401
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Withoff S, Li Y, Jonkers I, Wijmenga C. Understanding Celiac Disease by Genomics. Trends Genet 2016; 32:295-308. [PMID: 26972670 DOI: 10.1016/j.tig.2016.02.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/15/2016] [Accepted: 02/16/2016] [Indexed: 02/06/2023]
Abstract
Celiac disease (CeD) is a complex immune-mediated disease. Genetic studies have implicated 43 predisposing loci that collectively explain some 50% of the genetic variance in CeD. More than ∼90% of CeD-associated single nucleotide polymorphisms (SNPs) localize to the non-coding genome, which we need to better understand to translate genetic knowledge into clinical practice. New genomic technologies and resources are permitting a systematic analysis of the functional elements in the non-coding part of the genome. Here we explain how investigating the regulatory and epigenomic landscape will help to pinpoint the cell types involved in CeD, and the driver genes and gene regulatory networks that are affected by CeD-associated SNPs.
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Affiliation(s)
- Sebo Withoff
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
| | - Yang Li
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Iris Jonkers
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
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402
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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: 492] [Impact Index Per Article: 61.5] [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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403
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Nojima T, Gomes T, Carmo-Fonseca M, Proudfoot NJ. Mammalian NET-seq analysis defines nascent RNA profiles and associated RNA processing genome-wide. Nat Protoc 2016; 11:413-28. [PMID: 26844429 PMCID: PMC5152764 DOI: 10.1038/nprot.2016.012] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The transcription cycle of RNA polymerase II (Pol II) correlates with changes to the phosphorylation state of its large subunit C-terminal domain (CTD). We recently developed Native Elongation Transcript sequencing using mammalian cells (mNET-seq), which generates single-nucleotide-resolution genome-wide profiles of nascent RNA and co-transcriptional RNA processing that are associated with different CTD phosphorylation states. Here we provide a detailed protocol for mNET-seq. First, Pol II elongation complexes are isolated with specific phospho-CTD antibodies from chromatin solubilized by micrococcal nuclease digestion. Next, RNA derived from within the Pol II complex is size fractionated and Illumina sequenced. Using mNET-seq, we have previously shown that Pol II pauses at both ends of protein-coding genes but with different CTD phosphorylation patterns, and we have also detected phosphorylation at serine 5 (Ser5-P) CTD-specific splicing intermediates and Pol II accumulation over co-transcriptionally spliced exons. With moderate biochemical and bioinformatic skills, mNET-seq can be completed in ∼6 d, not including sequencing and data analysis.
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Affiliation(s)
- Takayuki Nojima
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Tomás Gomes
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
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404
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Flynn RA, Do BT, Rubin AJ, Calo E, Lee B, Kuchelmeister H, Rale M, Chu C, Kool ET, Wysocka J, Khavari PA, Chang HY. 7SK-BAF axis controls pervasive transcription at enhancers. Nat Struct Mol Biol 2016; 23:231-8. [PMID: 26878240 PMCID: PMC4982704 DOI: 10.1038/nsmb.3176] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 01/20/2016] [Indexed: 01/08/2023]
Abstract
RNA functions at enhancers remain mysterious. Here we show that the 7SK small nuclear RNA (snRNA) inhibits enhancer transcription by modulating nucleosome position. 7SK occupies enhancers and super enhancers genome-wide in mouse and human cells, and 7SK is required to limit eRNA initiation and synthesis in a manner distinct from promoter pausing. Clustered elements at super enhancers uniquely require 7SK to prevent convergent transcription and DNA damage signaling. 7SK physically interacts with the BAF chromatin remodeling complex, recruit BAF to enhancers, and inhibits enhancer transcription by modulating chromatin structure. In turn, 7SK occupancy at enhancers coincides with Brd4 and is exquisitely sensitive to the bromodomain inhibitor JQ1. Thus, 7SK employs distinct mechanisms to counteract diverse consequences of pervasive transcription that distinguish super enhancers, enhancers, and promoters.
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Affiliation(s)
- Ryan A Flynn
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Brian T Do
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Adam J Rubin
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Eliezer Calo
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Byron Lee
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | | | - Michael Rale
- The Genome Institute, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Ci Chu
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, California, USA
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
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405
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Pugh BF, Venters BJ. Genomic Organization of Human Transcription Initiation Complexes. PLoS One 2016; 11:e0149339. [PMID: 26866362 PMCID: PMC4750860 DOI: 10.1371/journal.pone.0149339] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 01/29/2016] [Indexed: 11/29/2022] Open
Abstract
A repertoire of transcription initiation factors engage the core promoter of mRNA genes to recruit RNA polymerase (Pol) II to initiate transcription, yet their precise spatial organization remains unclear. Using ChIP-exo, here we detail the interactions and genomic organization of initiation factors TBP, TFIIB, and Pol II at mRNA genes and within CpG islands. We find that when Pol II moves into a transcriptionally paused state, TBP/TFIIB remain at the promoter. We show that TBP and TFIIB bound to the core promoter at two separate, resolvable locations that coincided with sites of divergent transcription initiation. We also examine the precise binding of TBP at Pol III transcribed tRNA genes. We find that TBP crosslinked to tRNA genes in a similar manner as at Pol II transcribed genes. This comprehensive and high resolution genome-wide detection of the initiation machinery produces a consolidated view of transcription initiation events humans at Pol II coding and Pol III transcribed tRNA genes.
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Affiliation(s)
- B. Franklin Pugh
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Bryan J. Venters
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
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406
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407
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Andersson R, Chen Y, Core L, Lis JT, Sandelin A, Jensen TH. Human Gene Promoters Are Intrinsically Bidirectional. Mol Cell 2016; 60:346-7. [PMID: 26545074 DOI: 10.1016/j.molcel.2015.10.015] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark
| | - Yun Chen
- The Bioinformatics Centre, Section for Computational and RNA Biology, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark
| | - Leighton Core
- Department of Molecular & Cell Biology, Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Albin Sandelin
- The Bioinformatics Centre, Section for Computational and RNA Biology, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark.
| | - Torben Heick Jensen
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, C.F. Møllers Alle 3, Building 1130, 8000 Aarhus, Denmark.
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408
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Kalantari R, Chiang CM, Corey DR. Regulation of mammalian transcription and splicing by Nuclear RNAi. Nucleic Acids Res 2016; 44:524-37. [PMID: 26612865 PMCID: PMC4737150 DOI: 10.1093/nar/gkv1305] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 11/04/2015] [Accepted: 11/09/2015] [Indexed: 12/21/2022] Open
Abstract
RNA interference (RNAi) is well known as a mechanism for controlling mammalian mRNA translation in the cytoplasm, but what would be the consequences if it also functions in cell nuclei? Although RNAi has also been found in nuclei of plants, yeast, and other organisms, there has been relatively little progress towards understanding the potential involvement of mammalian RNAi factors in nuclear processes including transcription and splicing. This review summarizes evidence for mammalian RNAi factors in cell nuclei and mechanisms that might contribute to the control of gene expression. When RNAi factors bind small RNAs, they form ribonucleoprotein complexes that can be selective for target sequences within different classes of nuclear RNA substrates. The versatility of nuclear RNAi may supply a previously underappreciated layer of regulation to transcription, splicing, and other nuclear processes.
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Affiliation(s)
- Roya Kalantari
- Departments of Pharmacology & Biochemistry, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - Cheng-Ming Chiang
- Departments of Pharmacology & Biochemistry, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-8807, USA
| | - David R Corey
- Departments of Pharmacology & Biochemistry, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
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409
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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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410
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Haberle V, Lenhard B. Promoter architectures and developmental gene regulation. Semin Cell Dev Biol 2016; 57:11-23. [PMID: 26783721 DOI: 10.1016/j.semcdb.2016.01.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 01/08/2016] [Accepted: 01/11/2016] [Indexed: 01/03/2023]
Abstract
Core promoters are minimal regions sufficient to direct accurate initiation of transcription and are crucial for regulation of gene expression. They are highly diverse in terms of associated core promoter motifs, underlying sequence composition and patterns of transcription initiation. Distinctive features of promoters are also seen at the chromatin level, including nucleosome positioning patterns and presence of specific histone modifications. Recent advances in identifying and characterizing promoters using next-generation sequencing-based technologies have provided the basis for their classification into functional groups and have shed light on their modes of regulation, with important implications for transcriptional regulation in development. This review discusses the methodology and the results of genome-wide studies that provided insight into the diversity of RNA polymerase II promoter architectures in vertebrates and other Metazoa, and the association of these architectures with distinct modes of regulation in embryonic development and differentiation.
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Affiliation(s)
- Vanja Haberle
- Institute of Clinical Sciences and MRC Clinical Sciences Center, Faculty of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK; Department of Biology, University of Bergen, Thormøhlensgate 53A, N-5008 Bergen, Norway
| | - Boris Lenhard
- Institute of Clinical Sciences and MRC Clinical Sciences Center, Faculty of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK.
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411
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Stavreva DA, Hager GL. Chromatin structure and gene regulation: a dynamic view of enhancer function. Nucleus 2016; 6:442-8. [PMID: 26765055 DOI: 10.1080/19491034.2015.1107689] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Localized chromatin organization is now recognized as an important determinant of cell identity and developmental pathways. Recent studies have demonstrated that these epigenetic states are unexpectedly dynamic and malleable. In this Extra view we will highlight the transient nature of stimulus-induced enhancer accessibility and its importance for transcription regulation. Using glucocorticoid receptor (GR) as a model system we will discuss spatiotemporal relationships between receptor/chromatin interactions, lifetimes of the DNase I hypersensitivity sites (DHSs), long-range interactions, and gene regulation. We propose that differential temporal activation and utilization of distal regulatory elements plays a role in directing divergent stimulus-induced transcriptional programs.
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Affiliation(s)
- Diana A Stavreva
- a Laboratory of Receptor Biology and Gene Expression; National Cancer Institute; National Institutes of Health ; Bethesda , MD USA
| | - Gordon L Hager
- a Laboratory of Receptor Biology and Gene Expression; National Cancer Institute; National Institutes of Health ; Bethesda , MD USA
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412
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Carelli FN, Hayakawa T, Go Y, Imai H, Warnefors M, Kaessmann H. The life history of retrocopies illuminates the evolution of new mammalian genes. Genome Res 2016; 26:301-14. [PMID: 26728716 PMCID: PMC4772013 DOI: 10.1101/gr.198473.115] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 12/21/2015] [Indexed: 02/03/2023]
Abstract
New genes contribute substantially to adaptive evolutionary innovation, but the functional evolution of new mammalian genes has been little explored at a broad scale. Previous work established mRNA-derived gene duplicates, known as retrocopies, as models for the study of new gene origination. Here we combine mammalian transcriptomic and epigenomic data to unveil the processes underlying the evolution of stripped-down retrocopies into complex new genes. We show that although some robustly expressed retrocopies are transcribed from preexisting promoters, most evolved new promoters from scratch or recruited proto-promoters in their genomic vicinity. In particular, many retrocopy promoters emerged from ancestral enhancers (or bivalent regulatory elements) or are located in CpG islands not associated with other genes. We detected 88–280 selectively preserved retrocopies per mammalian species, illustrating that these mechanisms facilitated the birth of many functional retrogenes during mammalian evolution. The regulatory evolution of originally monoexonic retrocopies was frequently accompanied by exon gain, which facilitated co-option of distant promoters and allowed expression of alternative isoforms. While young retrogenes are often initially expressed in the testis, increased regulatory and structural complexities allowed retrogenes to functionally diversify and evolve somatic organ functions, sometimes as complex as those of their parents. Thus, some retrogenes evolved the capacity to temporarily substitute for their parents during the process of male meiotic X inactivation, while others rendered parental functions superfluous, allowing for parental gene loss. Overall, our reconstruction of the “life history” of mammalian retrogenes highlights retroposition as a general model for understanding new gene birth and functional evolution.
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Affiliation(s)
- Francesco Nicola Carelli
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Takashi Hayakawa
- Department of Wildlife Science (Nagoya Railroad Company, Limited), Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan; Japan Monkey Center, Inuyama, Aichi 484-0081, Japan
| | - Yasuhiro Go
- Department of Brain Sciences, Center for Novel Science Initiatives, National Institutes of Natural Sciences, Okazaki, Aichi 444-8585, Japan; Department of Developmental Physiology, National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan; Department of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 484-8585, Japan
| | - Hiroo Imai
- Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Maria Warnefors
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Henrik Kaessmann
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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413
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Identifying transcription start sites and active enhancer elements using BruUV-seq. Sci Rep 2015; 5:17978. [PMID: 26656874 PMCID: PMC4675984 DOI: 10.1038/srep17978] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/10/2015] [Indexed: 01/12/2023] Open
Abstract
BruUV-seq utilizes UV light to introduce transcription-blocking DNA lesions randomly in the genome prior to bromouridine-labeling and deep sequencing of nascent RNA. By inhibiting transcription elongation, but not initiation, pre-treatment with UV light leads to a redistribution of transcription reads resulting in the enhancement of nascent RNA signal towards the 5′-end of genes promoting the identification of transcription start sites (TSSs). Furthermore, transcripts associated with arrested RNA polymerases are protected from 3′–5′ degradation and thus, unstable transcripts such as putative enhancer RNA (eRNA) are dramatically increased. Validation of BruUV-seq against GRO-cap that identifies capped run-on transcripts showed that most BruUV-seq peaks overlapped with GRO-cap signal over both TSSs and enhancer elements. Finally, BruUV-seq identified putative enhancer elements induced by tumor necrosis factor (TNF) treatment concomitant with expression of nearby TNF-induced genes. Taken together, BruUV-seq is a powerful new approach for identifying TSSs and active enhancer elements genome-wide in intact cells.
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414
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Kleftogiannis D, Kalnis P, Bajic VB. Progress and challenges in bioinformatics approaches for enhancer identification. Brief Bioinform 2015; 17:967-979. [PMID: 26634919 PMCID: PMC5142011 DOI: 10.1093/bib/bbv101] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 10/22/2015] [Indexed: 12/20/2022] Open
Abstract
Enhancers are cis-acting DNA elements that play critical roles in distal regulation of gene expression. Identifying enhancers is an important step for understanding distinct gene expression programs that may reflect normal and pathogenic cellular conditions. Experimental identification of enhancers is constrained by the set of conditions used in the experiment. This requires multiple experiments to identify enhancers, as they can be active under specific cellular conditions but not in different cell types/tissues or cellular states. This has opened prospects for computational prediction methods that can be used for high-throughput identification of putative enhancers to complement experimental approaches. Potential functions and properties of predicted enhancers have been catalogued and summarized in several enhancer-oriented databases. Because the current methods for the computational prediction of enhancers produce significantly different enhancer predictions, it will be beneficial for the research community to have an overview of the strategies and solutions developed in this field. In this review, we focus on the identification and analysis of enhancers by bioinformatics approaches. First, we describe a general framework for computational identification of enhancers, present relevant data types and discuss possible computational solutions. Next, we cover over 30 existing computational enhancer identification methods that were developed since 2000. Our review highlights advantages, limitations and potentials, while suggesting pragmatic guidelines for development of more efficient computational enhancer prediction methods. Finally, we discuss challenges and open problems of this topic, which require further consideration.
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415
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Roman TS, Marvelle AF, Fogarty MP, Vadlamudi S, Gonzalez AJ, Buchkovich ML, Huyghe JR, Fuchsberger C, Jackson AU, Wu Y, Civelek M, Lusis AJ, Gaulton KJ, Sethupathy P, Kangas AJ, Soininen P, Ala-Korpela M, Kuusisto J, Collins FS, Laakso M, Boehnke M, Mohlke KL. Multiple Hepatic Regulatory Variants at the GALNT2 GWAS Locus Associated with High-Density Lipoprotein Cholesterol. Am J Hum Genet 2015; 97:801-15. [PMID: 26637976 PMCID: PMC4678431 DOI: 10.1016/j.ajhg.2015.10.016] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 10/28/2015] [Indexed: 11/24/2022] Open
Abstract
Genome-wide association studies (GWASs) have identified more than 150 loci associated with blood lipid and cholesterol levels; however, the functional and molecular mechanisms for many associations are unknown. We examined the functional regulatory effects of candidate variants at the GALNT2 locus associated with high-density lipoprotein cholesterol (HDL-C). Fine-mapping and conditional analyses in the METSIM study identified a single locus harboring 25 noncoding variants (r(2) > 0.7 with the lead GWAS variants) strongly associated with total cholesterol in medium-sized HDL (e.g., rs17315646, p = 3.5 × 10(-12)). We used luciferase reporter assays in HepG2 cells to test all 25 variants for allelic differences in regulatory enhancer activity. rs2281721 showed allelic differences in transcriptional activity (75-fold [T] versus 27-fold [C] more than the empty-vector control), as did a separate 780-bp segment containing rs4846913, rs2144300, and rs6143660 (49-fold [AT(-) haplotype] versus 16-fold [CC(+) haplotype] more). Using electrophoretic mobility shift assays, we observed differential CEBPB binding to rs4846913, and we confirmed this binding in a native chromatin context by performing chromatin-immunoprecipitation (ChIP) assays in HepG2 and Huh-7 cell lines of differing genotypes. Additionally, sequence reads in HepG2 DNase-I-hypersensitivity and CEBPB ChIP-seq signals spanning rs4846913 showed significant allelic imbalance. Allelic-expression-imbalance assays performed with RNA from primary human hepatocyte samples and expression-quantitative-trait-locus (eQTL) data in human subcutaneous adipose tissue samples confirmed that alleles associated with increased HDL-C are associated with a modest increase in GALNT2 expression. Together, these data suggest that at least rs4846913 and rs2281721 play key roles in influencing GALNT2 expression at this HDL-C locus.
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Affiliation(s)
- Tamara S Roman
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Amanda F Marvelle
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marie P Fogarty
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Swarooparani Vadlamudi
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Arlene J Gonzalez
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Martin L Buchkovich
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeroen R Huyghe
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christian Fuchsberger
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anne U Jackson
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ying Wu
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mete Civelek
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biomedical Engineering, Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Aldons J Lusis
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Deparment of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kyle J Gaulton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Praveen Sethupathy
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Antti J Kangas
- Computational Medicine, Institute of Health Sciences, University of Oulu, 90014 Oulu, Finland
| | - Pasi Soininen
- Computational Medicine, Institute of Health Sciences, University of Oulu, 90014 Oulu, Finland; Nuclear Magnetic Resonance Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, 70211 Kuopio, Finland
| | - Mika Ala-Korpela
- Computational Medicine, Institute of Health Sciences, University of Oulu, 90014 Oulu, Finland; Nuclear Magnetic Resonance Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, 70211 Kuopio, Finland; Oulu University Hospital, 90220 Oulu, Finland; Computational Medicine, School of Social and Community Medicine and Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK
| | - Johanna Kuusisto
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, 70210 Kuopio, Finland
| | - Francis S Collins
- National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, 70210 Kuopio, Finland
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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416
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Kim TK, Shiekhattar R. Architectural and Functional Commonalities between Enhancers and Promoters. Cell 2015; 162:948-59. [PMID: 26317464 DOI: 10.1016/j.cell.2015.08.008] [Citation(s) in RCA: 221] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Indexed: 01/23/2023]
Abstract
With the explosion of genome-wide studies of regulated transcription, it has become clear that traditional definitions of enhancers and promoters need to be revisited. These control elements can now be characterized in terms of their local and regional architecture, their regulatory components, including histone modifications and associated binding factors, and their functional contribution to transcription. This Review discusses unifying themes between promoters and enhancers in transcriptional regulatory mechanisms.
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Affiliation(s)
- Tae-Kyung Kim
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA.
| | - Ramin Shiekhattar
- University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Department of Human Genetics, Biomedical Research Building, Room 719, 1501 NW 10(th) Avenue, Miami, FL 33136, USA.
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417
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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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418
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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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419
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Albrecht AS, Ørom UA. Bidirectional expression of long ncRNA/protein-coding gene pairs in cancer. Brief Funct Genomics 2015; 15:167-73. [DOI: 10.1093/bfgp/elv048] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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420
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Nadel J, Athanasiadou R, Lemetre C, Wijetunga NA, Ó Broin P, Sato H, Zhang Z, Jeddeloh J, Montagna C, Golden A, Seoighe C, Greally JM. RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships. Epigenetics Chromatin 2015; 8:46. [PMID: 26579211 PMCID: PMC4647656 DOI: 10.1186/s13072-015-0040-6] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 10/29/2015] [Indexed: 01/01/2023] Open
Abstract
Background RNA:DNA hybrids represent a non-canonical nucleic acid structure that has been associated with a range of human diseases and potential transcriptional regulatory functions. Mapping of RNA:DNA hybrids in human cells reveals them to have a number of characteristics that give insights into their functions. Results We find RNA:DNA hybrids to occupy millions of base pairs in the human genome. A directional sequencing approach shows the RNA component of the RNA:DNA hybrid to be purine-rich, indicating a thermodynamic contribution to their in vivo stability. The RNA:DNA hybrids are enriched at loci with decreased DNA methylation and increased DNase hypersensitivity, and within larger domains with characteristics of heterochromatin formation, indicating potential transcriptional regulatory properties. Mass spectrometry studies of chromatin at RNA:DNA hybrids shows the presence of the ILF2 and ILF3 transcription factors, supporting a model of certain transcription factors binding preferentially to the RNA:DNA conformation. Conclusions Overall, there is little to indicate a dependence for RNA:DNA hybrids forming co-transcriptionally, with results from the ribosomal DNA repeat unit instead supporting the intriguing model of RNA generating these structures intrans. The results of the study indicate heterogeneous functions of these genomic elements and new insights into their formation and stability in vivo. Electronic supplementary material The online version of this article (doi:10.1186/s13072-015-0040-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julie Nadel
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Rodoniki Athanasiadou
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA ; Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY 10003 USA
| | - Christophe Lemetre
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA ; Integrated Genomics Operation, Memorial Sloan-Kettering Cancer Center, New York, NY 10065 USA
| | - N Ari Wijetunga
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Pilib Ó Broin
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Hanae Sato
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Zhengdong Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | | | - Cristina Montagna
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Aaron Golden
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Cathal Seoighe
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, Galway, Ireland
| | - John M Greally
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA ; Department of Genetics, Center for Epigenomics and Division of Computational Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461 USA
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421
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Austenaa L, Barozzi I, Simonatto M, Masella S, Della Chiara G, Ghisletti S, Curina A, de Wit E, Bouwman B, de Pretis S, Piccolo V, Termanini A, Prosperini E, Pelizzola M, de Laat W, Natoli G. Transcription of Mammalian cis-Regulatory Elements Is Restrained by Actively Enforced Early Termination. Mol Cell 2015; 60:460-74. [DOI: 10.1016/j.molcel.2015.09.018] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 08/13/2015] [Accepted: 09/17/2015] [Indexed: 12/12/2022]
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422
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Li Y, Chen CY, Kaye AM, Wasserman WW. The identification of cis-regulatory elements: A review from a machine learning perspective. Biosystems 2015; 138:6-17. [PMID: 26499213 DOI: 10.1016/j.biosystems.2015.10.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 10/09/2015] [Accepted: 10/14/2015] [Indexed: 01/06/2023]
Abstract
The majority of the human genome consists of non-coding regions that have been called junk DNA. However, recent studies have unveiled that these regions contain cis-regulatory elements, such as promoters, enhancers, silencers, insulators, etc. These regulatory elements can play crucial roles in controlling gene expressions in specific cell types, conditions, and developmental stages. Disruption to these regions could contribute to phenotype changes. Precisely identifying regulatory elements is key to deciphering the mechanisms underlying transcriptional regulation. Cis-regulatory events are complex processes that involve chromatin accessibility, transcription factor binding, DNA methylation, histone modifications, and the interactions between them. The development of next-generation sequencing techniques has allowed us to capture these genomic features in depth. Applied analysis of genome sequences for clinical genetics has increased the urgency for detecting these regions. However, the complexity of cis-regulatory events and the deluge of sequencing data require accurate and efficient computational approaches, in particular, machine learning techniques. In this review, we describe machine learning approaches for predicting transcription factor binding sites, enhancers, and promoters, primarily driven by next-generation sequencing data. Data sources are provided in order to facilitate testing of novel methods. The purpose of this review is to attract computational experts and data scientists to advance this field.
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Affiliation(s)
- Yifeng Li
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia Vancouver, British Columbia V5Z 4H4, Canada; Information and Communications Technologies, National Research Council of Canada, Ottawa, Ontario K1A 0R6, Canada.
| | - Chih-Yu Chen
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia Vancouver, British Columbia V5Z 4H4, Canada.
| | - Alice M Kaye
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia Vancouver, British Columbia V5Z 4H4, Canada.
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia Vancouver, British Columbia V5Z 4H4, Canada.
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423
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Savic D, Roberts BS, Carleton JB, Partridge EC, White MA, Cohen BA, Cooper GM, Gertz J, Myers RM. Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/ enhancer-binding protein beta binding sites. Genome Res 2015; 25:1791-800. [PMID: 26486725 PMCID: PMC4665001 DOI: 10.1101/gr.191593.115] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 10/14/2015] [Indexed: 01/20/2023]
Abstract
Transcription factors (TFs) bind to thousands of DNA sequences in mammalian genomes, but most of these binding events appear to have no direct effect on gene expression. It is unclear why only a subset of TF bound sites are actively involved in transcriptional regulation. Moreover, the key genomic features that accurately discriminate between active and inactive TF binding events remain ambiguous. Recent studies have identified promoter-distal RNA polymerase II (RNAP2) binding at enhancer elements, suggesting that these interactions may serve as a marker for active regulatory sequences. Despite these correlative analyses, a thorough functional validation of these genomic co-occupancies is still lacking. To characterize the gene regulatory activity of DNA sequences underlying promoter-distal TF binding events that co-occur with RNAP2 and TF sites devoid of RNAP2 occupancy using a functional reporter assay, we performed cis-regulatory element sequencing (CRE-seq). We tested more than 1000 promoter-distal CCAAT/enhancer-binding protein beta (CEBPB)-bound sites in HepG2 and K562 cells, and found that CEBPB-bound sites co-occurring with RNAP2 were more likely to exhibit enhancer activity. CEBPB-bound sites further maintained substantial cell-type specificity, indicating that local DNA sequence can accurately convey cell-type-specific regulatory information. By comparing our CRE-seq results to a comprehensive set of genome annotations, we identified a variety of genomic features that are strong predictors of regulatory element activity and cell-type-specific activity. Collectively, our functional assay results indicate that RNAP2 occupancy can be used as a key genomic marker that can distinguish active from inactive TF bound sites.
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Affiliation(s)
- Daniel Savic
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Brian S Roberts
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Julia B Carleton
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | | | - Michael A White
- Washington University at St. Louis, Center for Genome Sciences and Systems Biology, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Barak A Cohen
- Washington University at St. Louis, Center for Genome Sciences and Systems Biology, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Jason Gertz
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
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424
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Welsh IC, Kwak H, Chen FL, Werner M, Shopland LS, Danko CG, Lis JT, Zhang M, Martin JF, Kurpios NA. Chromatin Architecture of the Pitx2 Locus Requires CTCF- and Pitx2-Dependent Asymmetry that Mirrors Embryonic Gut Laterality. Cell Rep 2015; 13:337-49. [PMID: 26411685 PMCID: PMC4617833 DOI: 10.1016/j.celrep.2015.08.075] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/20/2015] [Accepted: 08/24/2015] [Indexed: 11/24/2022] Open
Abstract
Expression of Pitx2 on the left side of the embryo patterns left-right (LR) organs including the dorsal mesentery (DM), whose asymmetric cell behavior directs gut looping. Despite the importance of organ laterality, chromatin-level regulation of Pitx2 remains undefined. Here, we show that genes immediately neighboring Pitx2 in chicken and mouse, including a long noncoding RNA (Pitx2 locus-asymmetric regulated RNA or Playrr), are expressed on the right side and repressed by Pitx2. CRISPR/Cas9 genome editing of Playrr, 3D fluorescent in situ hybridization (FISH), and variations of chromatin conformation capture (3C) demonstrate that mutual antagonism between Pitx2 and Playrr is coordinated by asymmetric chromatin interactions dependent on Pitx2 and CTCF. We demonstrate that transcriptional and morphological asymmetries driving gut looping are mirrored by chromatin architectural asymmetries at the Pitx2 locus. We propose a model whereby Pitx2 auto-regulation directs chromatin topology to coordinate LR transcription of this locus essential for LR organogenesis.
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Affiliation(s)
- Ian C Welsh
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Frances L Chen
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Melissa Werner
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Lindsay S Shopland
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA; Eastern Maine Medical Center Cancer Care, 33 Whiting Hill Road, Brewer, ME 04412, USA
| | - Charles G Danko
- Department of Biomedical Sciences, The Baker Institute for Animal Health, Cornell University, Ithaca, NY 14853, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Min Zhang
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - James F Martin
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Heart Institute, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Natasza A Kurpios
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.
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425
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Scheidegger A, Nechaev S. RNA polymerase II pausing as a context-dependent reader of the genome. Biochem Cell Biol 2015; 94:82-92. [PMID: 26555214 DOI: 10.1139/bcb-2015-0045] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The RNA polymerase II (Pol II) transcribes all mRNA genes in eukaryotes and is among the most highly regulated enzymes in the cell. The classic model of mRNA gene regulation involves recruitment of the RNA polymerase to gene promoters in response to environmental signals. Higher eukaryotes have an additional ability to generate multiple cell types. This extra level of regulation enables each cell to interpret the same genome by committing to one of the many possible transcription programs and executing it in a precise and robust manner. Whereas multiple mechanisms are implicated in cell type-specific transcriptional regulation, how one genome can give rise to distinct transcriptional programs and what mechanisms activate and maintain the appropriate program in each cell remains unclear. This review focuses on the process of promoter-proximal Pol II pausing during early transcription elongation as a key step in context-dependent interpretation of the metazoan genome. We highlight aspects of promoter-proximal Pol II pausing, including its interplay with epigenetic mechanisms, that may enable cell type-specific regulation, and emphasize some of the pertinent questions that remain unanswered and open for investigation.
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Affiliation(s)
- Adam Scheidegger
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58201, USA.,Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58201, USA
| | - Sergei Nechaev
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58201, USA.,Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58201, USA
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426
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Abstract
While a role of promoter-proximal RNA Polymerase II (Pol II) pausing in regulation of eukaryotic gene expression is implied, the mechanisms and dynamics of this process are poorly understood. We performed genome-wide analysis of short capped RNAs (scRNAs) and Pol II chromatin immunoprecipitation sequencing (ChIP-seq) in human breast cancer MCF-7 cells to better understand Pol II pausing (Samarakkody, A., Abbas, A., Scheidegger, A., Warns, J., Nnoli, O., Jokinen, B., Zarns, K., Kubat, B., Dhasarathy, A. and Nechaev, S. (2015) RNA polymerase II pausing can be retained or acquired during activation of genes involved in the epithelial to mesenchymal transition. Nucleic Acids Res43, 3938–3949). The data are available at the NCBI Gene Expression Omnibus under accession number GSE67041. For both ChIP and scRNA samples, we used paired end sequencing on the Illumina MiSeq instrument. For ChIP-seq, the use of paired end sequencing allowed us to avoid ambiguities in center-read definition. For scRNA seq, this allowed us to identify both the 5′-end and the 3′-end in the same run that represent, respectively, the transcription start sites and the locations of Pol II pausing. The sharpening of Pol II ChIP-seq metagene profiles when aligned against 5′-ends of scRNAs indicates that these RNAs can be used to define the start sites for the majority of mRNA transcription events.
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427
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Romanoski CE, Link VM, Heinz S, Glass CK. Exploiting genomics and natural genetic variation to decode macrophage enhancers. Trends Immunol 2015; 36:507-18. [PMID: 26298065 PMCID: PMC4548828 DOI: 10.1016/j.it.2015.07.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 07/15/2015] [Accepted: 07/17/2015] [Indexed: 12/18/2022]
Abstract
The mammalian genome contains on the order of a million enhancer-like regions that are required to establish the identities and functions of specific cell types. Here, we review recent studies in immune cells that have provided insight into the mechanisms that selectively activate certain enhancers in response to cell lineage and environmental signals. We describe a working model wherein distinct classes of transcription factors define the repertoire of active enhancers in macrophages through collaborative and hierarchical interactions, and discuss important challenges to this model, specifically providing examples from T cells. We conclude by discussing the use of natural genetic variation as a powerful approach for decoding transcription factor combinations that play dominant roles in establishing the enhancer landscapes, and the potential that these insights have for advancing our understanding of the molecular causes of human disease.
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Affiliation(s)
- Casey E Romanoski
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA
| | - Verena M Link
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA; Faculty of Biology, Department II, Ludwig-Maximilians Universität München, Planegg-Martinsried 85152, Germany
| | - Sven Heinz
- Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA.
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428
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Fraser J, Williamson I, Bickmore WA, Dostie J. An Overview of Genome Organization and How We Got There: from FISH to Hi-C. Microbiol Mol Biol Rev 2015; 79:347-72. [PMID: 26223848 PMCID: PMC4517094 DOI: 10.1128/mmbr.00006-15] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In humans, nearly two meters of genomic material must be folded to fit inside each micrometer-scale cell nucleus while remaining accessible for gene transcription, DNA replication, and DNA repair. This fact highlights the need for mechanisms governing genome organization during any activity and to maintain the physical organization of chromosomes at all times. Insight into the functions and three-dimensional structures of genomes comes mostly from the application of visual techniques such as fluorescence in situ hybridization (FISH) and molecular approaches including chromosome conformation capture (3C) technologies. Recent developments in both types of approaches now offer the possibility of exploring the folded state of an entire genome and maybe even the identification of how complex molecular machines govern its shape. In this review, we present key methodologies used to study genome organization and discuss what they reveal about chromosome conformation as it relates to transcription regulation across genomic scales in mammals.
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Affiliation(s)
- James Fraser
- Department of Biochemistry, and Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada
| | - Iain Williamson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Wendy A Bickmore
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Josée Dostie
- Department of Biochemistry, and Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada
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429
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Feuerborn A, Cook PR. Why the activity of a gene depends on its neighbors. Trends Genet 2015; 31:483-90. [PMID: 26259670 DOI: 10.1016/j.tig.2015.07.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 06/25/2015] [Accepted: 07/15/2015] [Indexed: 11/15/2022]
Abstract
Sixty years ago, the position of a gene on a chromosome was seen to be a major determinant of gene activity; however, position effects are rarely central to current discussions of gene expression. We describe a comprehensive and simplifying view of how position in 1D sequence and 3D nuclear space underlies expression. We suggest that apparently-different regulatory motifs including enhancers, silencers, insulators, barriers, and boundaries act similarly - they are active promoters that tether target genes close to, or distant from, appropriate transcription sites or 'factories'. We also suggest that any active transcription unit regulates the firing of its neighbors - and thus can be categorized as one or other type of motif; this is consistent with expression quantitative trait loci (eQTLs) being widely dispersed.
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Affiliation(s)
- Alexander Feuerborn
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Peter R Cook
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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430
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Nilson KA, Guo J, Turek ME, Brogie JE, Delaney E, Luse DS, Price DH. THZ1 Reveals Roles for Cdk7 in Co-transcriptional Capping and Pausing. Mol Cell 2015; 59:576-87. [PMID: 26257281 DOI: 10.1016/j.molcel.2015.06.032] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 06/01/2015] [Accepted: 06/23/2015] [Indexed: 12/31/2022]
Abstract
The Cdk7 subunit of TFIIH phosphorylates RNA polymerase II (Pol II) during initiation, and, while recent studies show that inhibition of human Cdk7 negatively influences transcription, the mechanisms involved are unclear. Using in vitro transcription with nuclear extract, we demonstrate that THZ1, a covalent Cdk7 inhibitor, causes defects in Pol II phosphorylation, co-transcriptional capping, promoter proximal pausing, and productive elongation. THZ1 does not affect initiation but blocks essentially all Pol II large subunit C-terminal domain (CTD) phosphorylation. We found that guanylylation of nascent RNAs is length dependent and modulated by a THZ1-sensitive factor present in nuclear extract. THZ1 impacts pausing through a capping-independent block of DSIF and NELF loading. The P-TEFb-dependent transition into productive elongation was also inhibited by THZ1, likely due to loss of DSIF. Capping and pausing were also reduced in THZ1-treated cells. Our results provide mechanistic insights into THZ1 action and how Cdk7 broadly influences transcription and capping.
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Affiliation(s)
- Kyle A Nilson
- Molecular and Cellular Biology Program, University of Iowa, Iowa City, IA 52242, USA
| | - Jiannan Guo
- Biochemistry Department, University of Iowa, Iowa City, IA 52242, USA
| | - Michael E Turek
- Biochemistry Department, University of Iowa, Iowa City, IA 52242, USA
| | - John E Brogie
- Biochemistry Department, University of Iowa, Iowa City, IA 52242, USA
| | - Elizabeth Delaney
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Donal S Luse
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - David H Price
- Molecular and Cellular Biology Program, University of Iowa, Iowa City, IA 52242, USA; Biochemistry Department, University of Iowa, Iowa City, IA 52242, USA.
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431
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Liu X, Kraus WL, Bai X. Ready, pause, go: regulation of RNA polymerase II pausing and release by cellular signaling pathways. Trends Biochem Sci 2015; 40:516-25. [PMID: 26254229 DOI: 10.1016/j.tibs.2015.07.003] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 06/07/2015] [Accepted: 07/06/2015] [Indexed: 01/06/2023]
Abstract
Promoter-proximal pausing by RNA polymerase II (Pol II) is a well-established mechanism to control the timing, rate, and possibly the magnitude of transcriptional responses. Recent studies have shown that cellular signaling pathways can regulate gene transcription and signaling outcomes by controlling Pol II pausing in a wide array of biological systems. Identification of the proteins and small molecules that affect the establishment and release of paused Pol II is shedding new light on the mechanisms and biology of Pol II pausing. This review focuses on the interplay between cellular signaling pathways and Pol II pausing during normal development and under disease conditions.
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Affiliation(s)
- Xiuli Liu
- Molecular Genetics of Blood Development Laboratory, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center at Dallas, TX 75390, USA; Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - W Lee Kraus
- Signaling and Gene Regulation Laboratory, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center at Dallas, TX 75390, USA; Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaoying Bai
- Molecular Genetics of Blood Development Laboratory, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center at Dallas, TX 75390, USA; Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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432
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433
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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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434
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Pundhir S, Gorodkin J. Differential and coherent processing patterns from small RNAs. Sci Rep 2015; 5:12062. [PMID: 26166713 PMCID: PMC4499813 DOI: 10.1038/srep12062] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 06/16/2015] [Indexed: 12/16/2022] Open
Abstract
Post-transcriptional processing events related to short RNAs are often reflected in their read profile patterns emerging from high-throughput sequencing data. MicroRNA arm switching across different tissues is a well-known example of what we define as differential processing. Here, short RNAs from the nine cell lines of the ENCODE project, irrespective of their annotation status, were analyzed for genomic loci representing differential or coherent processing. We observed differential processing predominantly in RNAs annotated as miRNA, snoRNA or tRNA. Four out of five known cases of differentially processed miRNAs that were in the input dataset were recovered and several novel cases were discovered. In contrast to differential processing, coherent processing is observed widespread in both annotated and unannotated regions. While the annotated loci predominantly consist of ~24 nt short RNAs, the unannotated loci comparatively consist of ~17 nt short RNAs. Furthermore, these ~17 nt short RNAs are significantly enriched for overlap to transcription start sites and DNase I hypersensitive sites (p-value < 0.01) that are characteristic features of transcription initiation RNAs. We discuss how the computational pipeline developed in this study has the potential to be applied to other forms of RNA-seq data for further transcriptome-wide studies of differential and coherent processing.
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Affiliation(s)
- Sachin Pundhir
- Center for non-coding RNA in Technology and Health, IKVH, University of Copenhagen, Grønnegårdsvej 3, 1870, Frederiksberg C, Denmark
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health, IKVH, University of Copenhagen, Grønnegårdsvej 3, 1870, Frederiksberg C, Denmark
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435
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Hu J, Adar S, Selby CP, Lieb JD, Sancar A. Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution. Genes Dev 2015; 29:948-60. [PMID: 25934506 PMCID: PMC4421983 DOI: 10.1101/gad.261271.115] [Citation(s) in RCA: 192] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hu et al. developed a method for genome-wide mapping of DNA excision repair named XR-seq (excision repair sequencing) and used it to produce stranded, nucleotide-resolution maps of repair of two UV-induced DNA damages in human cells. XR-seq and the resulting repair maps will facilitate studies of the effects of genomic location, chromatin context, transcription, and replication on DNA repair in human cells. We developed a method for genome-wide mapping of DNA excision repair named XR-seq (excision repair sequencing). Human nucleotide excision repair generates two incisions surrounding the site of damage, creating an ∼30-mer. In XR-seq, this fragment is isolated and subjected to high-throughput sequencing. We used XR-seq to produce stranded, nucleotide-resolution maps of repair of two UV-induced DNA damages in human cells: cyclobutane pyrimidine dimers (CPDs) and (6-4) pyrimidine–pyrimidone photoproducts [(6-4)PPs]. In wild-type cells, CPD repair was highly associated with transcription, specifically with the template strand. Experiments in cells defective in either transcription-coupled excision repair or general excision repair isolated the contribution of each pathway to the overall repair pattern and showed that transcription-coupled repair of both photoproducts occurs exclusively on the template strand. XR-seq maps capture transcription-coupled repair at sites of divergent gene promoters and bidirectional enhancer RNA (eRNA) production at enhancers. XR-seq data also uncovered the repair characteristics and novel sequence preferences of CPDs and (6-4)PPs. XR-seq and the resulting repair maps will facilitate studies of the effects of genomic location, chromatin context, transcription, and replication on DNA repair in human cells.
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Affiliation(s)
- Jinchuan Hu
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
| | - Sheera Adar
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Christopher P Selby
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
| | - Jason D Lieb
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA;
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436
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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: 137] [Impact Index Per Article: 15.2] [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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437
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Abstract
Recent advances in experimental and computational methodologies are enabling ultra-high resolution genome-wide profiles of protein-DNA binding events. For example, the ChIP-exo protocol precisely characterizes protein-DNA cross-linking patterns by combining chromatin immunoprecipitation (ChIP) with 5' → 3' exonuclease digestion. Similarly, deeply sequenced chromatin accessibility assays (e.g. DNase-seq and ATAC-seq) enable the detection of protected footprints at protein-DNA binding sites. With these techniques and others, we have the potential to characterize the individual nucleotides that interact with transcription factors, nucleosomes, RNA polymerases and other regulatory proteins in a particular cellular context. In this review, we explain the experimental assays and computational analysis methods that enable high-resolution profiling of protein-DNA binding events. We discuss the challenges and opportunities associated with such approaches.
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Affiliation(s)
- Shaun Mahony
- a Department of Biochemistry & Molecular Biology , Center for Eukaryotic Gene Regulation, The Pennsylvania State University , University Park , PA , USA
| | - B Franklin Pugh
- a Department of Biochemistry & Molecular Biology , Center for Eukaryotic Gene Regulation, The Pennsylvania State University , University Park , PA , USA
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438
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Erokhin M, Vassetzky Y, Georgiev P, Chetverina D. Eukaryotic enhancers: common features, regulation, and participation in diseases. Cell Mol Life Sci 2015; 72:2361-75. [PMID: 25715743 PMCID: PMC11114076 DOI: 10.1007/s00018-015-1871-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 02/07/2015] [Accepted: 02/20/2015] [Indexed: 01/01/2023]
Abstract
Enhancers are positive DNA regulatory sequences controlling temporal and tissue-specific gene expression. These elements act independently of their orientation and distance relative to the promoters of target genes. Enhancers act through a variety of transcription factors that ensure their correct match with target promoters and consequent gene activation. There is a growing body of evidence on association of enhancers with transcription factors, co-activators, histone chromatin marks, and lncRNAs. Alterations in enhancers lead to misregulation of gene expression, causing a number of human diseases. In this review, we focus on the common characteristics of enhancers required for transcription stimulation.
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Affiliation(s)
- Maksim Erokhin
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334 Russia
- LIA 1066, Laboratoire Franco-Russe de recherche en oncologie, 119334 Moscow, Russia
| | - Yegor Vassetzky
- LIA 1066, Laboratoire Franco-Russe de recherche en oncologie, 119334 Moscow, Russia
- UMR8126, Université Paris-Sud, CNRS, Institut de cancérologie Gustave Roussy, 94805 Villejuif, France
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334 Russia
- LIA 1066, Laboratoire Franco-Russe de recherche en oncologie, 119334 Moscow, Russia
| | - Darya Chetverina
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334 Russia
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439
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Scruggs BS, Gilchrist DA, Nechaev S, Muse GW, Burkholder A, Fargo DC, Adelman K. Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin. Mol Cell 2015; 58:1101-12. [PMID: 26028540 DOI: 10.1016/j.molcel.2015.04.006] [Citation(s) in RCA: 158] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 01/29/2015] [Accepted: 04/01/2015] [Indexed: 11/26/2022]
Abstract
Anti-sense transcription originating upstream of mammalian protein-coding genes is a well-documented phenomenon, but remarkably little is known about the regulation or function of anti-sense promoters and the non-coding RNAs they generate. Here we define at nucleotide resolution the divergent transcription start sites (TSSs) near mouse mRNA genes. We find that coupled sense and anti-sense TSSs precisely define the boundaries of a nucleosome-depleted region (NDR) that is highly enriched in transcription factor (TF) motifs. Notably, as the distance between sense and anti-sense TSSs increases, so does the size of the NDR, the level of signal-dependent TF binding, and gene activation. We further discover a group of anti-sense TSSs in macrophages with an enhancer-like chromatin signature. Interestingly, this signature identifies divergent promoters that are activated during immune challenge. We propose that anti-sense promoters serve as platforms for TF binding and establishment of active chromatin to further regulate or enhance sense-strand mRNA expression.
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Affiliation(s)
- Benjamin S Scruggs
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Daniel A Gilchrist
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Sergei Nechaev
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Ginger W Muse
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Adam Burkholder
- Center for Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - David C Fargo
- Center for Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Karen Adelman
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.
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440
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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: 127] [Impact Index Per Article: 14.1] [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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441
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Danino YM, Even D, Ideses D, Juven-Gershon T. The core promoter: At the heart of gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1116-31. [PMID: 25934543 DOI: 10.1016/j.bbagrm.2015.04.003] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/19/2015] [Accepted: 04/23/2015] [Indexed: 12/17/2022]
Abstract
The identities of different cells and tissues in multicellular organisms are determined by tightly controlled transcriptional programs that enable accurate gene expression. The mechanisms that regulate gene expression comprise diverse multiplayer molecular circuits of multiple dedicated components. The RNA polymerase II (Pol II) core promoter establishes the center of this spatiotemporally orchestrated molecular machine. Here, we discuss transcription initiation, diversity in core promoter composition, interactions of the basal transcription machinery with the core promoter, enhancer-promoter specificity, core promoter-preferential activation, enhancer RNAs, Pol II pausing, transcription termination, Pol II recycling and translation. We further discuss recent findings indicating that promoters and enhancers share similar features and may not substantially differ from each other, as previously assumed. Taken together, we review a broad spectrum of studies that highlight the importance of the core promoter and its pivotal role in the regulation of metazoan gene expression and suggest future research directions and challenges.
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Affiliation(s)
- Yehuda M Danino
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Dan Even
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Diana Ideses
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Tamar Juven-Gershon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel.
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442
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Abstract
INTRODUCTION Regulation of gene expression involves a variety of mechanisms driven by a complex regulatory network of factors. Control of transcription is an important step in gene expression regulation, which integrates the function of cis-acting and trans-acting elements. Among cis-regulatory elements, enhancer RNA (eRNA)-producing domains recently emerged as widespread and potent regulators of transcription and cell fate decision. Thus, manipulation of eRNA levels becomes a novel and appealing avenue for the design of new therapeutic treatments. AREAS COVERED In this review, we focus on eRNA-producing domains. We describe mechanisms involved in their cell-type specific selection and activation as well as their epigenetic features. In addition, we present their function and the growing evidences of their deregulation in human diseases. Finally, we discuss eRNAs as potential therapeutic targets. EXPERT OPINION As key factors in the control of transcription, eRNAs appear to possess a great potential for the establishment of new therapy options. However, thorough testing as well as providing the genetic toolbox to target eRNAs will be needed to fully assess the practical and clinical possibilities.
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Affiliation(s)
- Nicolas Léveillé
- The Netherlands Cancer Institute, Division of Biological Stress Response , Plesmanlaan 121, 1066 CX, Amsterdam , The Netherlands
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443
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Samarakkody A, Abbas A, Scheidegger A, Warns J, Nnoli O, Jokinen B, Zarns K, Kubat B, Dhasarathy A, Nechaev S. RNA polymerase II pausing can be retained or acquired during activation of genes involved in the epithelial to mesenchymal transition. Nucleic Acids Res 2015; 43:3938-49. [PMID: 25820424 PMCID: PMC4417172 DOI: 10.1093/nar/gkv263] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 03/17/2015] [Indexed: 12/26/2022] Open
Abstract
Promoter-proximal RNA polymerase II (Pol II) pausing is implicated in the regulation of gene transcription. However, the mechanisms of pausing including its dynamics during transcriptional responses remain to be fully understood. We performed global analysis of short capped RNAs and Pol II Chromatin Immunoprecipitation sequencing in MCF-7 breast cancer cells to map Pol II pausing across the genome, and used permanganate footprinting to specifically follow pausing during transcriptional activation of several genes involved in the epithelial to mesenchymal transition (EMT). We find that the gene for EMT master regulator Snail (SNAI1), but not Slug (SNAI2), shows evidence of Pol II pausing before activation. Transcriptional activation of the paused SNAI1 gene is accompanied by a further increase in Pol II pausing signal, whereas activation of non-paused SNAI2 gene results in the acquisition of a typical pausing signature. The increase in pausing signal reflects increased transcription initiation without changes in Pol II pausing. Activation of the heat shock HSP70 gene involves pausing release that speeds up Pol II turnover, but does not change pausing location. We suggest that Pol II pausing is retained during transcriptional activation and can further undergo regulated release in a signal-specific manner.
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Affiliation(s)
- Ann Samarakkody
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
| | - Ata Abbas
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
| | - Adam Scheidegger
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
| | - Jessica Warns
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
| | - Oscar Nnoli
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
| | - Bradley Jokinen
- Department of Computer Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Kris Zarns
- Department of Computer Sciences, University of North Dakota, Grand Forks, ND 58202, USA
| | - Brooke Kubat
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
| | - Archana Dhasarathy
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
| | - Sergei Nechaev
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58202, USA
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444
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Jonkers I, Lis JT. Getting up to speed with transcription elongation by RNA polymerase II. Nat Rev Mol Cell Biol 2015; 16:167-77. [PMID: 25693130 PMCID: PMC4782187 DOI: 10.1038/nrm3953] [Citation(s) in RCA: 586] [Impact Index Per Article: 65.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent advances in sequencing techniques that measure nascent transcripts and that reveal the positioning of RNA polymerase II (Pol II) have shown that the pausing of Pol II in promoter-proximal regions and its release to initiate a phase of productive elongation are key steps in transcription regulation. Moreover, after the release of Pol II from the promoter-proximal region, elongation rates are highly dynamic throughout the transcription of a gene, and vary on a gene-by-gene basis. Interestingly, Pol II elongation rates affect co-transcriptional processes such as splicing, termination and genome stability. Increasing numbers of factors and regulatory mechanisms have been associated with the steps of transcription elongation by Pol II, revealing that elongation is a highly complex process. Elongation is thus now recognized as a key phase in the regulation of transcription by Pol II.
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Affiliation(s)
- Iris Jonkers
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, 416 Biotechnology Building, 14853, Ithaca, New York, USA
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445
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Heinz S, Romanoski CE, Benner C, Glass CK. The selection and function of cell type-specific enhancers. Nat Rev Mol Cell Biol 2015; 16:144-54. [PMID: 25650801 PMCID: PMC4517609 DOI: 10.1038/nrm3949] [Citation(s) in RCA: 670] [Impact Index Per Article: 74.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The human body contains several hundred cell types, all of which share the same genome. In metazoans, much of the regulatory code that drives cell type-specific gene expression is located in distal elements called enhancers. Although mammalian genomes contain millions of potential enhancers, only a small subset of them is active in a given cell type. Cell type-specific enhancer selection involves the binding of lineage-determining transcription factors that prime enhancers. Signal-dependent transcription factors bind to primed enhancers, which enables these broadly expressed factors to regulate gene expression in a cell type-specific manner. The expression of genes that specify cell type identity and function is associated with densely spaced clusters of active enhancers known as super-enhancers. The functions of enhancers and super-enhancers are influenced by, and affect, higher-order genomic organization.
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Affiliation(s)
| | | | | | - Christopher K. Glass
- Department of Cellular and Molecular Medicine, UC San Diego
- Department of Medicine, UC San Diego
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446
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Roy AL, Singer DS. Core promoters in transcription: old problem, new insights. Trends Biochem Sci 2015; 40:165-71. [PMID: 25680757 DOI: 10.1016/j.tibs.2015.01.007] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 01/09/2015] [Accepted: 01/15/2015] [Indexed: 12/11/2022]
Abstract
Early studies established that transcription initiates within an approximately 50 bp DNA segment capable of nucleating the assembly of RNA polymerase II (Pol II) and associated general transcription factors (GTFs) necessary for transcriptional initiation; this region is called a core promoter. Subsequent analyses identified a series of conserved DNA sequence elements, present in various combinations or not at all, in core promoters. Recent genome-wide analyses have provided further insights into the complexity of core promoter architecture and function. Here we review recent studies that delineate the active role of core promoters in the transcriptional regulation of diverse physiological systems.
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Affiliation(s)
- Ananda L Roy
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA.
| | - Dinah S Singer
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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447
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Abstract
A new study detects unstable nascent RNAs and uncovers thousands of transcription initiation sites in promoters and enhancers. Detailed analysis shows that these initiation sites have a similar architecture and that they are differentiated by post-transcriptional regulation rather than transcription initiation.
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448
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Sequencing of first-strand cDNA library reveals full-length transcriptomes. Nat Commun 2015; 6:6002. [PMID: 25607527 DOI: 10.1038/ncomms7002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 12/02/2014] [Indexed: 11/09/2022] Open
Abstract
Massively parallel strand-specific sequencing of RNA (ssRNA-seq) has emerged as a powerful tool for profiling complex transcriptomes. However, many current methods for ssRNA-seq suffer from the underrepresentation of both the 5' and 3' ends of RNAs, which can be attributed to second-strand cDNA synthesis. The 5' and 3' ends of RNA harbour crucial information for gene regulation; namely, transcription start sites (TSSs) and polyadenylation sites. Here we report a novel ssRNA-seq method that does not involve second-strand cDNA synthesis, as we Directly Ligate sequencing Adaptors to the First-strand cDNA (DLAF). This novel method with fewer enzymatic reactions results in a higher quality of the libraries than the conventional method. Sequencing of DLAF libraries followed by a novel analysis pipeline enables the profiling of both 5' ends and polyadenylation sites at near-base resolution. Therefore, DLAF offers the first genomics tool to obtain the 'full-length' transcriptome with a single library.
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449
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Gulko B, Hubisz MJ, Gronau I, Siepel A. A method for calculating probabilities of fitness consequences for point mutations across the human genome. Nat Genet 2015; 47:276-83. [PMID: 25599402 PMCID: PMC4342276 DOI: 10.1038/ng.3196] [Citation(s) in RCA: 181] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 12/19/2014] [Indexed: 12/17/2022]
Abstract
We describe a novel computational method for estimating the probability that a point mutation at each position in a genome will influence fitness. These fitness consequence (fitCons) scores serve as evolution-based measures of potential genomic function. Our approach is to cluster genomic positions into groups exhibiting distinct “fingerprints” based on high-throughput functional genomic data, then to estimate a probability of fitness consequences for each group from associated patterns of genetic polymorphism and divergence. We have generated fitCons scores for three human cell types based on public data from ENCODE. Compared with conventional conservation scores, fitCons scores show considerably improved prediction power for cis-regulatory elements. In addition, fitCons scores indicate that 4.2–7.5% of nucleotides in the human genome have influenced fitness since the human-chimpanzee divergence, and they suggest that recent evolutionary turnover has had limited impact on the functional content of the genome.
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Affiliation(s)
- Brad Gulko
- Graduate Field of Computer Science, Cornell University, Ithaca, New York, USA
| | - Melissa J Hubisz
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
| | - Ilan Gronau
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
| | - Adam Siepel
- 1] Graduate Field of Computer Science, Cornell University, Ithaca, New York, USA. [2] Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
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