analysis accessible to a wide range of users-from novice to practiced computational biologists. Availability and Implementation https://github.com/Mathelab/ALTRE. Contact ewy.mathe@osumc.edu. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Elizabeth Baskin
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Rick Farouni
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Ewy A Mathé
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
- To whom correspondence should be addressed.
| |
Collapse
|
10
|
Goldstein I, Baek S, Presman DM, Paakinaho V, Swinstead EE, Hager GL. Transcription factor assisted loading and enhancer dynamics dictate the hepatic fasting response. Genome Res 2016; 27:427-439. [PMID: 28031249 PMCID: PMC5340970 DOI: 10.1101/gr.212175.116] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 12/21/2016] [Indexed: 02/03/2023]
Abstract
Fasting elicits transcriptional programs in hepatocytes leading to glucose and ketone production. This transcriptional program is regulated by many transcription factors (TFs). To understand how this complex network regulates the metabolic response to fasting, we aimed at isolating the enhancers and TFs dictating it. Measuring chromatin accessibility revealed that fasting massively reorganizes liver chromatin, exposing numerous fasting-induced enhancers. By utilizing computational methods in combination with dissecting enhancer features and TF cistromes, we implicated four key TFs regulating the fasting response: glucocorticoid receptor (GR), cAMP responsive element binding protein 1 (CREB1), peroxisome proliferator activated receptor alpha (PPARA), and CCAAT/enhancer binding protein beta (CEBPB). These TFs regulate fuel production by two distinctly operating modules, each controlling a separate metabolic pathway. The gluconeogenic module operates through assisted loading, whereby GR doubles the number of sites occupied by CREB1 as well as enhances CREB1 binding intensity and increases accessibility of CREB1 binding sites. Importantly, this GR-assisted CREB1 binding was enhancer-selective and did not affect all CREB1-bound enhancers. Single-molecule tracking revealed that GR increases the number and DNA residence time of a portion of chromatin-bound CREB1 molecules. These events collectively result in rapid synergistic gene expression and higher hepatic glucose production. Conversely, the ketogenic module operates via a GR-induced TF cascade, whereby PPARA levels are increased following GR activation, facilitating gradual enhancer maturation next to PPARA target genes and delayed ketogenic gene expression. Our findings reveal a complex network of enhancers and TFs that dynamically cooperate to restore homeostasis upon fasting.
Collapse
Affiliation(s)
- Ido Goldstein
- Laboratory of Receptor Biology and Gene Expression, The National Cancer Institute, The National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, The National Cancer Institute, The National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Diego M Presman
- Laboratory of Receptor Biology and Gene Expression, The National Cancer Institute, The National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Ville Paakinaho
- Laboratory of Receptor Biology and Gene Expression, The National Cancer Institute, The National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Erin E Swinstead
- Laboratory of Receptor Biology and Gene Expression, The National Cancer Institute, The National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, The National Cancer Institute, The National Institutes of Health, Bethesda, Maryland 20892, USA
| |
Collapse
|
11
|
Identification of Binding Targets of a Pyrrole-Imidazole Polyamide KR12 in the LS180 Colorectal Cancer Genome. PLoS One 2016; 11:e0165581. [PMID: 27798693 PMCID: PMC5087912 DOI: 10.1371/journal.pone.0165581] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 10/16/2016] [Indexed: 01/06/2023] Open
Abstract
Pyrrole-imidazole polyamides are versatile DNA minor groove binders and attractive therapeutic options against oncological targets, especially upon functionalization with an alkylating agent such as seco-CBI. These molecules also provide an alternative for oncogenes deemed "undruggable" at the protein level, where the absence of solvent-accessible pockets or structural crevices prevent the formation of protein-inhibitor ligands; nevertheless, the genome-wide effect of pyrrole-imidazole polyamide binding remain largely unclear to-date. Here we propose a next-generation sequencing-based workflow combined with whole genome expression arrays to address such issue using a candidate anti-cancer alkylating agent, KR12, against codon 12 mutant KRAS. Biotinylating KR12 enables the means to identify its genome-wide effects in living cells and possible biological implications via a coupled workflow of enrichment-based sequencing and expression microarrays. The subsequent computational pathway and expression analyses allow the identification of its genomic binding sites, as well as a route to explore a polyamide's possible genome-wide effects. Among the 3,343 KR12 binding sites identified in the human LS180 colorectal cancer genome, the reduction of KR12-bound gene expressions was also observed. Additionally, the coupled microarray-sequencing analysis also revealed some insights about the effect of local chromatin structure on pyrrole-imidazole polyamide, which had not been fully understood to-date. A comparative analysis with KR12 in a different human colorectal cancer genome SW480 also showed agreeable agreements of KR12 binding affecting gene expressions. Combination of these analyses thus suggested the possibility of applying this approach to other pyrrole-imidazole polyamides to reveal further biological details about the effect of polyamide binding in a genome.
Collapse
|
12
|
Genome-wide footprinting: ready for prime time? Nat Methods 2016; 13:222-228. [PMID: 26914206 DOI: 10.1038/nmeth.3766] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 12/31/2015] [Indexed: 01/16/2023]
Abstract
High-throughput sequencing technologies have allowed many gene locus-level molecular biology assays to become genome-wide profiling methods. DNA-cleaving enzymes such as DNase I have been used to probe accessible chromatin. The accessible regions contain functional regulatory sites, including promoters, insulators and enhancers. Deep sequencing of DNase-seq libraries and computational analysis of the cut profiles have been used to infer protein occupancy in the genome at the nucleotide level, a method introduced as 'digital genomic footprinting'. The approach has been proposed as an attractive alternative to the analysis of transcription factors (TFs) by chromatin immunoprecipitation followed by sequencing (ChIP-seq), and in theory it should overcome antibody issues, poor resolution and batch effects. Recent reports point to limitations of the DNase-based genomic footprinting approach and call into question the scope of detectable protein occupancy, especially for TFs with short-lived chromatin binding. The genomics community is grappling with issues concerning the utility of genomic footprinting and is reassessing the proposed approaches in terms of robust deliverables. Here we summarize the consensus as well as different views emerging from recent reports, and we describe the remaining issues and hurdles for genomic footprinting.
Collapse
|
13
|
Thompson B, Varticovski L, Baek S, Hager GL. Genome-Wide Chromatin Landscape Transitions Identify Novel Pathways in Early Commitment to Osteoblast Differentiation. PLoS One 2016; 11:e0148619. [PMID: 26890492 PMCID: PMC4759368 DOI: 10.1371/journal.pone.0148619] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 01/20/2016] [Indexed: 12/17/2022] Open
Abstract
Bone continuously undergoes remodeling by a tightly regulated process that involves osteoblast differentiation from Mesenchymal Stem Cells (MSC). However, commitment of MSC to osteoblastic lineage is a poorly understood process. Chromatin organization functions as a molecular gatekeeper of DNA functions. Detection of sites that are hypersensitive to Dnase I has been used for detailed examination of changes in response to hormones and differentiation cues. To investigate the early steps in commitment of MSC to osteoblasts, we used a model human temperature-sensitive cell line, hFOB. When shifted to non-permissive temperature, these cells undergo "spontaneous" differentiation that takes several weeks, a process that is greatly accelerated by osteogenic induction media. We performed Dnase I hypersensitivity assays combined with deep sequencing to identify genome-wide potential regulatory events in cells undergoing early steps of commitment to osteoblasts. Massive reorganization of chromatin occurred within hours of differentiation. Whereas ~30% of unique DHS sites were located in the promoters, the majority was outside of the promoters, designated as enhancers. Many of them were at novel genomic sites and need to be confirmed experimentally. We developed a novel method for identification of cellular networks based solely on DHS enhancers signature correlated to gene expression. The analysis of enhancers that were unique to differentiating cells led to identification of bone developmental program encompassing 147 genes that directly or indirectly participate in osteogenesis. Identification of these pathways provided an unprecedented view of genomic regulation during early steps of differentiation and changes related to WNT, AP-1 and other pathways may have therapeutic implications.
Collapse
Affiliation(s)
- Bethtrice Thompson
- Laboratory of Receptor Biology and Gene Expression, NCI, NIH, Bethesda, MD, United States of America
- Center for Cancer Research and Therapeutic Development, Clark Atlanta University, Atlanta, GA, United States of America
| | - Lyuba Varticovski
- Laboratory of Receptor Biology and Gene Expression, NCI, NIH, Bethesda, MD, United States of America
- * E-mail:
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, NCI, NIH, Bethesda, MD, United States of America
| | - Gordon L. Hager
- Laboratory of Receptor Biology and Gene Expression, NCI, NIH, Bethesda, MD, United States of America
| |
Collapse
|
14
|
Baek S, Sung MH. Genome-Scale Analysis of Cell-Specific Regulatory Codes Using Nuclear Enzymes. Methods Mol Biol 2016; 1418:225-40. [PMID: 27008018 DOI: 10.1007/978-1-4939-3578-9_12] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
High-throughput sequencing technologies have made it possible for biologists to generate genome-wide profiles of chromatin features at the nucleotide resolution. Enzymes such as nucleases or transposes have been instrumental as a chromatin-probing agent due to their ability to target accessible chromatin for cleavage or insertion. On the scale of a few hundred base pairs, preferential action of the nuclear enzymes on accessible chromatin allows mapping of cell state-specific accessibility in vivo. Such accessible regions contain functionally important regulatory sites, including promoters and enhancers, which undergo active remodeling for cells adapting in a dynamic environment. DNase-seq and the more recent ATAC-seq are two assays that are gaining popularity. Deep sequencing of DNA libraries from these assays, termed genomic footprinting, has been proposed to enable the comprehensive construction of protein occupancy profiles over the genome at the nucleotide level. Recent studies have discovered limitations of genomic footprinting which reduce the scope of detectable proteins. In addition, the identification of putative factors that bind to the observed footprints remains challenging. Despite these caveats, the methodology still presents significant advantages over alternative techniques such as ChIP-seq or FAIRE-seq. Here we describe computational approaches and tools for analysis of chromatin accessibility and genomic footprinting. Proper experimental design and assay-specific data analysis ensure the detection sensitivity and maximize retrievable information. The enzyme-based chromatin profiling approaches represent a powerful and evolving methodology which facilitates our understanding of how the genome is regulated.
Collapse
Affiliation(s)
- Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, 41 Library Drive, Bethesda, MD, 20892, USA
| | - Myong-Hee Sung
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, 41 Library Drive, Bethesda, MD, 20892, USA. .,Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD, 21224, USA.
| |
Collapse
|
15
|
Wang C, Lv Y, Wang B, Yin C, Lin Y, Pan L. Survey of protein-DNA interactions in Aspergillus oryzae on a genomic scale. Nucleic Acids Res 2015; 43:4429-46. [PMID: 25883143 PMCID: PMC4482085 DOI: 10.1093/nar/gkv334] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 03/31/2015] [Indexed: 01/23/2023] Open
Abstract
The genome-scale delineation of in vivo protein–DNA interactions is key to understanding genome function. Only ∼5% of transcription factors (TFs) in the Aspergillus genus have been identified using traditional methods. Although the Aspergillus oryzae genome contains >600 TFs, knowledge of the in vivo genome-wide TF-binding sites (TFBSs) in aspergilli remains limited because of the lack of high-quality antibodies. We investigated the landscape of in vivo protein–DNA interactions across the A. oryzae genome through coupling the DNase I digestion of intact nuclei with massively parallel sequencing and the analysis of cleavage patterns in protein–DNA interactions at single-nucleotide resolution. The resulting map identified overrepresented de novo TF-binding motifs from genomic footprints, and provided the detailed chromatin remodeling patterns and the distribution of digital footprints near transcription start sites. The TFBSs of 19 known Aspergillus TFs were also identified based on DNase I digestion data surrounding potential binding sites in conjunction with TF binding specificity information. We observed that the cleavage patterns of TFBSs were dependent on the orientation of TF motifs and independent of strand orientation, consistent with the DNA shape features of binding motifs with flanking sequences.
Collapse
Affiliation(s)
- Chao Wang
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, 510006, China
| | - Yangyong Lv
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, 510006, China
| | - Bin Wang
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, 510006, China
| | - Chao Yin
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, 510006, China
| | - Ying Lin
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, 510006, China
| | - Li Pan
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, 510006, China
| |
Collapse
|
16
|
Transcriptional activation by the thyroid hormone receptor through ligand-dependent receptor recruitment and chromatin remodelling. Nat Commun 2015; 6:7048. [PMID: 25916672 DOI: 10.1038/ncomms8048] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/26/2015] [Indexed: 02/03/2023] Open
Abstract
A bimodal switch model is widely used to describe transcriptional regulation by the thyroid hormone receptor (TR). In this model, the unliganded TR forms stable, chromatin-bound complexes with transcriptional co-repressors to repress transcription. Binding of hormone dissociates co-repressors and facilitates recruitment of co-activators to activate transcription. Here we show that in addition to hormone-independent TR occupancy, ChIP-seq against endogenous TR in mouse liver tissue demonstrates considerable hormone-induced TR recruitment to chromatin associated with chromatin remodelling and activated gene transcription. Genome-wide footprinting analysis using DNase-seq provides little evidence for TR footprints both in the absence and presence of hormone, suggesting that unliganded TR engagement with repressive complexes on chromatin is, similar to activating receptor complexes, a highly dynamic process. This dynamic and ligand-dependent interaction with chromatin is likely shared by all steroid hormone receptors regardless of their capacity to repress transcription in the absence of ligand.
Collapse
|
17
|
Tsompana M, Buck MJ. Chromatin accessibility: a window into the genome. Epigenetics Chromatin 2014; 7:33. [PMID: 25473421 PMCID: PMC4253006 DOI: 10.1186/1756-8935-7-33] [Citation(s) in RCA: 270] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/05/2014] [Indexed: 01/09/2023] Open
Abstract
Transcriptional activation throughout the eukaryotic lineage has been tightly linked with disruption of nucleosome organization at promoters, enhancers, silencers, insulators and locus control regions due to transcription factor binding. Regulatory DNA thus coincides with open or accessible genomic sites of remodeled chromatin. Current chromatin accessibility assays are used to separate the genome by enzymatic or chemical means and isolate either the accessible or protected locations. The isolated DNA is then quantified using a next-generation sequencing platform. Wide application of these assays has recently focused on the identification of the instrumental epigenetic changes responsible for differential gene expression, cell proliferation, functional diversification and disease development. Here we discuss the limitations and advantages of current genome-wide chromatin accessibility assays with especial attention on experimental precautions and sequence data analysis. We conclude with our perspective on future improvements necessary for moving the field of chromatin profiling forward.
Collapse
Affiliation(s)
- Maria Tsompana
- New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, 701 Ellicott St, Buffalo, NY 14203 USA
| | - Michael J Buck
- New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, 701 Ellicott St, Buffalo, NY 14203 USA ; Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY USA
| |
Collapse
|
18
|
Hsiung CCS, Morrissey CS, Udugama M, Frank CL, Keller CA, Baek S, Giardine B, Crawford GE, Sung MH, Hardison RC, Blobel GA. Genome accessibility is widely preserved and locally modulated during mitosis. Genome Res 2014; 25:213-25. [PMID: 25373146 PMCID: PMC4315295 DOI: 10.1101/gr.180646.114] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Mitosis entails global alterations to chromosome structure and nuclear architecture, concomitant with transient silencing of transcription. How cells transmit transcriptional states through mitosis remains incompletely understood. While many nuclear factors dissociate from mitotic chromosomes, the observation that certain nuclear factors and chromatin features remain associated with individual loci during mitosis originated the hypothesis that such mitotically retained molecular signatures could provide transcriptional memory through mitosis. To understand the role of chromatin structure in mitotic memory, we performed the first genome-wide comparison of DNase I sensitivity of chromatin in mitosis and interphase, using a murine erythroblast model. Despite chromosome condensation during mitosis visible by microscopy, the landscape of chromatin accessibility at the macromolecular level is largely unaltered. However, mitotic chromatin accessibility is locally dynamic, with individual loci maintaining none, some, or all of their interphase accessibility. Mitotic reduction in accessibility occurs primarily within narrow, highly DNase hypersensitive sites that frequently coincide with transcription factor binding sites, whereas broader domains of moderate accessibility tend to be more stable. In mitosis, proximal promoters generally maintain their accessibility more strongly, whereas distal regulatory elements tend to lose accessibility. Large domains of DNA hypomethylation mark a subset of promoters that retain accessibility during mitosis and across many cell types in interphase. Erythroid transcription factor GATA1 exerts site-specific changes in interphase accessibility that are most pronounced at distal regulatory elements, but has little influence on mitotic accessibility. We conclude that features of open chromatin are remarkably stable through mitosis, but are modulated at the level of individual genes and regulatory elements.
Collapse
Affiliation(s)
- Chris C-S Hsiung
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Christapher S Morrissey
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Maheshi Udugama
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Christopher L Frank
- Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27708, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Gregory E Crawford
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA; Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina 27708, USA
| | - Myong-Hee Sung
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA;
| |
Collapse
|
19
|
Koohy H, Down TA, Spivakov M, Hubbard T. A comparison of peak callers used for DNase-Seq data. PLoS One 2014; 9:e96303. [PMID: 24810143 PMCID: PMC4014496 DOI: 10.1371/journal.pone.0096303] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 04/06/2014] [Indexed: 11/19/2022] Open
Abstract
Genome-wide profiling of open chromatin regions using DNase I and high-throughput sequencing (DNase-seq) is an increasingly popular approach for finding and studying regulatory elements. A variety of algorithms have been developed to identify regions of open chromatin from raw sequence-tag data, which has motivated us to assess and compare their performance. In this study, four published, publicly available peak calling algorithms used for DNase-seq data analysis (F-seq, Hotspot, MACS and ZINBA) are assessed at a range of signal thresholds on two published DNase-seq datasets for three cell types. The results were benchmarked against an independent dataset of regulatory regions derived from ENCODE in vivo transcription factor binding data for each particular cell type. The level of overlap between peak regions reported by each algorithm and this ENCODE-derived reference set was used to assess sensitivity and specificity of the algorithms. Our study suggests that F-seq has a slightly higher sensitivity than the next best algorithms. Hotspot and the ChIP-seq oriented method, MACS, both perform competitively when used with their default parameters. However the generic peak finder ZINBA appears to be less sensitive than the other three. We also assess accuracy of each algorithm over a range of signal thresholds. In particular, we show that the accuracy of F-Seq can be considerably improved by using a threshold setting that is different from the default value.
Collapse
Affiliation(s)
- Hashem Koohy
- The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Thomas A. Down
- The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Mikhail Spivakov
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Tim Hubbard
- The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| |
Collapse
|
20
|
Kieffer-Kwon KR, Tang Z, Mathe E, Qian J, Sung MH, Li G, Resch W, Baek S, Pruett N, Grøntved L, Vian L, Nelson S, Zare H, Hakim O, Reyon D, Yamane A, Nakahashi H, Kovalchuk AL, Zou J, Joung JK, Sartorelli V, Wei CL, Ruan X, Hager GL, Ruan Y, Casellas R. Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation. Cell 2014; 155:1507-20. [PMID: 24360274 DOI: 10.1016/j.cell.2013.11.039] [Citation(s) in RCA: 249] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 11/01/2013] [Accepted: 11/25/2013] [Indexed: 12/31/2022]
Abstract
A key finding of the ENCODE project is that the enhancer landscape of mammalian cells undergoes marked alterations during ontogeny. However, the nature and extent of these changes are unclear. As part of the NIH Mouse Regulome Project, we here combined DNaseI hypersensitivity, ChIP-seq, and ChIA-PET technologies to map the promoter-enhancer interactomes of pluripotent ES cells and differentiated B lymphocytes. We confirm that enhancer usage varies widely across tissues. Unexpectedly, we find that this feature extends to broadly transcribed genes, including Myc and Pim1 cell-cycle regulators, which associate with an entirely different set of enhancers in ES and B cells. By means of high-resolution CpG methylomes, genome editing, and digital footprinting, we show that these enhancers recruit lineage-determining factors. Furthermore, we demonstrate that the turning on and off of enhancers during development correlates with promoter activity. We propose that organisms rely on a dynamic enhancer landscape to control basic cellular functions in a tissue-specific manner.
Collapse
Affiliation(s)
| | - Zhonghui Tang
- The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, CT 06030, USA
| | - Ewy Mathe
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jason Qian
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Myong-Hee Sung
- Laboratory of Receptor Biology and Gene Expression, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Guoliang Li
- The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, CT 06030, USA
| | - Wolfgang Resch
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nathanael Pruett
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lars Grøntved
- Laboratory of Receptor Biology and Gene Expression, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Laura Vian
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Steevenson Nelson
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hossein Zare
- Laboratory of Muscle Stem Cells and Gene Regulation, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ofir Hakim
- Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Deepak Reyon
- Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA; Department of Pathology, Harvard Medical School, Boston, MA 02115 USA
| | - Arito Yamane
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hirotaka Nakahashi
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexander L Kovalchuk
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Jizhong Zou
- Laboratory of Stem Cell Biology, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - J Keith Joung
- Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA; Department of Pathology, Harvard Medical School, Boston, MA 02115 USA
| | - Vittorio Sartorelli
- Laboratory of Muscle Stem Cells and Gene Regulation, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chia-Lin Wei
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Xiaoan Ruan
- The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, CT 06030, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, and Department of Genetic and Development Biology, University of Connecticut, 400 Farmington, CT 06030, USA
| | - Rafael Casellas
- Genomics and Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA; Center of Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
21
|
Morris SA, Baek S, Sung MH, John S, Wiench M, Johnson TA, Schiltz RL, Hager GL. Overlapping chromatin-remodeling systems collaborate genome wide at dynamic chromatin transitions. Nat Struct Mol Biol 2013; 21:73-81. [PMID: 24317492 PMCID: PMC3947387 DOI: 10.1038/nsmb.2718] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 10/17/2013] [Indexed: 12/24/2022]
Abstract
ATP-dependent chromatin remodeling is an essential process required for the dynamic organization of chromatin structure. Here we describe the genome-wide location and activity of three remodeler proteins with diverse physiological functions in the mouse genome: Brg1, Chd4, and Snf2h. The localization patterns of all three proteins significantly overlap with one another and with regions of accessible chromatin. Furthermore, using inducible mutant variants, we demonstrate that the catalytic activity of these proteins contributes to the remodeling of chromatin genome-wide, and that each of these remodelers can independently regulate chromatin reorganization at distinct sites. Many regions require the activity of more than one remodeler to regulate accessibility. These findings provide a dynamic view of chromatin organization, and highlight the differential contributions of remodelers to chromatin maintenance in higher eukaryotes.
Collapse
Affiliation(s)
- Stephanie A Morris
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Myong-Hee Sung
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Sam John
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Malgorzata Wiench
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Thomas A Johnson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - R Louis Schiltz
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| |
Collapse
|
22
|
Miranda TB, Voss TC, Sung MH, Baek S, John S, Hawkins M, Grøntved L, Schiltz RL, Hager GL. Reprogramming the chromatin landscape: interplay of the estrogen and glucocorticoid receptors at the genomic level. Cancer Res 2013; 73:5130-9. [PMID: 23803465 PMCID: PMC3799864 DOI: 10.1158/0008-5472.can-13-0742] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cross-talk between estrogen receptors (ER) and glucocorticoid receptors (GR) has been shown to contribute to the development and progression of breast cancer. Importantly, the ER and GR status in breast cancer cells is a significant factor in determining the outcome of the disease. However, mechanistic details defining the cellular interactions between ER and GR are poorly understood. We investigated genome-wide binding profiles for ER and GR upon coactivation and characterized the status of the chromatin landscape. We describe a novel mechanism dictating the molecular interplay between ER and GR. Upon induction, GR modulates access of ER to specific sites in the genome by reorganization of the chromatin configuration for these elements. Binding to these newly accessible sites occurs either by direct recognition of ER response elements or indirectly through interactions with other factors. The unveiling of this mechanism is important for understanding cellular interactions between ER and GR and may represent a general mechanism for cross-talk between nuclear receptors in human disease.
Collapse
Affiliation(s)
- Tina B. Miranda
- Laboratory of Receptor Biology and Gene Expression, Building 41, B602, 41 Library Dr., National Cancer Institute, NIH, Bethesda, MD 20892-5055
| | - Ty C. Voss
- Laboratory of Receptor Biology and Gene Expression, Building 41, B602, 41 Library Dr., National Cancer Institute, NIH, Bethesda, MD 20892-5055
| | - Myong-Hee Sung
- Laboratory of Receptor Biology and Gene Expression, Building 41, B602, 41 Library Dr., National Cancer Institute, NIH, Bethesda, MD 20892-5055
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, Building 41, B602, 41 Library Dr., National Cancer Institute, NIH, Bethesda, MD 20892-5055
| | - Sam John
- Laboratory of Receptor Biology and Gene Expression, Building 41, B602, 41 Library Dr., National Cancer Institute, NIH, Bethesda, MD 20892-5055
| | - Mary Hawkins
- Laboratory of Receptor Biology and Gene Expression, Building 41, B602, 41 Library Dr., National Cancer Institute, NIH, Bethesda, MD 20892-5055
| | - Lars Grøntved
- Laboratory of Receptor Biology and Gene Expression, Building 41, B602, 41 Library Dr., National Cancer Institute, NIH, Bethesda, MD 20892-5055
| | - R. Louis Schiltz
- Laboratory of Receptor Biology and Gene Expression, Building 41, B602, 41 Library Dr., National Cancer Institute, NIH, Bethesda, MD 20892-5055
| | - Gordon L. Hager
- Laboratory of Receptor Biology and Gene Expression, Building 41, B602, 41 Library Dr., National Cancer Institute, NIH, Bethesda, MD 20892-5055
| |
Collapse
|
23
|
Grøntved L, John S, Baek S, Liu Y, Buckley JR, Vinson C, Aguilera G, Hager GL. C/EBP maintains chromatin accessibility in liver and facilitates glucocorticoid receptor recruitment to steroid response elements. EMBO J 2013; 32:1568-83. [PMID: 23665916 DOI: 10.1038/emboj.2013.106] [Citation(s) in RCA: 178] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 04/10/2013] [Indexed: 01/22/2023] Open
Abstract
Mechanisms regulating transcription factor interaction with chromatin in intact mammalian tissues are poorly understood. Exploiting an adrenalectomized mouse model with depleted endogenous glucocorticoids, we monitor changes of the chromatin landscape in intact liver tissue following glucocorticoid injection. Upon activation of the glucocorticoid receptor (GR), proximal regions of activated and repressed genes are remodelled, and these remodelling events correlate with RNA polymerase II occupancy of regulated genes. GR is exclusively associated with accessible chromatin and 62% percent of GR-binding sites are occupied by C/EBPβ. At the majority of these sites, chromatin is preaccessible suggesting a priming function of C/EBPβ for GR recruitment. Disruption of C/EBPβ binding to chromatin results in attenuation of pre-programmed chromatin accessibility, GR recruitment and GR-induced chromatin remodelling specifically at sites co-occupied by GR and C/EBPβ. Collectively, we demonstrate a highly cooperative mechanism by which C/EBPβ regulates selective GR binding to the genome in liver tissue. We suggest that selective targeting of GR in other tissues is likely mediated by the combined action of cell-specific priming proteins and chromatin remodellers.
Collapse
Affiliation(s)
- Lars Grøntved
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | | | | | | | | | | | | | | |
Collapse
|
24
|
Hakim O, Sung MH, Nakayamada S, Voss TC, Baek S, Hager GL. Spatial congregation of STAT binding directs selective nuclear architecture during T-cell functional differentiation. Genome Res 2012; 23:462-72. [PMID: 23212947 PMCID: PMC3589535 DOI: 10.1101/gr.147652.112] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Higher-order genome organization shows tissue-specific patterns. However, functional relevance and the mechanisms shaping the genome architecture are poorly understood. Here we report a profound shift from promiscuous to highly selective genome organization that accompanies the effector lineage choice of differentiating T cells. As multipotent naive cells receive antigenic signals and commit to a T helper (Th) pathway, the genome-wide contacts of a lineage-specific cytokine locus are preferentially enriched for functionally relevant genes. Despite the establishment of divergent interactomes and global reprogramming of transcription in Th1 versus Th2, the overall expression status of the contact genes is surprisingly similar between the two lineages. Importantly, during differentiation, the genomic contacts are retained and strengthened precisely at DNA binding sites of the specific lineage-determining STAT transcription factor. In cells from the specific STAT knock-out mouse, the signature cytokine locus is unable to shed the promiscuous contacts established in the naive T cells, indicating the importance of genomic STAT binding. Altogether, the global aggregation of STAT binding loci from genic and nongenic regions highlights a new role for differentiation-promoting transcription factors in direct specification of higher-order nuclear architecture through interacting with regulatory regions. Such subnuclear environments have significant implications for efficient functioning of the mature effector lymphocytes.
Collapse
Affiliation(s)
- Ofir Hakim
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | | | | | | | | | | |
Collapse
|
25
|
Khozoie C, Borland MG, Zhu B, Baek S, John S, Hager GL, Shah YM, Gonzalez FJ, Peters JM. Analysis of the peroxisome proliferator-activated receptor-β/δ (PPARβ/δ) cistrome reveals novel co-regulatory role of ATF4. BMC Genomics 2012; 13:665. [PMID: 23176727 PMCID: PMC3556323 DOI: 10.1186/1471-2164-13-665] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 11/22/2012] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The present study coupled expression profiling with chromatin immunoprecipitation sequencing (ChIP-seq) to examine peroxisome proliferator-activated receptor-β/δ (PPARβ/δ)-dependent regulation of gene expression in mouse keratinocytes, a cell type that expresses PPARβ/δ in high concentration. RESULTS Microarray analysis elucidated eight different types of regulation that modulated PPARβ/δ-dependent gene expression of 612 genes ranging from repression or activation without an exogenous ligand, repression or activation with an exogenous ligand, or a combination of these effects. Bioinformatic analysis of ChIP-seq data demonstrated promoter occupancy of PPARβ/δ for some of these genes, and also identified the presence of other transcription factor binding sites in close proximity to PPARβ/δ bound to chromatin. For some types of regulation, ATF4 is required for ligand-dependent induction of PPARβ/δ target genes. CONCLUSIONS PPARβ/δ regulates constitutive expression of genes in keratinocytes, thus suggesting the presence of one or more endogenous ligands. The diversity in the types of gene regulation carried out by PPARβ/δ is consistent with dynamic binding and interactions with chromatin and indicates the presence of complex regulatory networks in cells expressing high levels of this nuclear receptor such as keratinocytes. Results from these studies are the first to demonstrate that differences in DNA binding of other transcription factors can directly influence the transcriptional activity of PPARβ/δ.
Collapse
Affiliation(s)
- Combiz Khozoie
- Department of Veterinary and Biomedical Sciences and The Center for Molecular Toxicology and Carcinogenesis, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Michael G Borland
- Department of Veterinary and Biomedical Sciences and The Center for Molecular Toxicology and Carcinogenesis, The Pennsylvania State University, University Park, PA, 16802, USA
- Present address: Department of Chemistry and Biochemistry, Bloomsburg University of Pennsylvania, Bloomsburg, PA, USA
| | - Bokai Zhu
- Department of Veterinary and Biomedical Sciences and The Center for Molecular Toxicology and Carcinogenesis, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Sam John
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, 20892, USA
- Present address: Genome Sciences, University of Washington, Seattle, WA, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Yatrik M Shah
- Laboratory of Metabolism, National Cancer Institute, Bethesda, MD, 20892, USA
- Present address: Department of Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Frank J Gonzalez
- Laboratory of Metabolism, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Jeffrey M Peters
- Department of Veterinary and Biomedical Sciences and The Center for Molecular Toxicology and Carcinogenesis, The Pennsylvania State University, University Park, PA, 16802, USA
| |
Collapse
|
26
|
Madrigal P, Krajewski P. Current bioinformatic approaches to identify DNase I hypersensitive sites and genomic footprints from DNase-seq data. Front Genet 2012; 3:230. [PMID: 23118738 PMCID: PMC3484326 DOI: 10.3389/fgene.2012.00230] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Accepted: 10/13/2012] [Indexed: 12/16/2022] Open
Affiliation(s)
- Pedro Madrigal
- Laboratory of Biometry, Institute of Plant Genetics, Polish Academy of Sciences Poznań, Poland
| | | |
Collapse
|
27
|
King HA, Trotter KW, Archer TK. Chromatin remodeling during glucocorticoid receptor regulated transactivation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:716-26. [PMID: 22425674 DOI: 10.1016/j.bbagrm.2012.02.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 02/24/2012] [Accepted: 02/28/2012] [Indexed: 12/21/2022]
Abstract
Steroid hormone receptor (SR) signaling leads to widespread changes in gene expression, and aberrant SR signaling can lead to malignancies including breast, prostate, and lung cancers. Chromatin remodeling is an essential component of SR signaling, and defining the process of chromatin and nucleosome remodeling during signaling is critical to the continued development of related therapies. The glucocorticoid receptor (GR) is a key SR that activates numerous promoters including the well defined MMTV promoter. The activation of MMTV by GR provides an excellent model for teasing apart the sequence of events between hormone treatment and changes in gene expression. Comparing hormone-induced transcription from stably integrated promoters with defined nucleosomal structure to that from transiently expressed, unstructured promoters permits key distinctions between interactions that require remodeling and those that do not. The importance of co-activators and histone modifications prior to remodeling and the formation of the preinitiation complex that follows can also be clarified by defining key transition points in the propagation of hormonal signals. Combined with detailed mapping of proteins along the promoter, a temporal and spatial understanding of the signaling and remodeling processes begins to emerge. In this review, we examine SR signaling with a focus on GR activation of the MMTV promoter. We also discuss the ATP-dependent remodeling complex SWI/SNF, which provides the necessary remodeling activity during GR signaling and interacts with several SRs. BRG1, the central ATPase of SWI/SNF, also interacts with a set of BAF proteins that help determine the specialized function and fine-tuned regulation of BRG1 remodeling activity. BRG1 regulation comes from its own subdomains as well as its interactive partners. In particular, the HSA domain region of BRG1 and unique features of its ATPase homology appear to play key roles in regulating remodeling function. Details of the inter-workings of this chromatin remodeling protein continue to be revealed and promise to improve our understanding of the mechanism of chromatin remodeling during steroid hormone signaling. This article is part of a Special Issue entitled: Chromatin in time and space.
Collapse
Affiliation(s)
- Heather A King
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | | | | |
Collapse
|