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Gavrilov AA, Evko GS, Galitsyna AA, Ulianov SV, Kochetkova TV, Merkel AY, Tyakht AV, Razin SV. RNA-DNA interactomes of three prokaryotes uncovered by proximity ligation. Commun Biol 2023; 6:473. [PMID: 37120653 PMCID: PMC10148824 DOI: 10.1038/s42003-023-04853-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 04/19/2023] [Indexed: 05/01/2023] Open
Abstract
Proximity ligation approaches, which are widely used to study the spatial organization of the genome, also make it possible to reveal patterns of RNA-DNA interactions. Here, we use RedC, an RNA-DNA proximity ligation approach, to assess the distribution of major RNA types along the genomes of E. coli, B. subtilis, and thermophilic archaeon T. adornatum. We find that (i) messenger RNAs preferentially interact with their cognate genes and the genes located downstream in the same operon, which is consistent with polycistronic transcription; (ii) ribosomal RNAs preferentially interact with active protein-coding genes in both bacteria and archaea, indicating co-transcriptional translation; and (iii) 6S noncoding RNA, a negative regulator of bacterial transcription, is depleted from active genes in E. coli and B. subtilis. We conclude that the RedC data provide a rich resource for studying both transcription dynamics and the function of noncoding RNAs in microbial organisms.
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Affiliation(s)
- Alexey A Gavrilov
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
| | - Grigory S Evko
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
| | | | - Sergey V Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Tatiana V Kochetkova
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, 117312, Moscow, Russia
| | - Alexander Y Merkel
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, 117312, Moscow, Russia
| | - Alexander V Tyakht
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
| | - Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia.
- Faculty of Biology, Lomonosov Moscow State University, 119991, Moscow, Russia.
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2
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Cheng K, McCarrey JR. Profiling the Epigenetic Landscape of the Spermatogonial Stem Cell-Part 1: Epigenomics Assays. Methods Mol Biol 2023; 2656:71-108. [PMID: 37249867 DOI: 10.1007/978-1-0716-3139-3_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Epigenomics encompasses analyses of a variety of different epigenetic parameters which, collectively, make up the epigenetic programming that dictates cell fate and function. Here, protocols are provided for four different epigenomic methods including whole-genome bisulfite sequencing (WGBS) to assess DNA methylation patterns, chromatin immunoprecipitation-sequencing (ChIP-seq) to assess genomic patterns of either specific histone modifications or bound transcription factors, the assay for transposase-accessible chromatin-sequencing (ATAC-seq) to assess genomic patterns of chromatin accessibility, and high-throughput chromosome conformation capture-sequencing (Hi-C-seq) to assess three-dimensional interactions among distant genomic regions, plus computational methodology to integrate data from those four methodologies using Chromatin State Discovery and Characterization (ChromHMM) to obtain the most comprehensive overall assessment of epigenetic programming.
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Affiliation(s)
- Keren Cheng
- Department of Neuroscience, Developmental and Regenerative Biology, University of Texas at San Antonio, San Antonio, TX, USA
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - John R McCarrey
- Department of Neuroscience, Developmental and Regenerative Biology, University of Texas at San Antonio, San Antonio, TX, USA.
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3
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Regulation of KDM5C stability and enhancer reprogramming in breast cancer. Cell Death Dis 2022; 13:843. [PMID: 36192394 PMCID: PMC9530161 DOI: 10.1038/s41419-022-05296-5] [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: 04/15/2022] [Revised: 09/10/2022] [Accepted: 09/23/2022] [Indexed: 01/23/2023]
Abstract
Abnormality of enhancer regulation has emerged as one of the critical features for cancer cells. KDM5C is a histone H3K4 demethylase and frequently mutated in several types of cancer. It is critical for H3K4me3 and activity of enhancers, but its regulatory mechanisms remain elusive. Here, we identify TRIM11 as one ubiquitin E3 ligase for KDM5C. TRIM11 interacts with KDM5C, catalyzes K48-linked ubiquitin chain on KDM5C, and promotes KDM5C degradation through proteasome. TRIM11 deficiency in an animal model represses the growth of breast tumor and stabilizes KDM5C. In breast cancer patient tissues, TRIM11 is highly expressed and KDM5C is lower expressed, and their expression is negatively correlated. Mechanistically, TRIM11 regulates the enhancer activity of genes involved in cell migration and immune response by targeting KDM5C. TRIM11 and KDM5C regulate MCAM expression and cell migration through targeting H3K4me3 on MCAM enhancer. Taken together, our study reveals novel mechanisms for enhancer regulation during breast cancer tumorigenesis and development.
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4
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MacKenzie A, Hay EA, McEwan AR. Context-dependant enhancers as a reservoir of functional polymorphisms and epigenetic markers linked to alcohol use disorders and comorbidities. ADDICTION NEUROSCIENCE 2022; 2:None. [PMID: 35712020 PMCID: PMC9101288 DOI: 10.1016/j.addicn.2022.100014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/18/2022] [Accepted: 03/22/2022] [Indexed: 10/25/2022]
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5
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Zhu T, Liu J, Beck S, Pan S, Capper D, Lechner M, Thirlwell C, Breeze CE, Teschendorff AE. A pan-tissue DNA methylation atlas enables in silico decomposition of human tissue methylomes at cell-type resolution. Nat Methods 2022; 19:296-306. [PMID: 35277705 PMCID: PMC8916958 DOI: 10.1038/s41592-022-01412-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 01/28/2022] [Indexed: 02/07/2023]
Abstract
Bulk-tissue DNA methylomes represent an average over many different cell types, hampering our understanding of cell-type-specific contributions to disease development. As single-cell methylomics is not scalable to large cohorts of individuals, cost-effective computational solutions are needed, yet current methods are limited to tissues such as blood. Here we leverage the high-resolution nature of tissue-specific single-cell RNA-sequencing datasets to construct a DNA methylation atlas defined for 13 solid tissue types and 40 cell types. We comprehensively validate this atlas in independent bulk and single-nucleus DNA methylation datasets. We demonstrate that it correctly predicts the cell of origin of diverse cancer types and discovers new prognostic associations in olfactory neuroblastoma and stage 2 melanoma. In brain, the atlas predicts a neuronal origin for schizophrenia, with neuron-specific differential DNA methylation enriched for corresponding genome-wide association study risk loci. In summary, the DNA methylation atlas enables the decomposition of 13 different human tissue types at a high cellular resolution, paving the way for an improved interpretation of epigenetic data. This resource presents an in silico generated DNA methylation atlas that can be used for cell-type deconvolution of human tissues.
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6
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McCarrey JR, Cheng K. Germ cells: ENCODE's forgotten cell type. Biol Reprod 2021; 105:761-766. [PMID: 34250539 DOI: 10.1093/biolre/ioab135] [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: 03/04/2021] [Revised: 06/15/2021] [Accepted: 07/06/2021] [Indexed: 11/12/2022] Open
Abstract
More than a decade ago, the ENCODE and NIH Epigenomics Roadmap consortia organized large multi-laboratory efforts to profile the epigenomes of >110 different mammalian somatic cell types. This generated valuable publicly accessible datasets that are being mined to reveal genome-wide patterns of a variety of different epigenetic parameters. This consortia approach facilitated the powerful and comprehensive multiparametric integrative analysis of the epigenomes in each cell type. However, no germ cell types were included among the cell types characterized by either of these consortia. Thus, comprehensive epigenetic profiling data is not generally available for the most evolutionarily important cells, male and female germ cells. We discuss the need for reproductive biologists to generate similar multiparametric epigenomic profiling datasets for both male and female germ cells at different developmental stages, and summarize our recent effort to derive such data for mammalian spermatogonial stem cells and progenitor spermatogonia.
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Affiliation(s)
- John R McCarrey
- Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249 USA
| | - Keren Cheng
- Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249 USA
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7
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Wang J, Clay-Gilmour AI, Karaesmen E, Rizvi A, Zhu Q, Yan L, Preus L, Liu S, Wang Y, Griffiths E, Stram DO, Pooler L, Sheng X, Haiman C, Van Den Berg D, Webb A, Brock G, Spellman S, Pasquini M, McCarthy P, Allan J, Stölzel F, Onel K, Hahn T, Sucheston-Campbell LE. Genome-Wide Association Analyses Identify Variants in IRF4 Associated With Acute Myeloid Leukemia and Myelodysplastic Syndrome Susceptibility. Front Genet 2021; 12:554948. [PMID: 34220922 PMCID: PMC8248805 DOI: 10.3389/fgene.2021.554948] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 04/19/2021] [Indexed: 12/22/2022] Open
Abstract
The role of common genetic variation in susceptibility to acute myeloid leukemia (AML), and myelodysplastic syndrome (MDS), a group of rare clonal hematologic disorders characterized by dysplastic hematopoiesis and high mortality, remains unclear. We performed AML and MDS genome-wide association studies (GWAS) in the DISCOVeRY-BMT cohorts (2,309 cases and 2,814 controls). Association analysis based on subsets (ASSET) was used to conduct a summary statistics SNP-based analysis of MDS and AML subtypes. For each AML and MDS case and control we used PrediXcan to estimate the component of gene expression determined by their genetic profile and correlate this imputed gene expression level with risk of developing disease in a transcriptome-wide association study (TWAS). ASSET identified an increased risk for de novo AML and MDS (OR = 1.38, 95% CI, 1.26-1.51, Pmeta = 2.8 × 10-12) in patients carrying the T allele at s12203592 in Interferon Regulatory Factor 4 (IRF4), a transcription factor which regulates myeloid and lymphoid hematopoietic differentiation. Our TWAS analyses showed increased IRF4 gene expression is associated with increased risk of de novo AML and MDS (OR = 3.90, 95% CI, 2.36-6.44, Pmeta = 1.0 × 10-7). The identification of IRF4 by both GWAS and TWAS contributes valuable insight on the role of genetic variation in AML and MDS susceptibility.
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Affiliation(s)
- Junke Wang
- College of Pharmacy, The Ohio State University, Columbus, OH, United States
| | - Alyssa I. Clay-Gilmour
- Department of Epidemiology, Mayo Clinic, Rochester, MN, United States
- Department of Epidemiology & Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, United States
| | - Ezgi Karaesmen
- College of Pharmacy, The Ohio State University, Columbus, OH, United States
| | - Abbas Rizvi
- College of Pharmacy, The Ohio State University, Columbus, OH, United States
| | - Qianqian Zhu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Li Yan
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Leah Preus
- College of Pharmacy, The Ohio State University, Columbus, OH, United States
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Yiwen Wang
- College of Pharmacy, The Ohio State University, Columbus, OH, United States
| | - Elizabeth Griffiths
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Daniel O. Stram
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, United States
| | - Loreall Pooler
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, United States
| | - Xin Sheng
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, United States
| | - Christopher Haiman
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, United States
| | - David Van Den Berg
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, United States
| | - Amy Webb
- Department on Biomedical Informatics, The Ohio State University, Columbus, OH, United States
| | - Guy Brock
- Department on Biomedical Informatics, The Ohio State University, Columbus, OH, United States
| | - Stephen Spellman
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN, United States
| | - Marcelo Pasquini
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Philip McCarthy
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - James Allan
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Friedrich Stölzel
- Department of Internal Medicine I, University Hospital Carl Gustav Carus Dresden, Technical University Dresden, Dresden, Germany
| | - Kenan Onel
- Department of Pediatrics, Mount Sinai Medical Center, Miami Beach, NY, United States
| | - Theresa Hahn
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Lara E. Sucheston-Campbell
- College of Pharmacy, The Ohio State University, Columbus, OH, United States
- College of Veterinary Medicine, The Ohio State University, Columbus, OH, United States
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8
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McEwan AR, MacKenzie A. Perspective: Quality Versus Quantity; Is It Important to Assess the Role of Enhancers in Complex Disease from an In Vivo Perspective? Int J Mol Sci 2020; 21:E7856. [PMID: 33113946 PMCID: PMC7660172 DOI: 10.3390/ijms21217856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/15/2020] [Accepted: 10/20/2020] [Indexed: 12/18/2022] Open
Abstract
Sequencing of the human genome has permitted the development of genome-wide association studies (GWAS) to analyze the genetics of a number of complex disorders such as depression, anxiety and substance abuse. Thanks to their ability to analyze huge cohort sizes, these studies have successfully identified thousands of loci associated with a broad spectrum of complex diseases. Disconcertingly, the majority of these GWAS hits occur in non-coding regions of the genome, much of which controls the cell-type-specific expression of genes essential to health. In contrast to gene coding sequences, it is a challenge to understand the function of this non-coding regulatory genome using conventional biochemical techniques in cell lines. The current commentary scrutinizes the field of complex genetics from the standpoint of the large-scale whole-genome functional analysis of the promoters and cis-regulatory elements using chromatin markers. We contrast these large scale quantitative techniques against comparative genomics and in vivo analyses including CRISPR/CAS9 genome editing to determine the functional characteristics of these elements and to understand how polymorphic variation and epigenetic changes within these elements might contribute to complex disease and drug response. Most importantly, we suggest that, although the role of chromatin markers will continue to be important in identifying and characterizing enhancers, more emphasis must be placed on their analysis in relevant in-vivo models that take account of the appropriate cell-type-specific roles of these elements. It is hoped that offering these insights might refocus progress in analyzing the data tsunami of non-coding GWAS and whole-genome sequencing "hits" that threatens to overwhelm progress in the field.
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Affiliation(s)
| | - Alasdair MacKenzie
- School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, Foresterhill, University of Aberdeen, Aberdeen AB25 2ZD, UK;
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9
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Multiple functional variants in the IL1RL1 region are pretransplant markers for risk of GVHD and infection deaths. Blood Adv 2020; 3:2512-2524. [PMID: 31455667 DOI: 10.1182/bloodadvances.2019000075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 06/16/2019] [Indexed: 01/31/2023] Open
Abstract
Graft-versus-host disease (GVHD) and infections are the 2 main causes of death without relapse after allogeneic hematopoietic cell transplantation (HCT). Elevated soluble serum simulation-2 (sST2), the product of IL1RL1 in plasma/serum post-HCT, is a validated GVHD biomarker. Hundreds of SNPs at 2q12.1 have been shown to be strongly associated with sST2 concentrations in healthy populations. We therefore hypothesized that the donor genetic variants in IL1RL1 correlate with sST2 protein levels associated with patient survival outcomes after HCT. We used DISCOVeRY-BMT (Determining the Influence of Susceptibility Conveying Variants Related to 1-Year Mortality after Blood and Marrow Transplantation), a genomic study of >3000 donor-recipient pairs, to inform our hypothesis. We first measured pre-HCT plasma/serum sST2 levels in a subset of DISCOVeRY-BMT donors (n = 757) and tested the association of donor sST2 levels with donor single nucleotide polymorphisms (SNPs) in the 2q12.1 region. Donor SNPs associated with sST2 levels were then tested for association with recipient death caused by acute GVHD (aGVHD)-, infection-, and transplant-related mortality in cohorts 1 and 2. Meta-analyses of cohorts 1 and 2 were performed using fixed-effects inverse variance weighting, and P values were corrected for multiple comparisons. Donor risk alleles in rs22441131 (P meta = .00026) and rs2310241 (P meta = .00033) increased the cumulative incidence of aGVHD death up to fourfold and were associated with high sST2 levels. Donor risk alleles at rs4851601 (P meta = 9.7 × 10-7), rs13019803 (P meta = 8.9 × 10-6), and rs13015714 (P meta = 5.3 × 10-4) increased cumulative incidence of infection death to almost sevenfold and were associated with low sST2 levels. These functional variants are biomarkers of infection or aGVHD death and could facilitate donor selection, prophylaxis, and a conditioning regimen to reduce post-HCT mortality.
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10
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Hay EA, Cowie P, McEwan AR, Ross R, Pertwee RG, MacKenzie A. Disease-associated polymorphisms within the conserved ECR1 enhancer differentially regulate the tissue-specific activity of the cannabinoid-1 receptor gene promoter; implications for cannabinoid pharmacogenetics. Hum Mutat 2019; 41:291-298. [PMID: 31608546 PMCID: PMC6973010 DOI: 10.1002/humu.23931] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/19/2019] [Accepted: 09/26/2019] [Indexed: 12/14/2022]
Abstract
Cannabinoid receptor‐1 (CB1) represents a potential drug target against conditions that include obesity and substance abuse. However, drug trials targeting CB1 (encoded by the CNR1 gene) have been compromised by differences in patient response. Toward addressing the hypothesis that genetic changes within the regulatory regions controlling CNR1 expression contribute to these differences, we characterized the effects of disease‐associated allelic variation within a conserved regulatory sequence (ECR1) in CNR1 intron 2 that had previously been shown to modulate cannabinoid response, alcohol intake, and anxiety‐like behavior. We used primary cell analysis of reporters carrying different allelic variants of the human ECR1 and found that human‐specific C‐allele variants of ECR1 (ECR1(C)) drove higher levels of CNR1prom activity in primary hippocampal cells than did the ancestral T‐allele and demonstrated a differential response to CB1 agonism. We further demonstrate a role for the AP‐1 transcription factor in driving higher ECR1(C) activity and evidence that the ancestral t‐allele variant of ECR1 interacted with higher affinity with the insulator binding factor CTCF. The cell‐specific approaches used in our study represent an important step in gaining a mechanistic understanding of the roles of noncoding polymorphic variation in disease and in the increasingly important field of cannabinoid pharmacogenetics.
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Affiliation(s)
- Elizabeth A Hay
- School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, Foresterhill, University of Aberdeen, Aberdeen, UK
| | - Philip Cowie
- School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, Foresterhill, University of Aberdeen, Aberdeen, UK
| | - Andrew R McEwan
- School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, Foresterhill, University of Aberdeen, Aberdeen, UK
| | - Ruth Ross
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Roger G Pertwee
- School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, Foresterhill, University of Aberdeen, Aberdeen, UK
| | - Alasdair MacKenzie
- School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, Foresterhill, University of Aberdeen, Aberdeen, UK
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11
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Xia JH, Wei GH. Enhancer Dysfunction in 3D Genome and Disease. Cells 2019; 8:cells8101281. [PMID: 31635067 PMCID: PMC6830074 DOI: 10.3390/cells8101281] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/10/2019] [Accepted: 10/14/2019] [Indexed: 12/13/2022] Open
Abstract
Spatiotemporal patterns of gene expression depend on enhancer elements and other factors during individual development and disease progression. The rapid progress of high-throughput techniques has led to well-defined enhancer chromatin properties. Various genome-wide methods have revealed a large number of enhancers and the discovery of three-dimensional (3D) genome architecture showing the distant interacting mechanisms of enhancers that loop to target gene promoters. Whole genome sequencing projects directed at cancer have led to the discovery of substantial enhancer dysfunction in misregulating gene expression and in tumor initiation and progression. Results from genome-wide association studies (GWAS) combined with functional genomics analyses have elucidated the functional impacts of many cancer risk-associated variants that are enriched within the enhancer regions of chromatin. Risk variants dysregulate the expression of enhancer variant-associated genes via 3D genomic interactions. Moreover, these enhancer variants often alter the chromatin binding affinity for cancer-relevant transcription factors, which in turn leads to aberrant expression of the genes associated with cancer susceptibility. In this review, we investigate the extent to which these genetic regulatory circuits affect cancer predisposition and how the recent development of genome-editing methods have enabled the determination of the impacts of genomic variation and alteration on cancer phenotype, which will eventually lead to better management plans and treatment responses to human cancer in the clinic.
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Affiliation(s)
- Ji-Han Xia
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland.
| | - Gong-Hong Wei
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland.
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12
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van Steensel B, Furlong EEM. The role of transcription in shaping the spatial organization of the genome. Nat Rev Mol Cell Biol 2019; 20:327-337. [PMID: 30886333 PMCID: PMC7116054 DOI: 10.1038/s41580-019-0114-6] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The spatial organization of the genome into compartments and topologically associated domains can have an important role in the regulation of gene expression. But could gene expression conversely regulate genome organization? Here, we review recent studies that assessed the requirement of transcription and/or the transcription machinery for the establishment or maintenance of genome topology. The results reveal different requirements at different genomic scales. Transcription is generally not required for higher-level genome compartmentalization, has only moderate effects on domain organization and is not sufficient to create new domain boundaries. However, on a finer scale, transcripts or transcription does seem to have a role in the formation of subcompartments and subdomains and in stabilizing enhancer-promoter interactions. Recent evidence suggests a dynamic, reciprocal interplay between fine-scale genome organization and transcription, in which each is able to modulate or reinforce the activity of the other.
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Affiliation(s)
- Bas van Steensel
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands.
- Department of Cell Biology, Erasmus University Medical Centre, Rotterdam, Netherlands.
| | - Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
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13
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Li QL, Wang DY, Ju LG, Yao J, Gao C, Lei PJ, Li LY, Zhao XL, Wu M. The hyper-activation of transcriptional enhancers in breast cancer. Clin Epigenetics 2019; 11:48. [PMID: 30867030 PMCID: PMC6417266 DOI: 10.1186/s13148-019-0645-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 03/01/2019] [Indexed: 12/25/2022] Open
Abstract
Background Activation of transcription enhancers, especially super-enhancers, is one of the critical epigenetic features of tumorigenesis. However, very few studies have systematically identified the enhancers specific in cancer tissues. Methods Here, we studied the change of histone modifications in MMTV-PyVT breast cancer model, combining mass spectrometry-based proteomics and ChIP-seq-based epigenomics approaches. Some of the proteomic results were confirmed with western blotting and IHC staining. An inhibitor of H3K27ac was applied to study its effect on cancer development. Results H3K27ac and H4K8ac are elevated in cancer, which was confirmed in patient tissue chips. ChIP-seq revealed that H4K8ac is co-localized with H3K27ac on chromatin, especially on distal enhancers. Epigenomic studies further identified a subgroup of super-enhancers marked by H3K4me3 peaks in the intergenic regions. The H3K4me3-enriched regions enhancers are associated with higher level of H3K27ac and H4K8ac compared with the average level of conventional super-enhancers and are associated with higher transcription level of their adjacent genes. We identified 148 H3K4me3-enriched super-enhancers with higher gene expression in tumor, which may be critical for breast cancer. One inhibitor for p300 and H3K27ac, C646, repressed tumor formation probably through inhibiting Vegfa and other genes. Conclusions Taken together, our work identifies novel regulators and provides important resource to the genome-wide enhancer studies in breast cancer and raises the possibility of cancer treatment through modulating enhancer activity. Electronic supplementary material The online version of this article (10.1186/s13148-019-0645-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qing-Lan Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China.,Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, Wuhan University, Wuhan, 430072, Hubei, China
| | - Dan-Ya Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Lin-Gao Ju
- Department of Urology, Zhongnan Hospital, Wuhan University, Wuhan, 430072, Hubei, China
| | - Jie Yao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China.,Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, Wuhan University, Wuhan, 430072, Hubei, China
| | - Chuan Gao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China.,Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, Wuhan University, Wuhan, 430072, Hubei, China
| | - Pin-Ji Lei
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China.,Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, Wuhan University, Wuhan, 430072, Hubei, China
| | - Lian-Yun Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China.,Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, Wuhan University, Wuhan, 430072, Hubei, China
| | - Xiao-Lu Zhao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China.
| | - Min Wu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China. .,Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Enteropathy, Wuhan University, Wuhan, 430072, Hubei, China.
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14
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Panigrahi AK, Foulds CE, Lanz RB, Hamilton RA, Yi P, Lonard DM, Tsai MJ, Tsai SY, O'Malley BW. SRC-3 Coactivator Governs Dynamic Estrogen-Induced Chromatin Looping Interactions during Transcription. Mol Cell 2019; 70:679-694.e7. [PMID: 29775582 DOI: 10.1016/j.molcel.2018.04.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 02/15/2018] [Accepted: 04/18/2018] [Indexed: 01/09/2023]
Abstract
Enhancers are thought to activate transcription by physically contacting promoters via looping. However, direct assays demonstrating these contacts are required to mechanistically verify such cellular determinants of enhancer function. Here, we present versatile cell-free assays to further determine the role of enhancer-promoter contacts (EPCs). We demonstrate that EPC is linked to mutually stimulatory transcription at the enhancer and promoter in vitro. SRC-3 was identified as a critical looping determinant for the estradiol-(E2)-regulated GREB1 locus. Surprisingly, the GREB1 enhancer and promoter contact two internal gene body SRC-3 binding sites, GBS1 and GBS2, which stimulate their transcription. Utilizing time-course 3C assays, we uncovered SRC-3-dependent dynamic chromatin interactions involving the enhancer, promoter, GBS1, and GBS2. Collectively, these data suggest that the enhancer and promoter remain "poised" for transcription via their contacts with GBS1 and GBS2. Upon E2 induction, GBS1 and GBS2 disengage from the enhancer, allowing direct EPC for active transcription.
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Affiliation(s)
- Anil K Panigrahi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Charles E Foulds
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Center for Precision Environmental Health, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Rainer B Lanz
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Ross A Hamilton
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Ping Yi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - David M Lonard
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Ming-Jer Tsai
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Sophia Y Tsai
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
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15
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Booth KT, Azaiez H, Jahan I, Smith RJH, Fritzsch B. Intracellular Regulome Variability Along the Organ of Corti: Evidence, Approaches, Challenges, and Perspective. Front Genet 2018; 9:156. [PMID: 29868110 PMCID: PMC5951964 DOI: 10.3389/fgene.2018.00156] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/13/2018] [Indexed: 12/13/2022] Open
Abstract
The mammalian hearing organ is a regular array of two types of hair cells (HCs) surrounded by six types of supporting cells. Along the tonotopic axis, this conserved radial array of cell types shows longitudinal variations to enhance the tuning properties of basilar membrane. We present the current evidence supporting the hypothesis that quantitative local variations in gene expression profiles are responsible for local cell responses to global gene manipulations. With the advent of next generation sequencing and the unprecedented array of technologies offering high throughput analyses at the single cell level, transcriptomics will become a common tool to enhance our understanding of the inner ear. We provide an overview of the approaches and landmark studies undertaken to date to analyze single cell variations in the organ of Corti and discuss the current limitations. We next provide an overview of the complexity of known regulatory mechanisms in the inner ear. These mechanisms are tightly regulated temporally and spatially at the transcription, RNA-splicing, mRNA-regulation, and translation levels. Understanding the intricacies of regulatory mechanisms at play in the inner ear will require the use of complementary approaches, and most probably, a combinatorial strategy coupling transcriptomics, proteomics, and epigenomics technologies. We highlight how these data, in conjunction with recent insights into molecular cell transformation, can advance attempts to restore lost hair cells.
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Affiliation(s)
- Kevin T Booth
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa, Iowa City, IA, United States.,Interdisciplinary Graduate Program in Molecular Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Hela Azaiez
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa, Iowa City, IA, United States
| | - Israt Jahan
- Department of Biology, University of Iowa, Iowa City, IA, United States
| | - Richard J H Smith
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa, Iowa City, IA, United States
| | - Bernd Fritzsch
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa, Iowa City, IA, United States.,Department of Biology, University of Iowa, Iowa City, IA, United States
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16
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Huang D, Wang Y, Tang J, Luo S. Molecular mechanisms of suppressor of fused in regulating the hedgehog signalling pathway. Oncol Lett 2018; 15:6077-6086. [PMID: 29725392 DOI: 10.3892/ol.2018.8142] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 10/17/2017] [Indexed: 02/07/2023] Open
Abstract
Highly conserved throughout evolution, the hedgehog (Hh) signalling pathway has been demonstrated to be involved in embryonic development, stem cell maintenance and tissue homeostasis in animals ranging from invertebrates to vertebrates. In the human body, a variety of cancer types are associated with the aberrantly activated Hh signalling pathway. Multiple studies have revealed suppressor of fused (Sufu) as a key negative regulator of this signalling pathway. In vertebrates, Sufu primarily functions as a tumor suppressor factor by interacting with and inhibiting glioma-associated oncogene homologues (GLIs), which are the terminal transcription factors of the Hh signalling pathway and belong to the Kruppel family of zinc finger proteins; by contrast, the regulation of Sufu itself remains relatively unclear. In the present review article, we focus on the effects of Sufu on the Hh signalling pathway in tumourigenesis and the molecular mechanisms underlying the regulation of GLI by Sufu. In addition, the factors modulating the activity of Sufu at post-transcriptional levels are also discussed.
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Affiliation(s)
- Dengliang Huang
- Center for Experimental Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China.,Jiangxi Key Laboratory of Molecular Diagnostics and Precision Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Yiting Wang
- Center for Experimental Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China.,Jiangxi Key Laboratory of Molecular Diagnostics and Precision Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Jiabin Tang
- Center for Experimental Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Shiwen Luo
- Center for Experimental Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China.,Jiangxi Key Laboratory of Molecular Diagnostics and Precision Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
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17
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Sancisi V, Manzotti G, Gugnoni M, Rossi T, Gandolfi G, Gobbi G, Torricelli F, Catellani F, Faria do Valle I, Remondini D, Castellani G, Ragazzi M, Piana S, Ciarrocchi A. RUNX2 expression in thyroid and breast cancer requires the cooperation of three non-redundant enhancers under the control of BRD4 and c-JUN. Nucleic Acids Res 2017; 45:11249-11267. [PMID: 28981843 PMCID: PMC5737559 DOI: 10.1093/nar/gkx802] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 08/30/2017] [Indexed: 12/14/2022] Open
Abstract
Aberrant reactivation of embryonic pathways is a common feature of cancer. RUNX2 is a transcription factor crucial during embryogenesis that is aberrantly reactivated in many tumors, including thyroid and breast cancer, where it promotes aggressiveness and metastatic spreading. Currently, the mechanisms driving RUNX2 expression in cancer are still largely unknown. Here we showed that RUNX2 transcription in thyroid and breast cancer requires the cooperation of three distantly located enhancers (ENHs) brought together by chromatin three-dimensional looping. We showed that BRD4 controls RUNX2 by binding to the newly identified ENHs and we demonstrated that the anti-proliferative effects of bromodomain inhibitors (BETi) is associated with RUNX2 transcriptional repression. We demonstrated that each RUNX2 ENH is potentially controlled by a distinct set of TFs and we identified c-JUN as the principal pivot of this regulatory platform. We also observed that accumulation of genetic mutations within these elements correlates with metastatic behavior in human thyroid tumors. Finally, we identified RAINs, a novel family of ENH-associated long non-coding RNAs, transcribed from the identified RUNX2 regulatory unit. Our data provide a new model to explain how RUNX2 expression is reactivated in thyroid and breast cancer and how cancer-driving signaling pathways converge on the regulation of this gene.
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Affiliation(s)
- Valentina Sancisi
- Laboratory of Translational Research, Azienda USL Reggio Emilia - IRCCS, Reggio Emilia, Italy
| | - Gloria Manzotti
- Laboratory of Translational Research, Azienda USL Reggio Emilia - IRCCS, Reggio Emilia, Italy
| | - Mila Gugnoni
- Laboratory of Translational Research, Azienda USL Reggio Emilia - IRCCS, Reggio Emilia, Italy
| | - Teresa Rossi
- Laboratory of Translational Research, Azienda USL Reggio Emilia - IRCCS, Reggio Emilia, Italy
| | - Greta Gandolfi
- Laboratory of Translational Research, Azienda USL Reggio Emilia - IRCCS, Reggio Emilia, Italy
| | - Giulia Gobbi
- Laboratory of Translational Research, Azienda USL Reggio Emilia - IRCCS, Reggio Emilia, Italy
| | - Federica Torricelli
- Laboratory of Translational Research, Azienda USL Reggio Emilia - IRCCS, Reggio Emilia, Italy
| | - Francesca Catellani
- Laboratory of Translational Research, Azienda USL Reggio Emilia - IRCCS, Reggio Emilia, Italy
| | | | - Daniel Remondini
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Gastone Castellani
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Moira Ragazzi
- Pathology Unit, Azienda USL Reggio Emilia - IRCCS, Reggio Emilia, Italy
| | - Simonetta Piana
- Pathology Unit, Azienda USL Reggio Emilia - IRCCS, Reggio Emilia, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda USL Reggio Emilia - IRCCS, Reggio Emilia, Italy
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18
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Rosa-Garrido M, Chapski DJ, Schmitt AD, Kimball TH, Karbassi E, Monte E, Balderas E, Pellegrini M, Shih TT, Soehalim E, Liem D, Ping P, Galjart NJ, Ren S, Wang Y, Ren B, Vondriska TM. High-Resolution Mapping of Chromatin Conformation in Cardiac Myocytes Reveals Structural Remodeling of the Epigenome in Heart Failure. Circulation 2017; 136:1613-1625. [PMID: 28802249 PMCID: PMC5648689 DOI: 10.1161/circulationaha.117.029430] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 07/31/2017] [Indexed: 01/01/2023]
Abstract
BACKGROUND Cardiovascular disease is associated with epigenomic changes in the heart; however, the endogenous structure of cardiac myocyte chromatin has never been determined. METHODS To investigate the mechanisms of epigenomic function in the heart, genome-wide chromatin conformation capture (Hi-C) and DNA sequencing were performed in adult cardiac myocytes following development of pressure overload-induced hypertrophy. Mice with cardiac-specific deletion of CTCF (a ubiquitous chromatin structural protein) were generated to explore the role of this protein in chromatin structure and cardiac phenotype. Transcriptome analyses by RNA-seq were conducted as a functional readout of the epigenomic structural changes. RESULTS Depletion of CTCF was sufficient to induce heart failure in mice, and human patients with heart failure receiving mechanical unloading via left ventricular assist devices show increased CTCF abundance. Chromatin structural analyses revealed interactions within the cardiac myocyte genome at 5-kb resolution, enabling examination of intra- and interchromosomal events, and providing a resource for future cardiac epigenomic investigations. Pressure overload or CTCF depletion selectively altered boundary strength between topologically associating domains and A/B compartmentalization, measurements of genome accessibility. Heart failure involved decreased stability of chromatin interactions around disease-causing genes. In addition, pressure overload or CTCF depletion remodeled long-range interactions of cardiac enhancers, resulting in a significant decrease in local chromatin interactions around these functional elements. CONCLUSIONS These findings provide a high-resolution chromatin architecture resource for cardiac epigenomic investigations and demonstrate that global structural remodeling of chromatin underpins heart failure. The newly identified principles of endogenous chromatin structure have key implications for epigenetic therapy.
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Affiliation(s)
- Manuel Rosa-Garrido
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Douglas J Chapski
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Anthony D Schmitt
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Todd H Kimball
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Elaheh Karbassi
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Emma Monte
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Enrique Balderas
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Matteo Pellegrini
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Tsai-Ting Shih
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Elizabeth Soehalim
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - David Liem
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Peipei Ping
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Niels J Galjart
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Shuxun Ren
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Yibin Wang
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Bing Ren
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.)
| | - Thomas M Vondriska
- From Departments of Anesthesiology and Perioperative Medicine (M.R.-G., D.J.C., T.H.K., E.K., E.M., T.-T.S., E.S., S.R., Y.W., T.M.V.), Medicine (D.L., P.P., Y.W., T.M.V.), Physiology (P.P.,Y.W., T.M.V.), Molecular, Cellular and Developmental Biology (M.P.), UCLA, Los Angeles, CA; Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City (E.B.); Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, UCSD, San Diego, CA (A.D.S., B.R.); and Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands (N.J.G.).
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19
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Affiliation(s)
- David Gurwitz
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, 69978, Israel
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20
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Connected Gene Communities Underlie Transcriptional Changes in Cornelia de Lange Syndrome. Genetics 2017; 207:139-151. [PMID: 28679547 DOI: 10.1534/genetics.117.202291] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/28/2017] [Indexed: 12/25/2022] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a complex multisystem developmental disorder caused by mutations in cohesin subunits and regulators. While its precise molecular mechanisms are not well defined, they point toward a global deregulation of the transcriptional gene expression program. Cohesin is associated with the boundaries of chromosome domains and with enhancer and promoter regions connecting the three-dimensional genome organization with transcriptional regulation. Here, we show that connected gene communities, structures emerging from the interactions of noncoding regulatory elements and genes in the three-dimensional chromosomal space, provide a molecular explanation for the pathoetiology of CdLS associated with mutations in the cohesin-loading factor NIPBL and the cohesin subunit SMC1A NIPBL and cohesin are important constituents of connected gene communities that are centrally positioned at noncoding regulatory elements. Accordingly, genes deregulated in CdLS are positioned within reach of NIPBL- and cohesin-occupied regions through promoter-promoter interactions. Our findings suggest a dynamic model where NIPBL loads cohesin to connect genes in communities, offering an explanation for the gene expression deregulation in the CdLS.
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Delker RK, Mann RS. From Reductionism to Holism: Toward a More Complete View of Development Through Genome Engineering. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1016:45-74. [PMID: 29130153 PMCID: PMC6935049 DOI: 10.1007/978-3-319-63904-8_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Paradigm shifts in science are often coupled to technological advances. New techniques offer new roads of discovery; but, more than this, they shape the way scientists approach questions. Developmental biology exemplifies this idea both in its past and present. The rise of molecular biology and genetics in the late twentieth century shifted the focus from the anatomical to the molecular, nudging the underlying philosophy from holism to reductionism. Developmental biology is currently experiencing yet another transformation triggered by '-omics' technology and propelled forward by CRISPR genome engineering (GE). Together, these technologies are helping to reawaken a holistic approach to development. Herein, we focus on CRISPR GE and its potential to reveal principles of development at the level of the genome, the epigenome, and the cell. Within each stage we illustrate how GE can move past pure reductionism and embrace holism, ultimately delivering a more complete view of development.
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Affiliation(s)
- Rebecca K Delker
- Department of Biochemistry and Molecular Biophysics and Systems Biology, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, 612 West 130th Street, 9th Floor, New York, NY, 10027, USA.
| | - Richard S Mann
- Department of Biochemistry and Molecular Biophysics and Systems Biology, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, 612 West 130th Street, 9th Floor, New York, NY, 10027, USA
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