51
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Boyd M, Thodberg M, Vitezic M, Bornholdt J, Vitting-Seerup K, Chen Y, Coskun M, Li Y, Lo BZS, Klausen P, Jan Schweiger P, Pedersen AG, Rapin N, Skovgaard K, Dahlgaard K, Andersson R, Terkelsen TB, Lilje B, Troelsen JT, Petersen AM, Jensen KB, Gögenur I, Thielsen P, Seidelin JB, Nielsen OH, Bjerrum JT, Sandelin A. Characterization of the enhancer and promoter landscape of inflammatory bowel disease from human colon biopsies. Nat Commun 2018; 9:1661. [PMID: 29695774 PMCID: PMC5916929 DOI: 10.1038/s41467-018-03766-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 03/12/2018] [Indexed: 02/08/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic intestinal disorder, with two main types: Crohn’s disease (CD) and ulcerative colitis (UC), whose molecular pathology is not well understood. The majority of IBD-associated SNPs are located in non-coding regions and are hard to characterize since regulatory regions in IBD are not known. Here we profile transcription start sites (TSSs) and enhancers in the descending colon of 94 IBD patients and controls. IBD-upregulated promoters and enhancers are highly enriched for IBD-associated SNPs and are bound by the same transcription factors. IBD-specific TSSs are associated to genes with roles in both inflammatory cascades and gut epithelia while TSSs distinguishing UC and CD are associated to gut epithelia functions. We find that as few as 35 TSSs can distinguish active CD, UC, and controls with 85% accuracy in an independent cohort. Our data constitute a foundation for understanding the molecular pathology, gene regulation, and genetics of IBD. Many SNPs associated with inflammatory bowel disease are located in non-coding genomic regions. Here, the authors perform CAGE-sequencing on descending colon biopsies of Crohn’s disease and ulcerative colitis patients to map transcription start sites and enhancer activity for analysis of regulatory regions.
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Affiliation(s)
- Mette Boyd
- Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Malte Thodberg
- Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Morana Vitezic
- Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Jette Bornholdt
- Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Kristoffer Vitting-Seerup
- Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Yun Chen
- Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Mehmet Coskun
- Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Yuan Li
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, 2730, Herlev, Denmark
| | - Bobby Zhao Sheng Lo
- Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen N, Denmark.,Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, 2730, Herlev, Denmark
| | - Pia Klausen
- Department of Gastroenterology, Surgical Section, Herlev Hospital, 2730, Herlev, Denmark
| | - Pawel Jan Schweiger
- Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen N, Denmark
| | | | - Nicolas Rapin
- Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen N, Denmark.,The Finsen Laboratory, Rigshospitalet, University of Copenhagen, 2200, Copenhagen N, Denmark.,Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Kerstin Skovgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Katja Dahlgaard
- Department of Science and Environment (INM), Roskilde University, 4000, Roskilde, Denmark
| | - Robin Andersson
- Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Thilde Bagger Terkelsen
- Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Berit Lilje
- Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen N, Denmark
| | | | - Andreas Munk Petersen
- Hvidovre Hospital, Gastrounit Medical Division, University of Copenhagen, 2650, Hvidovre, Denmark.,Hvidovre Hospital, Department of Clinical Microbiology, University of Copenhagen, 2650, Hvidovre, Denmark
| | - Kim Bak Jensen
- Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen N, Denmark.,Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Ismail Gögenur
- Centre for Surgical Science, Department of Surgery, Zealand University Hospital, 4600, Koege, Denmark
| | - Peter Thielsen
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, 2730, Herlev, Denmark
| | - Jakob Benedict Seidelin
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, 2730, Herlev, Denmark
| | - Ole Haagen Nielsen
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, 2730, Herlev, Denmark
| | - Jacob Tveiten Bjerrum
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, 2730, Herlev, Denmark.
| | - Albin Sandelin
- Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark. .,Biotech Research and Innovation Centre, University of Copenhagen, 2200, Copenhagen N, Denmark.
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52
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Gao WW, Xiao RQ, Zhang WJ, Hu YR, Peng BL, Li WJ, He YH, Shen HF, Ding JC, Huang QX, Ye TY, Li Y, Liu ZY, Ding R, Rosenfeld MG, Liu W. JMJD6 Licenses ERα-Dependent Enhancer and Coding Gene Activation by Modulating the Recruitment of the CARM1/MED12 Co-activator Complex. Mol Cell 2018; 70:340-357.e8. [PMID: 29628309 PMCID: PMC6258263 DOI: 10.1016/j.molcel.2018.03.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 02/12/2018] [Accepted: 03/02/2018] [Indexed: 12/18/2022]
Abstract
Whereas the actions of enhancers in gene transcriptional regulation are well established, roles of JmjC-domain-containing proteins in mediating enhancer activation remain poorly understood. Here, we report that recruitment of the JmjC-domain-containing protein 6 (JMJD6) to estrogen receptor alpha (ERα)-bound active enhancers is required for RNA polymerase II recruitment and enhancer RNA production on enhancers, resulting in transcriptional pause release of cognate estrogen target genes. JMJD6 is found to interact with MED12 in the mediator complex to regulate its recruitment. Unexpectedly, JMJD6 is necessary for MED12 to interact with CARM1, which methylates MED12 at multiple arginine sites and regulates its chromatin binding. Consistent with its role in transcriptional activation, JMJD6 is required for estrogen/ERα-induced breast cancer cell growth and tumorigenesis. Our data have uncovered a critical regulator of estrogen/ERα-induced enhancer coding gene activation and breast cancer cell potency, providing a potential therapeutic target of ER-positive breast cancers.
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Affiliation(s)
- Wei-Wei Gao
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Rong-Quan Xiao
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Wen-Juan Zhang
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Yi-Ren Hu
- Howard Hughes Medical Institute, Department of Medicine, School of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Bing-Ling Peng
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Wen-Juan Li
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Yao-Hui He
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Hai-Feng Shen
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Jian-Cheng Ding
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Qi-Xuan Huang
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Tian-Yi Ye
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Ying Li
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Zhi-Ying Liu
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Rong Ding
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, Department of Medicine, School of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Wen Liu
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China; State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China.
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53
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Hayashi T, Ozaki H, Sasagawa Y, Umeda M, Danno H, Nikaido I. Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs. Nat Commun 2018; 9:619. [PMID: 29434199 PMCID: PMC5809388 DOI: 10.1038/s41467-018-02866-0] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 01/05/2018] [Indexed: 01/06/2023] Open
Abstract
Total RNA sequencing has been used to reveal poly(A) and non-poly(A) RNA expression, RNA processing and enhancer activity. To date, no method for full-length total RNA sequencing of single cells has been developed despite the potential of this technology for single-cell biology. Here we describe random displacement amplification sequencing (RamDA-seq), the first full-length total RNA-sequencing method for single cells. Compared with other methods, RamDA-seq shows high sensitivity to non-poly(A) RNA and near-complete full-length transcript coverage. Using RamDA-seq with differentiation time course samples of mouse embryonic stem cells, we reveal hundreds of dynamically regulated non-poly(A) transcripts, including histone transcripts and long noncoding RNA Neat1. Moreover, RamDA-seq profiles recursive splicing in >300-kb introns. RamDA-seq also detects enhancer RNAs and their cell type-specific activity in single cells. Taken together, we demonstrate that RamDA-seq could help investigate the dynamics of gene expression, RNA-processing events and transcriptional regulation in single cells.
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Affiliation(s)
- Tetsutaro Hayashi
- Bioinformatics Research Unit, Advanced Center for Computing and Communication, RIKEN, 2-1 Hirosawa Wako, Saitama, 351-0198, Japan
| | - Haruka Ozaki
- Bioinformatics Research Unit, Advanced Center for Computing and Communication, RIKEN, 2-1 Hirosawa Wako, Saitama, 351-0198, Japan
| | - Yohei Sasagawa
- Bioinformatics Research Unit, Advanced Center for Computing and Communication, RIKEN, 2-1 Hirosawa Wako, Saitama, 351-0198, Japan
| | - Mana Umeda
- Bioinformatics Research Unit, Advanced Center for Computing and Communication, RIKEN, 2-1 Hirosawa Wako, Saitama, 351-0198, Japan
| | - Hiroki Danno
- Bioinformatics Research Unit, Advanced Center for Computing and Communication, RIKEN, 2-1 Hirosawa Wako, Saitama, 351-0198, Japan
| | - Itoshi Nikaido
- Bioinformatics Research Unit, Advanced Center for Computing and Communication, RIKEN, 2-1 Hirosawa Wako, Saitama, 351-0198, Japan.
- Single-cell Omics Research Unit, Center for RIKEN Center for Developmental Biology, RIKEN, 2-1 Hirosawa Wako, Saitama, 351-0198, Japan.
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54
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Mikhaylichenko O, Bondarenko V, Harnett D, Schor IE, Males M, Viales RR, Furlong EEM. The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription. Genes Dev 2018; 32:42-57. [PMID: 29378788 PMCID: PMC5828394 DOI: 10.1101/gad.308619.117] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 12/21/2017] [Indexed: 12/03/2022]
Abstract
Here, Mikhaylichenko et al. investigate the transcriptional properties of enhancers during Drosophila embryogenesis using characterized developmental enhancers. The authors demonstrate that while the timing of enhancer transcription is correlated with enhancer activity, the levels and directionality of transcription are highly varied among active enhancers and conclude that this is likely an inherent sequence property of the elements themselves. Gene expression is regulated by promoters, which initiate transcription, and enhancers, which control their temporal and spatial activity. However, the discovery that mammalian enhancers also initiate transcription questions the inherent differences between enhancers and promoters. Here, we investigate the transcriptional properties of enhancers during Drosophila embryogenesis using characterized developmental enhancers. We show that while the timing of enhancer transcription is generally correlated with enhancer activity, the levels and directionality of transcription are highly varied among active enhancers. To assess how this impacts function, we developed a dual transgenic assay to simultaneously measure enhancer and promoter activities from a single element in the same embryo. Extensive transgenic analysis revealed a relationship between the direction of endogenous transcription and the ability to function as an enhancer or promoter in vivo, although enhancer RNA (eRNA) production and activity are not always strictly coupled. Some enhancers (mainly bidirectional) can act as weak promoters, producing overlapping spatio–temporal expression. Conversely, bidirectional promoters often act as strong enhancers, while unidirectional promoters generally cannot. The balance between enhancer and promoter activity is generally reflected in the levels and directionality of eRNA transcription and is likely an inherent sequence property of the elements themselves.
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Affiliation(s)
- Olga Mikhaylichenko
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
| | - Vladyslav Bondarenko
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
| | - Dermot Harnett
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
| | - Ignacio E Schor
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
| | - Matilda Males
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
| | - Rebecca R Viales
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
| | - Eileen E M Furlong
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
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55
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Bidirectional transcription initiation marks accessible chromatin and is not specific to enhancers. Genome Biol 2017; 18:242. [PMID: 29284524 PMCID: PMC5747114 DOI: 10.1186/s13059-017-1379-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 12/12/2017] [Indexed: 01/12/2023] Open
Abstract
Background Enhancers are modular regulatory elements that are central to the spatial and temporal regulation of gene expression. Bidirectional transcription initiating at enhancers has been proposed to mark active enhancers and as such has been utilized to experimentally identify active enhancers de novo. Results Here, we show that bidirectional transcription initiation is a pervasive feature of accessible chromatin, including at enhancers, promoters, and other DNase hypersensitive regions not marked with canonical histone modification profiles. Transcription is less predictive for enhancer activity than epigenetic modifications such as H3K4me1 or the accessibility of DNA when measured both in enhancer assays and at endogenous loci. The stability of enhancer initiated transcripts does not influence measures of enhancer activity and we cannot detect evidence of purifying selection on the resulting enhancer RNAs within the human population. Conclusions Our results indicate that bidirectional transcription initiation from accessible chromatin is not sufficient for, nor specific to, enhancer activity. Transcription initiating at enhancers may be a frequent by-product of promiscuous RNA polymerase initiation at accessible chromatin and is unlikely to generally play a functional role in enhancer activity. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1379-8) contains supplementary material, which is available to authorized users.
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56
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Yang XH, Nadadur RD, Hilvering CR, Bianchi V, Werner M, Mazurek SR, Gadek M, Shen KM, Goldman JA, Tyan L, Bekeny J, Hall JM, Lee N, Perez-Cervantes C, Burnicka-Turek O, Poss KD, Weber CR, de Laat W, Ruthenburg AJ, Moskowitz IP. Transcription-factor-dependent enhancer transcription defines a gene regulatory network for cardiac rhythm. eLife 2017; 6:31683. [PMID: 29280435 PMCID: PMC5745077 DOI: 10.7554/elife.31683] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 12/02/2017] [Indexed: 12/28/2022] Open
Abstract
The noncoding genome is pervasively transcribed. Noncoding RNAs (ncRNAs) generated from enhancers have been proposed as a general facet of enhancer function and some have been shown to be required for enhancer activity. Here we examine the transcription-factor-(TF)-dependence of ncRNA expression to define enhancers and enhancer-associated ncRNAs that are involved in a TF-dependent regulatory network. TBX5, a cardiac TF, regulates a network of cardiac channel genes to maintain cardiac rhythm. We deep sequenced wildtype and Tbx5-mutant mouse atria, identifying ~2600 novel Tbx5-dependent ncRNAs. Tbx5-dependent ncRNAs were enriched for tissue-specific marks of active enhancers genome-wide. Tbx5-dependent ncRNAs emanated from regions that are enriched for TBX5-binding and that demonstrated Tbx5-dependent enhancer activity. Tbx5-dependent ncRNA transcription provided a quantitative metric of Tbx5-dependent enhancer activity, correlating with target gene expression. We identified RACER, a novel Tbx5-dependent long noncoding RNA (lncRNA) required for the expression of the calcium-handling gene Ryr2. We illustrate that TF-dependent enhancer transcription can illuminate components of TF-dependent gene regulatory networks.
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Affiliation(s)
- Xinan H Yang
- Department of Pediatrics, The University of Chicago, Chicago, United States.,Department of Pathology, The University of Chicago, Chicago, United States.,Department of Human Genetics, The University of Chicago, Chicago, United States
| | - Rangarajan D Nadadur
- Department of Pediatrics, The University of Chicago, Chicago, United States.,Department of Pathology, The University of Chicago, Chicago, United States.,Department of Human Genetics, The University of Chicago, Chicago, United States
| | - Catharina Re Hilvering
- Hubrecht Institute-Koninklijke Nederlandse Akademie van Wetenschappen, University Medical Center Utrecht, Uppsalalaan, Netherlands
| | - Valerio Bianchi
- Hubrecht Institute-Koninklijke Nederlandse Akademie van Wetenschappen, University Medical Center Utrecht, Uppsalalaan, Netherlands
| | - Michael Werner
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States.,Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, United States
| | - Stefan R Mazurek
- Department of Pediatrics, The University of Chicago, Chicago, United States.,Department of Pathology, The University of Chicago, Chicago, United States.,Department of Human Genetics, The University of Chicago, Chicago, United States
| | - Margaret Gadek
- Department of Pediatrics, The University of Chicago, Chicago, United States.,Department of Pathology, The University of Chicago, Chicago, United States.,Department of Human Genetics, The University of Chicago, Chicago, United States
| | - Kaitlyn M Shen
- Department of Pediatrics, The University of Chicago, Chicago, United States.,Department of Pathology, The University of Chicago, Chicago, United States.,Department of Human Genetics, The University of Chicago, Chicago, United States
| | - Joseph Aaron Goldman
- Department of Cell Biology, Duke University School of Medicine, Durham, United States.,Regeneration Next, Duke University, Durham, United States
| | - Leonid Tyan
- Department of Pediatrics, The University of Chicago, Chicago, United States.,Department of Pathology, The University of Chicago, Chicago, United States.,Department of Human Genetics, The University of Chicago, Chicago, United States
| | - Jenna Bekeny
- Department of Pediatrics, The University of Chicago, Chicago, United States.,Department of Pathology, The University of Chicago, Chicago, United States.,Department of Human Genetics, The University of Chicago, Chicago, United States
| | - Johnathon M Hall
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States.,Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, United States
| | - Nutishia Lee
- Department of Cell Biology, Duke University School of Medicine, Durham, United States
| | - Carlos Perez-Cervantes
- Department of Pediatrics, The University of Chicago, Chicago, United States.,Department of Pathology, The University of Chicago, Chicago, United States.,Department of Human Genetics, The University of Chicago, Chicago, United States
| | - Ozanna Burnicka-Turek
- Department of Pediatrics, The University of Chicago, Chicago, United States.,Department of Pathology, The University of Chicago, Chicago, United States.,Department of Human Genetics, The University of Chicago, Chicago, United States
| | - Kenneth D Poss
- Department of Cell Biology, Duke University School of Medicine, Durham, United States.,Regeneration Next, Duke University, Durham, United States
| | - Christopher R Weber
- Department of Pediatrics, The University of Chicago, Chicago, United States.,Department of Pathology, The University of Chicago, Chicago, United States.,Department of Human Genetics, The University of Chicago, Chicago, United States
| | - Wouter de Laat
- Hubrecht Institute-Koninklijke Nederlandse Akademie van Wetenschappen, University Medical Center Utrecht, Uppsalalaan, Netherlands
| | - Alexander J Ruthenburg
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, United States.,Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, United States
| | - Ivan P Moskowitz
- Department of Pediatrics, The University of Chicago, Chicago, United States.,Department of Pathology, The University of Chicago, Chicago, United States.,Department of Human Genetics, The University of Chicago, Chicago, United States
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57
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Wang AH, Juan AH, Ko KD, Tsai PF, Zare H, Dell'Orso S, Sartorelli V. The Elongation Factor Spt6 Maintains ESC Pluripotency by Controlling Super-Enhancers and Counteracting Polycomb Proteins. Mol Cell 2017; 68:398-413.e6. [PMID: 29033324 DOI: 10.1016/j.molcel.2017.09.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/23/2017] [Accepted: 09/12/2017] [Indexed: 01/07/2023]
Abstract
Spt6 coordinates nucleosome dis- and re-assembly, transcriptional elongation, and mRNA processing. Here, we report that depleting Spt6 in embryonic stem cells (ESCs) reduced expression of pluripotency factors, increased expression of cell-lineage-affiliated developmental regulators, and induced cell morphological and biochemical changes indicative of ESC differentiation. Selective downregulation of pluripotency factors upon Spt6 depletion may be mechanistically explained by its enrichment at ESC super-enhancers, where Spt6 controls histone H3K27 acetylation and methylation and super-enhancer RNA transcription. In ESCs, Spt6 interacted with the PRC2 core subunit Suz12 and prevented H3K27me3 accumulation at ESC super-enhancers and associated promoters. Biochemical as well as functional experiments revealed that Spt6 could compete for binding of the PRC2 methyltransferase Ezh2 to Suz12 and reduce PRC2 chromatin engagement. Thus, in addition to serving as a histone chaperone and transcription elongation factor, Spt6 counteracts repression by opposing H3K27me3 deposition at critical genomic regulatory regions.
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Affiliation(s)
- A Hongjun Wang
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20829, USA
| | - Aster H Juan
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20829, USA
| | - Kyung Dae Ko
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20829, USA
| | - Pei-Fang Tsai
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20829, USA
| | - Hossein Zare
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20829, USA
| | - Stefania Dell'Orso
- High-Throughput Sequencing Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20829, USA
| | - Vittorio Sartorelli
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20829, USA.
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58
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Mutations in ACTRT1 and its enhancer RNA elements lead to aberrant activation of Hedgehog signaling in inherited and sporadic basal cell carcinomas. Nat Med 2017; 23:1226-1233. [PMID: 28869610 DOI: 10.1038/nm.4368] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 06/14/2017] [Indexed: 12/19/2022]
Abstract
Basal cell carcinoma (BCC), the most common human cancer, results from aberrant activation of the Hedgehog signaling pathway. Although most cases of BCC are sporadic, some forms are inherited, such as Bazex-Dupré-Christol syndrome (BDCS)-a cancer-prone genodermatosis with an X-linked, dominant inheritance pattern. We have identified mutations in the ACTRT1 gene, which encodes actin-related protein T1 (ARP-T1), in two of the six families with BDCS that were examined in this study. High-throughput sequencing in the four remaining families identified germline mutations in noncoding sequences surrounding ACTRT1. These mutations were located in transcribed sequences encoding enhancer RNAs (eRNAs) and were shown to impair enhancer activity and ACTRT1 expression. ARP-T1 was found to directly bind to the GLI1 promoter, thus inhibiting GLI1 expression, and loss of ARP-T1 led to activation of the Hedgehog pathway in individuals with BDCS. Moreover, exogenous expression of ACTRT1 reduced the in vitro and in vivo proliferation rates of cell lines with aberrant activation of the Hedgehog signaling pathway. In summary, our study identifies a disease mechanism in BCC involving mutations in regulatory noncoding elements and uncovers the tumor-suppressor properties of ACTRT1.
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59
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Elkon R, Agami R. Characterization of noncoding regulatory DNA in the human genome. Nat Biotechnol 2017; 35:732-746. [DOI: 10.1038/nbt.3863] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 03/31/2017] [Indexed: 12/22/2022]
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60
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Chen H, Du G, Song X, Li L. Non-coding Transcripts from Enhancers: New Insights into Enhancer Activity and Gene Expression Regulation. GENOMICS PROTEOMICS & BIOINFORMATICS 2017; 15:201-207. [PMID: 28599852 PMCID: PMC5487526 DOI: 10.1016/j.gpb.2017.02.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/23/2017] [Accepted: 02/07/2017] [Indexed: 02/05/2023]
Abstract
Long non-coding RNAs (lncRNAs) have gained widespread interest in the past decade owing to their enormous amount and surprising functions implicated in a variety of biological processes. Some lncRNAs exert function as enhancers, i.e., activating gene transcription by serving as the cis-regulatory molecules. Furthermore, recent studies have demonstrated that many enhancer elements can be transcribed and produce RNA molecules, which are termed as enhancer RNAs (eRNAs). The eRNAs are not merely the by-product of the enhancer transcription. In fact, many of them directly exert or regulate enhancer activity in gene activation through diverse mechanisms. Here, we provide an overview of enhancer activity, transcription of enhancer itself, characteristics of eRNAs, as well as their roles in regulating enhancer activity and gene expression.
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Affiliation(s)
- Hongjun Chen
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610064, China
| | - Guangshi Du
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610064, China
| | - Xu Song
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610064, China; State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Ling Li
- Center for Functional Genomics and Bioinformatics, Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu 610064, China.
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61
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Zhu Y, Tazearslan C, Suh Y. Challenges and progress in interpretation of non-coding genetic variants associated with human disease. Exp Biol Med (Maywood) 2017; 242:1325-1334. [PMID: 28581336 DOI: 10.1177/1535370217713750] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Genome-wide association studies have shown that the far majority of disease-associated variants reside in the non-coding regions of the genome, suggesting that gene regulatory changes contribute to disease risk. To identify truly causal non-coding variants and their affected target genes remains challenging but is a critical step to translate the genetic associations to molecular mechanisms and ultimately clinical applications. Here we review genomic/epigenomic resources and in silico tools that can be used to identify causal non-coding variants and experimental strategies to validate their functionalities. Impact statement Most signals from genome-wide association studies (GWASs) map to the non-coding genome, and functional interpretation of these associations remained challenging. We reviewed recent progress in methodologies of studying the non-coding genome and argued that no single approach allows one to effectively identify the causal regulatory variants from GWAS results. By illustrating the advantages and limitations of each method, our review potentially provided a guideline for taking a combinatorial approach to accurately predict, prioritize, and eventually experimentally validate the causal variants.
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Affiliation(s)
- Yizhou Zhu
- 1 Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Cagdas Tazearslan
- 1 Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Yousin Suh
- 1 Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.,2 Department of Ophthalmology & Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA.,3 Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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Fan Z, Zhao M, Joshi PD, Li P, Zhang Y, Guo W, Xu Y, Wang H, Zhao Z, Yan J. A class of circadian long non-coding RNAs mark enhancers modulating long-range circadian gene regulation. Nucleic Acids Res 2017; 45:5720-5738. [PMID: 28335007 PMCID: PMC5449593 DOI: 10.1093/nar/gkx156] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 02/24/2017] [Indexed: 12/30/2022] Open
Abstract
Circadian rhythm exerts its influence on animal physiology and behavior by regulating gene expression at various levels. Here we systematically explored circadian long non-coding RNAs (lncRNAs) in mouse liver and examined their circadian regulation. We found that a significant proportion of circadian lncRNAs are expressed at enhancer regions, mostly bound by two key circadian transcription factors, BMAL1 and REV-ERBα. These circadian lncRNAs showed similar circadian phases with their nearby genes. The extent of their nuclear localization is higher than protein coding genes but less than enhancer RNAs. The association between enhancer and circadian lncRNAs is also observed in tissues other than liver. Comparative analysis between mouse and rat circadian liver transcriptomes showed that circadian transcription at lncRNA loci tends to be conserved despite of low sequence conservation of lncRNAs. One such circadian lncRNA termed lnc-Crot led us to identify a super-enhancer region interacting with a cluster of genes involved in circadian regulation of metabolism through long-range interactions. Further experiments showed that lnc-Crot locus has enhancer function independent of lnc-Crot's transcription. Our results suggest that the enhancer-associated circadian lncRNAs mark the genomic loci modulating long-range circadian gene regulation and shed new lights on the evolutionary origin of lncRNAs.
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Affiliation(s)
- Zenghua Fan
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
- University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Meng Zhao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Parth D. Joshi
- Department of Genes and Behavior, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Ping Li
- Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Yan Zhang
- Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Weimin Guo
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yichi Xu
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
- University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Haifang Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhihu Zhao
- Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Jun Yan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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63
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Developmental Control of NRAMP1 (SLC11A1) Expression in Professional Phagocytes. BIOLOGY 2017; 6:biology6020028. [PMID: 28467369 PMCID: PMC5485475 DOI: 10.3390/biology6020028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/25/2017] [Accepted: 04/25/2017] [Indexed: 12/11/2022]
Abstract
NRAMP1 (SLC11A1) is a professional phagocyte membrane importer of divalent metals that contributes to iron recycling at homeostasis and to nutritional immunity against infection. Analyses of data generated by several consortia and additional studies were integrated to hypothesize mechanisms restricting NRAMP1 expression to mature phagocytes. Results from various epigenetic and transcriptomic approaches were collected for mesodermal and hematopoietic cell types and compiled for combined analysis with results of genetic studies associating single nucleotide polymorphisms (SNPs) with variations in NRAMP1 expression (eQTLs). Analyses establish that NRAMP1 is part of an autonomous topologically associated domain delimited by ubiquitous CCCTC-binding factor (CTCF) sites. NRAMP1 locus contains five regulatory regions: a predicted super-enhancer (S-E) key to phagocyte-specific expression; the proximal promoter; two intronic areas, including 3' inhibitory elements that restrict expression during development; and a block of upstream sites possibly extending the S-E domain. Also the downstream region adjacent to the 3' CTCF locus boundary may regulate expression during hematopoiesis. Mobilization of the locus 14 predicted transcriptional regulatory elements occurs in three steps, beginning with hematopoiesis; at the onset of myelopoiesis and through myelo-monocytic differentiation. Basal expression level in mature phagocytes is further influenced by genetic variation, tissue environment, and in response to infections that induce various epigenetic memories depending on microorganism nature. Constitutively associated transcription factors (TFs) include CCAAT enhancer binding protein beta (C/EBPb), purine rich DNA binding protein (PU.1), early growth response 2 (EGR2) and signal transducer and activator of transcription 1 (STAT1) while hypoxia-inducible factors (HIFs) and interferon regulatory factor 1 (IRF1) may stimulate iron acquisition in pro-inflammatory conditions. Mouse orthologous locus is generally conserved; chromatin patterns typify a de novo myelo-monocytic gene whose expression is tightly controlled by TFs Pu.1, C/ebps and Irf8; Irf3 and nuclear factor NF-kappa-B p 65 subunit (RelA) regulate expression in inflammatory conditions. Functional differences in the determinants identified at these orthologous loci imply that species-specific mechanisms control gene expression.
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64
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Bornholdt J, Saber AT, Lilje B, Boyd M, Jørgensen M, Chen Y, Vitezic M, Jacobsen NR, Poulsen SS, Berthing T, Bressendorff S, Vitting-Seerup K, Andersson R, Hougaard KS, Yauk CL, Halappanavar S, Wallin H, Vogel U, Sandelin A. Identification of Gene Transcription Start Sites and Enhancers Responding to Pulmonary Carbon Nanotube Exposure in Vivo. ACS NANO 2017; 11:3597-3613. [PMID: 28345861 DOI: 10.1021/acsnano.6b07533] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Increased use of nanomaterials in industry, medicine, and consumer products has raised concerns over their toxicity. To ensure safe use of nanomaterials, understanding their biological effects at the molecular level is crucial. In particular, the regulatory mechanisms responsible for the cascade of genes activated by nanomaterial exposure are not well-characterized. To this end, we profiled the genome-wide usage of gene transcription start sites and linked active enhancer regions in lungs of C57BL/6 mice 24 h after intratracheal instillation of a single dose of the multiwalled carbon nanotube (MWCNT) Mitsui-7. Our results revealed a massive gene regulatory response, where expression of key inflammatory genes (e.g., Csf3, Il24, and Fgf23) was increased >100-fold 24 h after Mitsui-7 exposure. Many of the Mitsui-7-responsive transcription start sites were alternative transcription start sites for known genes, and the number of alternative transcription start sites used in a given gene was correlated with overall Mitsui-7 response. Strikingly, genes that were up-regulated after Mitsui-7 exposure only through their main annotated transcription start site were linked to inflammatory and defense responses, while genes up-regulated only through alternative transcription start sites were functionally heterogeneous and not inflammation-associated. Furthermore, we identified almost 12 000 active enhancers, many of which were Mitsui-7-responsive, and we identified similarly responding putative target genes. Overall, our study provides the location and activity of Mitsui-7-induced enhancers and transcription start sites, providing a useful resource for targeted experiments elucidating the biological effects of nanomaterials and the identification of biomarkers for early detection of MWCNT-induced inflammation.
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Affiliation(s)
- Jette Bornholdt
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
| | | | - Berit Lilje
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
| | - Mette Boyd
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
| | - Mette Jørgensen
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
| | - Yun Chen
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
| | - Morana Vitezic
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
| | | | - Sarah Søs Poulsen
- National Research Centre for the Working Environment , 2100 Copenhagen, Denmark
| | - Trine Berthing
- National Research Centre for the Working Environment , 2100 Copenhagen, Denmark
| | - Simon Bressendorff
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
| | - Kristoffer Vitting-Seerup
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
| | - Robin Andersson
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
| | | | - Carole L Yauk
- Environmental and Radiation Health Sciences Directorate, Health Canada , Ottawa, Ontario K1A 0K9, Canada
| | - Sabina Halappanavar
- Environmental and Radiation Health Sciences Directorate, Health Canada , Ottawa, Ontario K1A 0K9, Canada
| | - Håkan Wallin
- National Research Centre for the Working Environment , 2100 Copenhagen, Denmark
- Department of Public Health, University of Copenhagen , 2200 Copenhagen, Denmark
| | - Ulla Vogel
- National Research Centre for the Working Environment , 2100 Copenhagen, Denmark
- Department of Micro and Nanotechnology, Technical University of Denmark , 2800 Kongens Lyngby, Denmark
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
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65
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Michel M, Demel C, Zacher B, Schwalb B, Krebs S, Blum H, Gagneur J, Cramer P. TT-seq captures enhancer landscapes immediately after T-cell stimulation. Mol Syst Biol 2017; 13:920. [PMID: 28270558 PMCID: PMC5371733 DOI: 10.15252/msb.20167507] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
To monitor transcriptional regulation in human cells, rapid changes in enhancer and promoter activity must be captured with high sensitivity and temporal resolution. Here, we show that the recently established protocol TT-seq ("transient transcriptome sequencing") can monitor rapid changes in transcription from enhancers and promoters during the immediate response of T cells to ionomycin and phorbol 12-myristate 13-acetate (PMA). TT-seq maps eRNAs and mRNAs every 5 min after T-cell stimulation with high sensitivity and identifies many new primary response genes. TT-seq reveals that the synthesis of 1,601 eRNAs and 650 mRNAs changes significantly within only 15 min after stimulation, when standard RNA-seq does not detect differentially expressed genes. Transcription of enhancers that are primed for activation by nucleosome depletion can occur immediately and simultaneously with transcription of target gene promoters. Our results indicate that enhancer transcription is a good proxy for enhancer regulatory activity in target gene activation, and establish TT-seq as a tool for monitoring the dynamics of enhancer landscapes and transcription programs during cellular responses and differentiation.
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Affiliation(s)
- Margaux Michel
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Carina Demel
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Benedikt Zacher
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Björn Schwalb
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Stefan Krebs
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Helmut Blum
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Julien Gagneur
- Department of Informatics, Technische Universität München, Garching, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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66
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Ko JY, Oh S, Yoo KH. Functional Enhancers As Master Regulators of Tissue-Specific Gene Regulation and Cancer Development. Mol Cells 2017; 40:169-177. [PMID: 28359147 PMCID: PMC5386954 DOI: 10.14348/molcells.2017.0033] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 03/29/2017] [Accepted: 03/30/2017] [Indexed: 12/30/2022] Open
Abstract
Tissue-specific transcription is critical for normal development, and abnormalities causing undesirable gene expression may lead to diseases such as cancer. Such highly organized transcription is controlled by enhancers with specific DNA sequences recognized by transcription factors. Enhancers are associated with chromatin modifications that are distinct epigenetic features in a tissue-specific manner. Recently, super-enhancers comprising enhancer clusters co-occupied by lineage-specific factors have been identified in diverse cell types such as adipocytes, hair follicle stem cells, and mammary epithelial cells. In addition, noncoding RNAs, named eRNAs, are synthesized at super-enhancer regions before their target genes are transcribed. Many functional studies revealed that super-enhancers and eRNAs are essential for the regulation of tissue-specific gene expression. In this review, we summarize recent findings concerning enhancer function in tissue-specific gene regulation and cancer development.
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Affiliation(s)
- Je Yeong Ko
- Molecular Medicine Laboratory, Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310,
Korea
| | - Sumin Oh
- Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310,
Korea
| | - Kyung Hyun Yoo
- Laboratory of Biomedical Genomics, Department of Biological Sciences, Sookmyung Women’s University, Seoul 04310,
Korea
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67
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Le Gras S, Keime C, Anthony A, Lotz C, De Longprez L, Brouillet E, Cassel JC, Boutillier AL, Merienne K. Altered enhancer transcription underlies Huntington's disease striatal transcriptional signature. Sci Rep 2017; 7:42875. [PMID: 28225006 PMCID: PMC5320509 DOI: 10.1038/srep42875] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 01/16/2017] [Indexed: 01/09/2023] Open
Abstract
Epigenetic and transcriptional alterations are both implicated in Huntington’s disease (HD), a progressive neurodegenerative disease resulting in degeneration of striatal neurons in the brain. However, how impaired epigenetic regulation leads to transcriptional dysregulation in HD is unclear. Here, we investigated enhancer RNAs (eRNAs), a class of long non-coding RNAs transcribed from active enhancers. We found that eRNAs are expressed from many enhancers of mouse striatum and showed that a subset of those eRNAs are deregulated in HD vs control mouse striatum. Enhancer regions producing eRNAs decreased in HD mouse striatum were associated with genes involved in striatal neuron identity. Consistently, they were enriched in striatal super-enhancers. Moreover, decreased eRNA expression in HD mouse striatum correlated with down-regulation of associated genes. Additionally, a significant number of RNA Polymerase II (RNAPII) binding sites were lost within enhancers associated with decreased eRNAs in HD vs control mouse striatum. Together, this indicates that loss of RNAPII at HD mouse enhancers contributes to reduced transcription of eRNAs, resulting in down-regulation of target genes. Thus, our data support the view that eRNA dysregulation in HD striatum is a key mechanism leading to altered transcription of striatal neuron identity genes, through reduced recruitment of RNAPII at super-enhancers.
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Affiliation(s)
- Stéphanie Le Gras
- GenomeEast Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS/INSERM/University of Strasbourg-UMR 7104, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Céline Keime
- GenomeEast Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS/INSERM/University of Strasbourg-UMR 7104, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Anne Anthony
- University of Strasbourg, Laboratory of Cognitive and Adaptive Neurosciences (LNCA), 12 rue Goethe, 67000 Strasbourg, France.,CNRS, LNCA UMR 7364, 12 rue Goethe, 67000 Strasbourg, France
| | - Caroline Lotz
- University of Strasbourg, Laboratory of Cognitive and Adaptive Neurosciences (LNCA), 12 rue Goethe, 67000 Strasbourg, France.,CNRS, LNCA UMR 7364, 12 rue Goethe, 67000 Strasbourg, France
| | - Lucie De Longprez
- Commissariat à l'Energie Atomique (CEA), Département de Recherches Fondamentales (DRF), Institut d'Imagerie Biomédicale (I2BM), Molecular Imaging Research Center (MIRCen), F-92260 Fontenay-aux-Roses, France.,Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, UMR 9199, Neurodegenerative Diseases Laboratory, F-92260 Fontenay-aux-Roses, France
| | - Emmanuel Brouillet
- Commissariat à l'Energie Atomique (CEA), Département de Recherches Fondamentales (DRF), Institut d'Imagerie Biomédicale (I2BM), Molecular Imaging Research Center (MIRCen), F-92260 Fontenay-aux-Roses, France.,Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, UMR 9199, Neurodegenerative Diseases Laboratory, F-92260 Fontenay-aux-Roses, France
| | - Jean-Christophe Cassel
- University of Strasbourg, Laboratory of Cognitive and Adaptive Neurosciences (LNCA), 12 rue Goethe, 67000 Strasbourg, France.,CNRS, LNCA UMR 7364, 12 rue Goethe, 67000 Strasbourg, France
| | - Anne-Laurence Boutillier
- University of Strasbourg, Laboratory of Cognitive and Adaptive Neurosciences (LNCA), 12 rue Goethe, 67000 Strasbourg, France.,CNRS, LNCA UMR 7364, 12 rue Goethe, 67000 Strasbourg, France
| | - Karine Merienne
- University of Strasbourg, Laboratory of Cognitive and Adaptive Neurosciences (LNCA), 12 rue Goethe, 67000 Strasbourg, France.,CNRS, LNCA UMR 7364, 12 rue Goethe, 67000 Strasbourg, France
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68
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Ehrlich KC, Paterson HL, Lacey M, Ehrlich M. DNA Hypomethylation in Intragenic and Intergenic Enhancer Chromatin of Muscle-Specific Genes Usually Correlates with their Expression. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2016; 89:441-455. [PMID: 28018137 PMCID: PMC5168824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Tissue-specific enhancers are critical for gene regulation. In this study, we help elucidate the contribution of muscle-associated differential DNA methylation to the enhancer activity of highly muscle-specific genes. By bioinformatic analysis of 44 muscle-associated genes, we show that preferential gene expression in skeletal muscle (SkM) correlates with SkM-specific intragenic and intergenic enhancer chromatin and overlapping foci of DNA hypomethylation. Some genes, e.g., CASQ1 and FBXO32, displayed broad regions of both SkM- and heart-specific enhancer chromatin but exhibited focal SkM-specific DNA hypomethylation. Half of the genes had SkM-specific super-enhancers. In contrast to simple enhancer/gene-expression correlations, a super-enhancer was associated with the myogenic MYOD1 gene in both SkM and myoblasts even though SkM has < 1 percent as much MYOD1 expression. Local chromatin differences in this super-enhancer probably contribute to the SkM/myoblast differential expression. Transfection assays confirmed the tissue-specificity of the 0.3-kb core enhancer within MYOD1's super-enhancer and demonstrated its repression by methylation of its three CG dinucleotides. Our study suggests that DNA hypomethylation increases enhancer tissue-specificity and that SkM super-enhancers sometimes are poised for physiologically important, rapid up-regulation.
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Affiliation(s)
- Kenneth C. Ehrlich
- Program in Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA
| | | | - Michelle Lacey
- Tulane Cancer Center, Tulane University Health Sciences Center, New Orleans, LA,Mathematics Department, Tulane University, New Orleans, LA
| | - Melanie Ehrlich
- Program in Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA,Tulane Cancer Center, Tulane University Health Sciences Center, New Orleans, LA,Hayward Genetics Center, Tulane University Health Sciences Center, New Orleans, LA,To whom all correspondence should be addressed: Melanie Ehrlich, PhD, Hayward Genetics Center, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112; Tele: 504-988-2449; Fax: 504-988-1763;
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69
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Ye J, Tucker NR, Weng LC, Clauss S, Lubitz SA, Ellinor PT. A Functional Variant Associated with Atrial Fibrillation Regulates PITX2c Expression through TFAP2a. Am J Hum Genet 2016; 99:1281-1291. [PMID: 27866707 PMCID: PMC5142106 DOI: 10.1016/j.ajhg.2016.10.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 10/03/2016] [Indexed: 01/22/2023] Open
Abstract
The most significantly associated genetic locus for atrial fibrillation (AF) is in chromosomal region 4q25, where four independent association signals have been identified. Although model-system studies suggest that altered PITX2c expression might underlie the association, the link between specific variants and the direction of effect on gene expression remains unknown for all four signals. In the present study, we analyzed the AF-associated region most proximal to PITX2 at 4q25. First, we identified candidate regulatory variants that might confer AF risk through a combination of mammalian conservation, DNase hypersensitivity, and histone modification from ENCODE and the Roadmap Epigenomics Project, as well as through in vivo analysis of enhancer activity in embryonic zebrafish. Within candidate regions, we then identified a single associated SNP, rs2595104, which displayed dramatically reduced enhancer activity with the AF risk allele. CRISPR-Cas9-mediated deletion of the rs2595104 region and editing of the rs2595104 risk allele in human stem-cell-derived cardiomyocytes resulted in diminished PITX2c expression in comparison to that of the non-risk allele. This differential activity was mediated by activating enhancer binding protein 2 alpha (TFAP2a), which bound robustly to the non-risk allele at rs2595104, but not to the risk allele, in cardiomyocytes. In sum, we found that the AF-associated SNP rs2595104 altered PITX2c expression via interaction with TFAP2a. Such a pathway could ultimately contribute to AF susceptibility at the PITX2 locus associated with AF.
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Affiliation(s)
- Jiangchuan Ye
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Nathan R Tucker
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Lu-Chen Weng
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Sebastian Clauss
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Steven A Lubitz
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Patrick T Ellinor
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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70
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Gokoolparsadh A, Sutton GJ, Charamko A, Green NFO, Pardy CJ, Voineagu I. Searching for convergent pathways in autism spectrum disorders: insights from human brain transcriptome studies. Cell Mol Life Sci 2016; 73:4517-4530. [PMID: 27405608 PMCID: PMC11108267 DOI: 10.1007/s00018-016-2304-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 06/16/2016] [Accepted: 07/05/2016] [Indexed: 01/07/2023]
Abstract
Autism spectrum disorder (ASD) is one of the most heritable neuropsychiatric conditions. The complex genetic landscape of the disorder includes both common and rare variants at hundreds of genetic loci. This marked heterogeneity has thus far hampered efforts to develop genetic diagnostic panels and targeted pharmacological therapies. Here, we give an overview of the current literature on the genetic basis of ASD, and review recent human brain transcriptome studies and their role in identifying convergent pathways downstream of the heterogeneous genetic variants. We also discuss emerging evidence on the involvement of non-coding genomic regions and non-coding RNAs in ASD.
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Affiliation(s)
- Akira Gokoolparsadh
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, NSW, 2052, Australia
| | - Gavin J Sutton
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, NSW, 2052, Australia
| | - Alexiy Charamko
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, NSW, 2052, Australia
| | - Nicole F Oldham Green
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, NSW, 2052, Australia
| | - Christopher J Pardy
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, NSW, 2052, Australia
| | - Irina Voineagu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, NSW, 2052, Australia.
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71
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Spitz F. Gene regulation at a distance: From remote enhancers to 3D regulatory ensembles. Semin Cell Dev Biol 2016; 57:57-67. [PMID: 27364700 DOI: 10.1016/j.semcdb.2016.06.017] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 06/24/2016] [Indexed: 10/21/2022]
Abstract
Large-scale identification of elements associated with gene expression revealed that many of them are located extremely far from gene transcriptional start sites. We review here the growing evidence that show that distal cis-acting elements provide key instructions to genes, as genetic variation affecting them is growingly identified as an importance source of phenotypic diversity and disease. We discuss the different mechanisms that allow these elements to exert their regulatory functions, in a robust and specific manner, despite the large genomic distances separating them from their target genes. We particularly focus on the role of the structural organization of the genome in guiding such regulatory interactions.
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Affiliation(s)
- François Spitz
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; Department of Developmental Biology and Stem Cells, Institut Pasteur, Paris, France.
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72
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Li W, Notani D, Rosenfeld MG. Enhancers as non-coding RNA transcription units: recent insights and future perspectives. Nat Rev Genet 2016; 17:207-23. [PMID: 26948815 DOI: 10.1038/nrg.2016.4] [Citation(s) in RCA: 487] [Impact Index Per Article: 60.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Networks of regulatory enhancers dictate distinct cell identities and cellular responses to diverse signals by instructing precise spatiotemporal patterns of gene expression. However, 35 years after their discovery, enhancer functions and mechanisms remain incompletely understood. Intriguingly, recent evidence suggests that many, if not all, functional enhancers are themselves transcription units, generating non-coding enhancer RNAs. This observation provides a fundamental insight into the inter-regulation between enhancers and promoters, which can both act as transcription units; it also raises crucial questions regarding the potential biological roles of the enhancer transcription process and non-coding enhancer RNAs. Here, we review research progress in this field and discuss several important, unresolved questions regarding the roles and mechanisms of enhancers in gene regulation.
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Affiliation(s)
- Wenbo Li
- Howard Hughes Medical Institute, Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92037-0648, USA
| | - Dimple Notani
- Howard Hughes Medical Institute, Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92037-0648, USA
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92037-0648, USA
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73
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Genomic Views of Transcriptional Enhancers: Essential Determinants of Cellular Identity and Activity-Dependent Responses in the CNS. J Neurosci 2016; 35:13819-26. [PMID: 26468181 DOI: 10.1523/jneurosci.2622-15.2015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
UNLABELLED Sprinkled throughout the genome are a million regulatory sequences called transcriptional enhancers that activate gene promoters in the right cells, at the right time. Enhancers endow the brain with its incredible diversity of cell types and also translate neural activity into gene induction. Thanks to rapid advances in genomic technologies, it is now possible to identify thousands of enhancers rapidly, test their transcriptional function en masse, and address their neurobiological functions via genome editing. Enhancers also promise to be a great technological opportunity for neuroscience, offering the potential for cell-type-specific genetic labeling and manipulation without the need for transgenesis. The objective of this review and the accompanying 2015 SfN mini-symposium is to highlight the use of new and emerging genomic technologies to probe enhancer function in the nervous system. SIGNIFICANCE STATEMENT Transcriptional enhancers turn on genes in the right cells, at the right time. Enhancers are also the genomic sequences that encode the incredible diversity of cell types in the brain and enable the brain to turn genes on in response to new experiences. New technology enables enhancers to be found and manipulated. The study of enhancers promises to inform our understanding of brain development and function. The application of enhancer technology holds promise in accelerating basic neuroscience research and enabling gene therapies to be targeted to specific cell types in the brain.
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74
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Merienne K, Boutillier AL. [Epigenetic regulations and cerebral plasticity: towards new therapeutic options in neurodegenerative diseases?]. Biol Aujourdhui 2016; 210:297-309. [PMID: 28327286 DOI: 10.1051/jbio/2017002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Indexed: 11/15/2022]
Abstract
Although revealed in the 1950's, epigenetics is still a fast-growing field. Its delineations continuously evolve and become clarified. In particular, "neuroepigenetics", a notion that encompasses epigenetic regulations associated with neuronal processes, appears very promising. Indeed, the challenge to be undertaken in this sub-field is double. On the one hand, it should bring molecular comprehension of specific neuronal processes, some of them falling within the long term regulations, such as learning and memory. On the other hand, it could bring therapeutic options for brain diseases, e.g. neurodegenerative diseases such as Alzheimer's or Huntington's diseases.
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75
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Rastegar S, Strähle U. The Zebrafish as Model for Deciphering the Regulatory Architecture of Vertebrate Genomes. GENETICS, GENOMICS AND FISH PHENOMICS 2016; 95:195-216. [DOI: 10.1016/bs.adgen.2016.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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76
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Yan L, Guo H, Hu B, Li R, Yong J, Zhao Y, Zhi X, Fan X, Guo F, Wang X, Wang W, Wei Y, Wang Y, Wen L, Qiao J, Tang F. Epigenomic Landscape of Human Fetal Brain, Heart, and Liver. J Biol Chem 2015; 291:4386-98. [PMID: 26719341 DOI: 10.1074/jbc.m115.672931] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Indexed: 11/06/2022] Open
Abstract
The epigenetic regulation of spatiotemporal gene expression is crucial for human development. Here, we present whole-genome chromatin immunoprecipitation followed by high throughput DNA sequencing (ChIP-seq) analyses of a wide variety of histone markers in the brain, heart, and liver of early human embryos shortly after their formation. We identified 40,181 active enhancers, with a large portion showing tissue-specific and developmental stage-specific patterns, pointing to their roles in controlling the ordered spatiotemporal expression of the developmental genes in early human embryos. Moreover, using sequential ChIP-seq, we showed that all three organs have hundreds to thousands of bivalent domains that are marked by both H3K4me3 and H3K27me3, probably to keep the progenitor cells in these organs ready for immediate differentiation into diverse cell types during subsequent developmental processes. Our work illustrates the potentially critical roles of tissue-specific and developmental stage-specific epigenomes in regulating the spatiotemporal expression of developmental genes during early human embryonic development.
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Affiliation(s)
- Liying Yan
- From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital, and the Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191
| | - Hongshan Guo
- From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital, and
| | - Boqiang Hu
- From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital, and
| | - Rong Li
- From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital, and the Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191
| | - Jun Yong
- From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital, and
| | - Yangyu Zhao
- From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital, and the Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191
| | - Xu Zhi
- From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital, and the Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191
| | - Xiaoying Fan
- From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital, and
| | - Fan Guo
- From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital, and
| | - Xiaoye Wang
- From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital, and the Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191
| | - Wei Wang
- From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital, and the Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191
| | - Yuan Wei
- From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital, and the Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191
| | - Yan Wang
- From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital, and the Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191
| | - Lu Wen
- From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital, and the Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, the Center for Molecular and Translational Medicine, Peking University Health Science Center, Beijing 100191, China
| | - Jie Qiao
- From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital, and the Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, the Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing 100871, and the Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871,
| | - Fuchou Tang
- From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital, and the Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, the Center for Molecular and Translational Medicine, Peking University Health Science Center, Beijing 100191, China the Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871,
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77
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Joo JY, Schaukowitch K, Farbiak L, Kilaru G, Kim TK. Stimulus-specific combinatorial functionality of neuronal c-fos enhancers. Nat Neurosci 2015; 19:75-83. [PMID: 26595656 PMCID: PMC4696896 DOI: 10.1038/nn.4170] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/09/2015] [Indexed: 12/16/2022]
Abstract
The c-fos gene is induced by a broad range of stimuli, and has been commonly used as a reliable marker for neural activity. Its induction mechanism and available reporter mouse lines are exclusively based on the c-fos promoter activity. Here, we demonstrate that multiple enhancers surrounding the c-fos gene are critical for ensuring robust c-fos response to various stimuli. Membrane depolarization, brain-derived neurotrophic factor (BDNF), and Forskolin activate distinct subsets of the enhancers to induce c-fos transcription in neurons, suggesting that stimulus-specific combinatorial activation of multiple enhancers underlies the broad inducibility of the c-fos gene. Accordingly, the functional requirement of key transcription factors varies depending on the type of stimulation. Combinatorial enhancer activation also occurs in the brain. Providing a comprehensive picture of the c-fos induction mechanism beyond the minimal promoter, our study should help in understanding the physiological nature of c-fos induction in relation to neural activity and plasticity.
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Affiliation(s)
- Jae-Yeol Joo
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Katie Schaukowitch
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Lukas Farbiak
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Gokhul Kilaru
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Tae-Kyung Kim
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
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78
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Mora A, Sandve GK, Gabrielsen OS, Eskeland R. In the loop: promoter-enhancer interactions and bioinformatics. Brief Bioinform 2015; 17:980-995. [PMID: 26586731 PMCID: PMC5142009 DOI: 10.1093/bib/bbv097] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 09/26/2015] [Indexed: 12/17/2022] Open
Abstract
Enhancer-promoter regulation is a fundamental mechanism underlying differential transcriptional regulation. Spatial chromatin organization brings remote enhancers in contact with target promoters in cis to regulate gene expression. There is considerable evidence for promoter-enhancer interactions (PEIs). In the recent years, genome-wide analyses have identified signatures and mapped novel enhancers; however, being able to precisely identify their target gene(s) requires massive biological and bioinformatics efforts. In this review, we give a short overview of the chromatin landscape and transcriptional regulation. We discuss some key concepts and problems related to chromatin interaction detection technologies, and emerging knowledge from genome-wide chromatin interaction data sets. Then, we critically review different types of bioinformatics analysis methods and tools related to representation and visualization of PEI data, raw data processing and PEI prediction. Lastly, we provide specific examples of how PEIs have been used to elucidate a functional role of non-coding single-nucleotide polymorphisms. The topic is at the forefront of epigenetic research, and by highlighting some future bioinformatics challenges in the field, this review provides a comprehensive background for future PEI studies.
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79
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Yao P, Lin P, Gokoolparsadh A, Assareh A, Thang MWC, Voineagu I. Coexpression networks identify brain region-specific enhancer RNAs in the human brain. Nat Neurosci 2015; 18:1168-74. [PMID: 26167905 DOI: 10.1038/nn.4063] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 06/18/2015] [Indexed: 12/17/2022]
Abstract
Despite major progress in identifying enhancer regions on a genome-wide scale, the majority of available data are limited to model organisms and human transformed cell lines. We have identified a robust set of enhancer RNAs (eRNAs) expressed in the human brain and constructed networks assessing eRNA-gene coexpression interactions across human fetal brain and multiple adult brain regions. Our data identify brain region-specific eRNAs and show that enhancer regions expressing eRNAs are enriched for genetic variants associated with autism spectrum disorders.
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Affiliation(s)
- Pu Yao
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Peijie Lin
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Akira Gokoolparsadh
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Amelia Assareh
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Mike W C Thang
- QFAB Bioinformatics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
| | - Irina Voineagu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
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80
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Condensin I and II Complexes License Full Estrogen Receptor α-Dependent Enhancer Activation. Mol Cell 2015; 59:188-202. [PMID: 26166704 DOI: 10.1016/j.molcel.2015.06.002] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 03/11/2015] [Accepted: 06/02/2015] [Indexed: 11/21/2022]
Abstract
Enhancers instruct spatio-temporally specific gene expression in a manner tightly linked to higher-order chromatin architecture. Critical chromatin architectural regulators condensin I and condensin II play non-redundant roles controlling mitotic chromosomes. But the chromosomal locations of condensins and their functional roles in interphase are poorly understood. Here we report that both condensin complexes exhibit an unexpected, dramatic estrogen-induced recruitment to estrogen receptor α (ER-α)-bound eRNA(+) active enhancers in interphase breast cancer cells, exhibiting non-canonical interaction with ER-α via its DNA-binding domain (DBD). Condensins positively regulate ligand-dependent enhancer activation at least in part by recruiting an E3 ubiquitin ligase, HECTD1, to modulate the binding of enhancer-associated coactivators/corepressors, including p300 and RIP140, permitting full eRNA transcription, formation of enhancer:promoter looping, and the resultant coding gene activation. Collectively, our results reveal an important, unanticipated transcriptional role of interphase condensins in modulating estrogen-regulated enhancer activation and coding gene transcriptional program.
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81
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Andersson R, Sandelin A, Danko CG. A unified architecture of transcriptional regulatory elements. Trends Genet 2015; 31:426-33. [PMID: 26073855 DOI: 10.1016/j.tig.2015.05.007] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/19/2015] [Accepted: 05/20/2015] [Indexed: 11/19/2022]
Abstract
Gene expression is precisely controlled in time and space through the integration of signals that act at gene promoters and gene-distal enhancers. Classically, promoters and enhancers are considered separate classes of regulatory elements, often distinguished by histone modifications. However, recent studies have revealed broad similarities between enhancers and promoters, blurring the distinction: active enhancers often initiate transcription, and some gene promoters have the potential to enhance transcriptional output of other promoters. Here, we propose a model in which promoters and enhancers are considered a single class of functional element, with a unified architecture for transcription initiation. The context of interacting regulatory elements and the surrounding sequences determine local transcriptional output as well as the enhancer and promoter activities of individual elements.
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Affiliation(s)
- Robin Andersson
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA; Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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82
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Dailey L. High throughput technologies for the functional discovery of mammalian enhancers: new approaches for understanding transcriptional regulatory network dynamics. Genomics 2015; 106:151-158. [PMID: 26072436 DOI: 10.1016/j.ygeno.2015.06.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 04/18/2015] [Accepted: 06/08/2015] [Indexed: 01/08/2023]
Abstract
Completion of the human and mouse genomes has inspired new initiatives to obtain a global understanding of the functional regulatory networks governing gene expression. Enhancers are primary regulatory DNA elements determining precise spatio- and temporal gene expression patterns, but the observation that they can function at any distance from the gene(s) they regulate has made their genome-wide characterization challenging. Since traditional, single reporter approaches would be unable to accomplish this enormous task, high throughput technologies for mapping chromatin features associated with enhancers have emerged as an effective surrogate for enhancer discovery. However, the last few years have witnessed the development of several new innovative approaches that can effectively screen for and discover enhancers based on their functional activation of transcription using massively parallel reporter systems. In addition to their application for genome annotation, these new high throughput functional approaches open new and exciting avenues for modeling gene regulatory networks.
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Affiliation(s)
- Lisa Dailey
- NYU School of Medicine, Department of Microbiology, Kimmel Center for Stem Cell Biology, 550 First Avenue, MSB 252, New York, NY 10016, United States.
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83
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Wang Z, Yuan W, Montana G. Sparse multi-view matrix factorization: a multivariate approach to multiple tissue comparisons. Bioinformatics 2015; 31:3163-71. [DOI: 10.1093/bioinformatics/btv344] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/29/2015] [Indexed: 12/25/2022] Open
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84
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Danko CG, Hyland SL, Core LJ, Martins AL, Waters CT, Lee HW, Cheung VG, Kraus WL, Lis JT, Siepel A. Identification of active transcriptional regulatory elements from GRO-seq data. Nat Methods 2015; 12:433-8. [PMID: 25799441 PMCID: PMC4507281 DOI: 10.1038/nmeth.3329] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 02/24/2015] [Indexed: 12/26/2022]
Abstract
Modifications to the global run-on and sequencing (GRO-seq) protocol that enrich for 5'-capped RNAs can be used to reveal active transcriptional regulatory elements (TREs) with high accuracy. Here, we introduce discriminative regulatory-element detection from GRO-seq (dREG), a sensitive machine learning method that uses support vector regression to identify active TREs from GRO-seq data without requiring cap-based enrichment (https://github.com/Danko-Lab/dREG/). This approach allows TREs to be assayed together with gene expression levels and other transcriptional features in a single experiment. Predicted TREs are more enriched for several marks of transcriptional activation—including expression quantitative trait loci, disease-associated polymorphisms, acetylated histone 3 lysine 27 (H3K27ac) and transcription factor binding—than those identified by alternative functional assays. Using dREG, we surveyed TREs in eight human cell types and provide new insights into global patterns of TRE function.
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Affiliation(s)
- Charles G. Danko
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY,USA
| | - Stephanie L. Hyland
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, New York, USA
| | - Leighton J. Core
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Andre L. Martins
- Graduate Field in Computational Biology, Cornell University, Ithaca, NY, USA
| | - Colin T Waters
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Hyung Won Lee
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Vivian G. Cheung
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - W. Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - John T. Lis
- Graduate Field in Computational Biology, Cornell University, Ithaca, NY, USA
| | - Adam Siepel
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY,USA
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85
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Abstract
A large part of the mammalian genome is transcribed into noncoding RNAs. Long noncoding RNAs (lncRNAs) have emerged as critical epigenetic regulators of gene expression. Distinct molecular mechanisms allow lncRNAs either to activate or to repress gene expression, thereby participating in the regulation of cellular and tissue function. LncRNAs, therefore, have important roles in healthy and diseased hearts, and might be targets for therapeutic intervention. In this Review, we summarize the current knowledge of the roles of lncRNAs in cardiac development and ageing. After describing the definition and classification of lncRNAs, we present an overview of the mechanisms by which lncRNAs regulate gene expression. We discuss the multiple roles of lncRNAs in the heart, and focus on the regulation of embryonic stem cell differentiation, cardiac cell fate and development, and cardiac ageing. We emphasize the importance of chromatin remodelling in this regulation. Finally, we discuss the therapeutic and biomarker potential of lncRNAs.
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Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AMN, Arner P, Axton R, Baillie JK, Beckhouse A, Bodega B, Briggs J, Brombacher F, Davis M, Detmar M, Ehrlund A, Endoh M, Eslami A, Fagiolini M, Fairbairn L, Faulkner GJ, Ferrai C, Fisher ME, Forrester L, Goldowitz D, Guler R, Ha T, Hara M, Herlyn M, Ikawa T, Kai C, Kawamoto H, Khachigian LM, Klinken SP, Kojima S, Koseki H, Klein S, Mejhert N, Miyaguchi K, Mizuno Y, Morimoto M, Morris KJ, Mummery C, Nakachi Y, Ogishima S, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov D, Passier R, Patrikakis M, Pombo A, Qin XY, Roy S, Sato H, Savvi S, Saxena A, Schwegmann A, Sugiyama D, Swoboda R, Tanaka H, Tomoiu A, Winteringham LN, Wolvetang E, Yanagi-Mizuochi C, Yoneda M, Zabierowski S, Zhang P, Abugessaisa I, Bertin N, Diehl AD, Fukuda S, Furuno M, Harshbarger J, Hasegawa A, Hori F, Ishikawa-Kato S, Ishizu Y, Itoh M, Kawashima T, Kojima M, Kondo N, Lizio M, Meehan TF, Mungall CJ, Murata M, Nishiyori-Sueki H, Sahin S, Nagao-Sato S, Severin J, de Hoon MJL, Kawai J, Kasukawa T, Lassmann T, Suzuki H, Kawaji H, Summers KM, Wells C, Hume DA, Forrest ARR, Sandelin A, Carninci P, Hayashizaki Y. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science 2015; 347:1010-4. [PMID: 25678556 PMCID: PMC4681433 DOI: 10.1126/science.1259418] [Citation(s) in RCA: 420] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Although it is generally accepted that cellular differentiation requires changes to transcriptional networks, dynamic regulation of promoters and enhancers at specific sets of genes has not been previously studied en masse. Exploiting the fact that active promoters and enhancers are transcribed, we simultaneously measured their activity in 19 human and 14 mouse time courses covering a wide range of cell types and biological stimuli. Enhancer RNAs, then messenger RNAs encoding transcription factors, dominated the earliest responses. Binding sites for key lineage transcription factors were simultaneously overrepresented in enhancers and promoters active in each cellular system. Our data support a highly generalizable model in which enhancer transcription is the earliest event in successive waves of transcriptional change during cellular differentiation or activation.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - David A. Hume
- Corresponding author. (D.A.H.); (A.R.R.F.); (A.S.); (P.C.); (Y.H.)
| | | | - Albin Sandelin
- Corresponding author. (D.A.H.); (A.R.R.F.); (A.S.); (P.C.); (Y.H.)
| | - Piero Carninci
- Corresponding author. (D.A.H.); (A.R.R.F.); (A.S.); (P.C.); (Y.H.)
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Andersson R. Promoter or enhancer, what's the difference? Deconstruction of established distinctions and presentation of a unifying model. Bioessays 2014; 37:314-23. [PMID: 25450156 DOI: 10.1002/bies.201400162] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Gene transcription is strictly controlled by the interplay of regulatory events at gene promoters and gene-distal regulatory elements called enhancers. Despite extensive studies of enhancers, we still have a very limited understanding of their mechanisms of action and their restricted spatio-temporal activities. A better understanding would ultimately lead to fundamental insights into the control of gene transcription and the action of regulatory genetic variants involved in disease. Here, I review and discuss pros and cons of state-of-the-art genomics methods to localize and infer the activity of enhancers. Among the different approaches, profiling of enhancer RNAs yields the highest specificity and may be superior in detecting in vivo activity. I discuss their apparent similarities to promoters, which challenge the established view of enhancers and promoters as distinct entities, and present a unifying model of regulatory elements in transcriptional regulation, in which activity, transcriptional output and regulatory function is context specific.
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Affiliation(s)
- Robin Andersson
- The Bioinformatics Centre, Section for Computational and RNA Biology, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Denmark
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Cao J. The functional role of long non-coding RNAs and epigenetics. Biol Proced Online 2014; 16:11. [PMID: 25276098 PMCID: PMC4177375 DOI: 10.1186/1480-9222-16-11] [Citation(s) in RCA: 246] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 09/06/2014] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides. The post-transcriptional regulation is influenced by these lncRNAs by interfering with the microRNA pathways, involving in diverse cellular processes. The regulation of gene expression by lncRNAs at the epigenetic level, transcriptional and post-transcriptional level have been well known and widely studied. Recent recognition that lncRNAs make effects in many biological and pathological processes such as stem cell pluripotency, neurogenesis, oncogenesis and etc. This review will focus on the functional roles of lncRNAs in epigenetics and related research progress will be summarized.
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Affiliation(s)
- Jinneng Cao
- Department of respiratory medicine, Fuyong People's Hospital, Baoan District, Shenzhen 518103, Guangdong, People's Republic of China
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