351
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Trinh LA, Chong-Morrison V, Gavriouchkina D, Hochgreb-Hägele T, Senanayake U, Fraser SE, Sauka-Spengler T. Biotagging of Specific Cell Populations in Zebrafish Reveals Gene Regulatory Logic Encoded in the Nuclear Transcriptome. Cell Rep 2017; 19:425-440. [PMID: 28402863 PMCID: PMC5400779 DOI: 10.1016/j.celrep.2017.03.045] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 12/21/2016] [Accepted: 03/13/2017] [Indexed: 11/22/2022] Open
Abstract
Interrogation of gene regulatory circuits in complex organisms requires precise tools for the selection of individual cell types and robust methods for biochemical profiling of target proteins. We have developed a versatile, tissue-specific binary in vivo biotinylation system in zebrafish termed biotagging that uses genetically encoded components to biotinylate target proteins, enabling in-depth genome-wide analyses of their molecular interactions. Using tissue-specific drivers and cell-compartment-specific effector lines, we demonstrate the specificity of the biotagging toolkit at the biochemical, cellular, and transcriptional levels. We use biotagging to characterize the in vivo transcriptional landscape of migratory neural crest and myocardial cells in different cellular compartments (ribosomes and nucleus). These analyses reveal a comprehensive network of coding and non-coding RNAs and cis-regulatory modules, demonstrating that tissue-specific identity is embedded in the nuclear transcriptomes. By eliminating background inherent to complex embryonic environments, biotagging allows analyses of molecular interactions at high resolution. Biotagging enables cell- and compartment-specific in vivo biotinylation in zebrafish Technique yields comprehensive nuclear transcriptional analysis of cardiomyocytes Biotagging finds bidirectionally transcribed neural crest cis-regulatory modules System reveals tissue-specific regulation of noncoding RNA species
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Affiliation(s)
- Le A Trinh
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Vanessa Chong-Morrison
- Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Daria Gavriouchkina
- Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Tatiana Hochgreb-Hägele
- Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Upeka Senanayake
- Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Scott E Fraser
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Tatjana Sauka-Spengler
- Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
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352
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Abstract
CpG islands (CGI) are critical genomic regulatory elements that support transcriptional initiation and are associated with the promoters of most human genes. CGI are distinguished from the bulk genome by their high CpG density, lack of DNA methylation, and euchromatic features. While CGI are canonically known as strong promoters, thousands of 'orphan' CGI lie far from any known transcript, leaving their function an open question. We undertook a comprehensive analysis of the epigenetic state of orphan CGI across over 100 cell types. Here we show that most orphan CGI display the chromatin features of active enhancers (H3K4me1, H3K27Ac) in at least one cell type. Relative to classical enhancers, these enhancer CGI (ECGI) are stronger, as gauged by chromatin state and in functional assays, are more broadly expressed, and are more highly conserved. Likewise, ECGI engage in more genomic contacts and are enriched for transcription factor binding relative to classical enhancers. In human cancers, these epigenetic differences between ECGI vs. classical enhancers manifest in distinct alterations in DNA methylation. Thus, ECGI define a class of highly active enhancers, strengthened by the broad transcriptional activity, CpG density, hypomethylation, and chromatin features they share with promoter CGI. In addition to indicating a role for thousands of orphan CGI, these findings suggests that enhancer activity may be an intrinsic function of CGI in general and provides new insights into the evolution of enhancers and their epigenetic regulation during development and tumorigenesis.
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Affiliation(s)
- Joshua S K Bell
- a Department of Radiation Oncology , Emory University School of Medicine , Atlanta , GA , USA.,b Winship Cancer Institute of Emory University , Atlanta , GA , USA.,c Graduate Program in Genetics & Molecular Biology , Emory University , Atlanta , GA, USA
| | - Paula M Vertino
- a Department of Radiation Oncology , Emory University School of Medicine , Atlanta , GA , USA.,b Winship Cancer Institute of Emory University , Atlanta , GA , USA
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353
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A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells. Nat Methods 2017; 14:629-635. [PMID: 28417999 PMCID: PMC5490986 DOI: 10.1038/nmeth.4264] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/15/2017] [Indexed: 12/20/2022]
Abstract
Millions of cis-regulatory elements are predicted in the human genome, but direct evidence for their biological function is still scarce. Here we report a high-throughput method, Cis-Regulatory Element Scan by Tiling-deletion and sequencing (CREST-seq), for unbiased discovery and functional assessment of cis regulatory sequences in the genome. We use it to interrogate the 2Mbp POU5F1 locus in the human embryonic stem cells and identify 45 cis-regulatory elements of POU5F1. A majority of these elements display active chromatin marks, DNase hypersensitivity and occupancy by multiple transcription factors, confirming the utility of chromatin signatures in cis elements mapping. Notably, 17 of them are previously annotated promoters of functionally unrelated genes, and like typical enhancers, they form extensive spatial contacts with the POU5F1 promoter. Taken together, these results support the utility of CREST-seq for large-scale cis regulatory element discovery and point to commonality of enhancer-like promoters in the human genome.
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354
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Sengupta S, George RE. Super-Enhancer-Driven Transcriptional Dependencies in Cancer. Trends Cancer 2017; 3:269-281. [PMID: 28718439 DOI: 10.1016/j.trecan.2017.03.006] [Citation(s) in RCA: 204] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 03/13/2017] [Accepted: 03/14/2017] [Indexed: 11/24/2022]
Abstract
Transcriptional deregulation is one of the core tenets of cancer biology and is underpinned by alterations in both protein-coding genes and noncoding regulatory elements. Large regulatory elements, so-called super-enhancers (SEs), are central to the maintenance of cancer cell identity and promote oncogenic transcription to which cancer cells become highly addicted. Such dependence on SE-driven transcription for proliferation and survival offers an Achilles heel for the therapeutic targeting of cancer cells. Indeed, inhibition of the cellular machinery required for the assembly and maintenance of SEs dampens oncogenic transcription and inhibits tumor growth. In this article, we review the organization, function, and regulation of oncogenic SEs and their contribution to the cancer cell state.
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Affiliation(s)
- Satyaki Sengupta
- Department of Pediatric Hematology and Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02215, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Rani E George
- Department of Pediatric Hematology and Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA 02215, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
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355
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Sarda S, Das A, Vinson C, Hannenhalli S. Distal CpG islands can serve as alternative promoters to transcribe genes with silenced proximal promoters. Genome Res 2017; 27:553-566. [PMID: 28223400 PMCID: PMC5378174 DOI: 10.1101/gr.212050.116] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 02/21/2017] [Indexed: 12/31/2022]
Abstract
DNA methylation at the promoter of a gene is presumed to render it silent, yet a sizable fraction of genes with methylated proximal promoters exhibit elevated expression. Here, we show, through extensive analysis of the methylome and transcriptome in 34 tissues, that in many such cases, transcription is initiated by a distal upstream CpG island (CGI) located several kilobases away that functions as an alternative promoter. Specifically, such genes are expressed precisely when the neighboring CGI is unmethylated but remain silenced otherwise. Based on CAGE and Pol II localization data, we found strong evidence of transcription initiation at the upstream CGI and a lack thereof at the methylated proximal promoter itself. Consistent with their alternative promoter activity, CGI-initiated transcripts are associated with signals of stable elongation and splicing that extend into the gene body, as evidenced by tissue-specific RNA-seq and other DNA-encoded splice signals. Furthermore, based on both inter- and intra-species analyses, such CGIs were found to be under greater purifying selection relative to CGIs upstream of silenced genes. Overall, our study describes a hitherto unreported conserved mechanism of transcription of genes with methylated proximal promoters in a tissue-specific fashion. Importantly, this phenomenon explains the aberrant expression patterns of some cancer driver genes, potentially due to aberrant hypomethylation of distal CGIs, despite methylation at proximal promoters.
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Affiliation(s)
- Shrutii Sarda
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland 20742, USA
| | - Avinash Das
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland 20742, USA
| | - Charles Vinson
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Sridhar Hannenhalli
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland 20742, USA
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356
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Qamra A, Xing M, Padmanabhan N, Kwok JJT, Zhang S, Xu C, Leong YS, Lee Lim AP, Tang Q, Ooi WF, Suling Lin J, Nandi T, Yao X, Ong X, Lee M, Tay ST, Keng ATL, Gondo Santoso E, Ng CCY, Ng A, Jusakul A, Smoot D, Ashktorab H, Rha SY, Yeoh KG, Peng Yong W, Chow PK, Chan WH, Ong HS, Soo KC, Kim KM, Wong WK, Rozen SG, Teh BT, Kappei D, Lee J, Connolly J, Tan P. Epigenomic Promoter Alterations Amplify Gene Isoform and Immunogenic Diversity in Gastric Adenocarcinoma. Cancer Discov 2017; 7:630-651. [DOI: 10.1158/2159-8290.cd-16-1022] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 10/27/2016] [Accepted: 03/16/2017] [Indexed: 01/08/2023]
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357
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Huang YF, Gulko B, Siepel A. Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data. Nat Genet 2017; 49:618-624. [PMID: 28288115 PMCID: PMC5395419 DOI: 10.1038/ng.3810] [Citation(s) in RCA: 221] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 02/13/2017] [Indexed: 12/17/2022]
Abstract
Many genetic variants that influence phenotypes of interest are located outside of protein-coding genes, yet existing methods for identifying such variants have poor predictive power. Here we introduce a new computational method, called LINSIGHT, that substantially improves the prediction of noncoding nucleotide sites at which mutations are likely to have deleterious fitness consequences, and which, therefore, are likely to be phenotypically important. LINSIGHT combines a generalized linear model for functional genomic data with a probabilistic model of molecular evolution. The method is fast and highly scalable, enabling it to exploit the 'big data' available in modern genomics. We show that LINSIGHT outperforms the best available methods in identifying human noncoding variants associated with inherited diseases. In addition, we apply LINSIGHT to an atlas of human enhancers and show that the fitness consequences at enhancers depend on cell type, tissue specificity, and constraints at associated promoters.
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Affiliation(s)
- Yi-Fei Huang
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Brad Gulko
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.,Graduate Field of Computer Science, Cornell University, Ithaca, New York, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
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358
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Curina A, Termanini A, Barozzi I, Prosperini E, Simonatto M, Polletti S, Silvola A, Soldi M, Austenaa L, Bonaldi T, Ghisletti S, Natoli G. High constitutive activity of a broad panel of housekeeping and tissue-specific cis-regulatory elements depends on a subset of ETS proteins. Genes Dev 2017; 31:399-412. [PMID: 28275002 PMCID: PMC5358759 DOI: 10.1101/gad.293134.116] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/03/2017] [Indexed: 11/24/2022]
Abstract
Here, Curina et al. found that a subgroup of ETS family transcription factors (the ELF proteins) shows a strong bias in its genomic distribution by binding in very close proximity (<60 nt) to the transcription start sites of housekeeping genes. They show that a limited number of highly active transcription factors can equip cis-regulatory elements with disparate functional roles and cell type specificity with the ability to efficiently promote transcription. Enhancers and promoters that control the transcriptional output of terminally differentiated cells include cell type-specific and broadly active housekeeping elements. Whether the high constitutive activity of these two groups of cis-regulatory elements relies on entirely distinct or instead also on shared regulators is unknown. By dissecting the cis-regulatory repertoire of macrophages, we found that the ELF subfamily of ETS proteins selectively bound within 60 base pairs (bp) from the transcription start sites of highly active housekeeping genes. ELFs also bound constitutively active, but not poised, macrophage-specific enhancers and promoters. The role of ELFs in promoting high-level constitutive transcription was suggested by multiple evidence: ELF sites enabled robust transcriptional activation by endogenous and minimal synthetic promoters, ELF recruitment was stabilized by the transcriptional machinery, and ELF proteins mediated recruitment of transcriptional and chromatin regulators to core promoters. These data suggest that the co-optation of a limited number of highly active transcription factors represents a broadly adopted strategy to equip both cell type-specific and housekeeping cis-regulatory elements with the ability to efficiently promote transcription.
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Affiliation(s)
- Alessia Curina
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | | | - Iros Barozzi
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Elena Prosperini
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Marta Simonatto
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Sara Polletti
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Alessio Silvola
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Monica Soldi
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Liv Austenaa
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Serena Ghisletti
- Humanitas Clinical and Research Center, 20089 Rozzano-Milan, Italy
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy.,Humanitas University, 20089 Rozzano-Milan, Italy
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359
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Identifying Novel Transcriptional and Epigenetic Features of Nuclear Lamina-associated Genes. Sci Rep 2017; 7:100. [PMID: 28273906 PMCID: PMC5427898 DOI: 10.1038/s41598-017-00176-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 02/13/2017] [Indexed: 01/10/2023] Open
Abstract
Because a large portion of the mammalian genome is associated with the nuclear lamina (NL), it is interesting to study how native genes resided there are transcribed and regulated. In this study, we report unique transcriptional and epigenetic features of nearly 3,500 NL-associated genes (NL genes). Promoter regions of active NL genes are often excluded from NL-association, suggesting that NL-promoter interactions may repress transcription. Active NL genes with higher RNA polymerase II (Pol II) recruitment levels tend to display Pol II promoter-proximal pausing, while Pol II recruitment and Pol II pausing are not correlated among non-NL genes. At the genome-wide scale, NL-association and H3K27me3 distinguishes two large gene classes with low transcriptional activities. Notably, NL-association is anti-correlated with both transcription and active histone mark levels among genes not significantly enriched with H3K9me3 or H3K27me3, suggesting that NL-association may represent a novel gene repression pathway. Interestingly, an NL gene subgroup is not significantly enriched with H3K9me3 or H3K27me3 and is transcribed at higher levels than the rest of NL genes. Furthermore, we identified distal enhancers associated with active NL genes and reported their epigenetic features.
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360
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An atlas of human long non-coding RNAs with accurate 5' ends. Nature 2017; 543:199-204. [PMID: 28241135 DOI: 10.1038/nature21374] [Citation(s) in RCA: 690] [Impact Index Per Article: 98.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 01/08/2017] [Indexed: 12/15/2022]
Abstract
Long non-coding RNAs (lncRNAs) are largely heterogeneous and functionally uncharacterized. Here, using FANTOM5 cap analysis of gene expression (CAGE) data, we integrate multiple transcript collections to generate a comprehensive atlas of 27,919 human lncRNA genes with high-confidence 5' ends and expression profiles across 1,829 samples from the major human primary cell types and tissues. Genomic and epigenomic classification of these lncRNAs reveals that most intergenic lncRNAs originate from enhancers rather than from promoters. Incorporating genetic and expression data, we show that lncRNAs overlapping trait-associated single nucleotide polymorphisms are specifically expressed in cell types relevant to the traits, implicating these lncRNAs in multiple diseases. We further demonstrate that lncRNAs overlapping expression quantitative trait loci (eQTL)-associated single nucleotide polymorphisms of messenger RNAs are co-expressed with the corresponding messenger RNAs, suggesting their potential roles in transcriptional regulation. Combining these findings with conservation data, we identify 19,175 potentially functional lncRNAs in the human genome.
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361
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Kleftogiannis D, Kalnis P, Arner E, Bajic VB. Discriminative identification of transcriptional responses of promoters and enhancers after stimulus. Nucleic Acids Res 2017; 45:e25. [PMID: 27789687 PMCID: PMC5389464 DOI: 10.1093/nar/gkw1015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 10/17/2016] [Indexed: 01/19/2023] Open
Abstract
Promoters and enhancers regulate the initiation of gene expression and maintenance of expression levels in spatial and temporal manner. Recent findings stemming from the Cap Analysis of Gene Expression (CAGE) demonstrate that promoters and enhancers, based on their expression profiles after stimulus, belong to different transcription response subclasses. One of the most promising biological features that might explain the difference in transcriptional response between subclasses is the local chromatin environment. We introduce a novel computational framework, PEDAL, for distinguishing effectively transcriptional profiles of promoters and enhancers using solely histone modification marks, chromatin accessibility and binding sites of transcription factors and co-activators. A case study on data from MCF-7 cell-line reveals that PEDAL can identify successfully the transcription response subclasses of promoters and enhancers from two different stimulations. Moreover, we report subsets of input markers that discriminate with minimized classification error MCF-7 promoter and enhancer transcription response subclasses. Our work provides a general computational approach for identifying effectively cell-specific and stimulation-specific promoter and enhancer transcriptional profiles, and thus, contributes to improve our understanding of transcriptional activation in human.
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Affiliation(s)
- Dimitrios Kleftogiannis
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,The Institute of Cancer Research (ICR), London, SW7 3RP, UK
| | - Panos Kalnis
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Erik Arner
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies) (CLST (DGT)), Yokohama, Kanagawa 230-0045, Japan
| | - Vladimir B Bajic
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
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362
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Evolution of Brain Active Gene Promoters in Human Lineage Towards the Increased Plasticity of Gene Regulation. Mol Neurobiol 2017; 55:1871-1904. [PMID: 28233272 DOI: 10.1007/s12035-017-0427-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/26/2017] [Indexed: 01/31/2023]
Abstract
Adaptability to a variety of environmental conditions is a prominent feature of Homo sapiens. We hypothesize that this feature can be explained by evolutionary changes in gene promoters active in the brain prefrontal cortex leading to a more flexible gene regulation network. The genotype-dependent range of gene expression can be broader in humans than in other higher primates. Thus, we searched for specific signatures of evolutionary changes in promoter architectures of multiple hominid genes, including the genes active in human cortical neurons that may indicate an increase of variability of gene expression rather than just changes in the level of expression, such as downregulation or upregulation of the genes. We performed a whole-genome search for genetic-based alterations that may impact gene regulation "flexibility" in a process of hominids evolution, such as (i) CpG dinucleotide content, (ii) predicted nucleosome-DNA dissociation constant, and (iii) predicted affinities for TATA-binding protein (TBP) in gene promoters. We tested all putative promoter regions across the human genome and especially gene promoters in active chromatin state in neurons of prefrontal cortex, the brain region critical for abstract thinking and social and behavioral adaptation. Our data imply that the origin of modern man has been associated with an increase of flexibility of promoter-driven gene regulation in brain. In contrast, after splitting from the ancestral lineages of H. sapiens, the evolution of ape species is characterized by reduced flexibility of gene promoter functioning, underlying reduced variability of the gene expression.
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363
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Wang L, Rinaldi FC, Singh P, Doyle EL, Dubrow ZE, Tran TT, Pérez-Quintero AL, Szurek B, Bogdanove AJ. TAL Effectors Drive Transcription Bidirectionally in Plants. MOLECULAR PLANT 2017; 10:285-296. [PMID: 27965000 DOI: 10.1016/j.molp.2016.12.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Revised: 11/29/2016] [Accepted: 12/01/2016] [Indexed: 06/06/2023]
Abstract
TAL effectors delivered by phytopathogenic Xanthomonas species are DNA-sequence-specific transcriptional activators of host susceptibility genes and sometimes resistance genes. The modularity of DNA recognition by TAL effectors makes them important also as tools for gene targeting and genome editing. Effector binding elements (EBEs) recognized by native TAL effectors in plants have been identified only on the forward strand of target promoters. Here, we demonstrate that TAL effectors can drive plant transcription from EBEs on either strand and in both directions. Furthermore, we show that a native TAL effector from Xanthomonas oryzae pv. oryzicola drives expression of a target with an EBE on each strand of its promoter. By inserting that promoter and derivatives between two reporter genes oriented head to head, we show that the TAL effector drives expression from either EBE in the respective orientations, and that activity at the reverse-strand EBE also potentiates forward transcription driven by activity at the forward-strand EBE. Our results reveal new modes of action for TAL effectors, suggesting the possibility of yet unrecognized targets important in plant disease, expanding the search space for off-targets of custom TAL effectors, and highlighting the potential of TAL effectors for probing fundamental aspects of plant transcription.
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Affiliation(s)
- Li Wang
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science Building, Ithaca, NY 14853, USA
| | - Fabio C Rinaldi
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science Building, Ithaca, NY 14853, USA
| | - Pallavi Singh
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science Building, Ithaca, NY 14853, USA
| | - Erin L Doyle
- Department of Biology, Doane University, 1014 Boswell Avenue, Crete, NE 68333, USA
| | - Zoe E Dubrow
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science Building, Ithaca, NY 14853, USA
| | - Tuan Tu Tran
- UMR Interactions-Plantes-Microorganismes-Environnement, IRD-Cirad-Université Montpellier, Montpellier, France
| | - Alvaro L Pérez-Quintero
- UMR Interactions-Plantes-Microorganismes-Environnement, IRD-Cirad-Université Montpellier, Montpellier, France
| | - Boris Szurek
- UMR Interactions-Plantes-Microorganismes-Environnement, IRD-Cirad-Université Montpellier, Montpellier, France
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science Building, Ithaca, NY 14853, USA.
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364
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Abstract
The leap from simple unicellularity to complex multicellularity remains one of life's major enigmas. The origins of metazoan developmental gene regulatory mechanisms are sought by analyzing gene regulation in extant eumetazoans, sponges, and unicellular organisms. The main hypothesis of this manuscript is that, developmental enhancers evolved from unicellular inducible promoters that diversified the expression of regulatory genes during metazoan evolution. Promoters and enhancers are functionally similar; both can regulate the transcription of distal promoters and both direct local transcription. Additionally, enhancers have experimentally characterized structural features that reveal their origin from inducible promoters. The distal co-operative regulation among promoters identified in unicellular opisthokonts possibly represents the precursor of distal regulation of promoters by enhancers. During metazoan evolution, constitutive-type promoters of regulatory genes would have acquired novel receptivity to distal regulatory inputs from promoters of inducible genes that eventually specialized as enhancers. The novel regulatory interactions would have caused constitutively expressed genes controlling differential gene expression in unicellular organisms to become themselves differentially expressed. The consequence of the novel regulatory interactions was that regulatory pathways of unicellular organisms became interlaced and ultimately evolved into the intricate developmental gene regulatory networks (GRNs) of extant metazoans.
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Affiliation(s)
- César Arenas-Mena
- Department of Biology, College of Staten Island and Graduate Center, The City University of New York (CUNY), Staten Island, NY 10314, USA
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365
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The human initiator is a distinct and abundant element that is precisely positioned in focused core promoters. Genes Dev 2017; 31:6-11. [PMID: 28108474 PMCID: PMC5287114 DOI: 10.1101/gad.293837.116] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 12/19/2016] [Indexed: 12/19/2022]
Abstract
Vo ngoc et al. show that the human initiator has the consensus of BBCA+1BW at focused promoters in which transcription initiates at a single site or a narrow cluster of sites. DNA sequence signals in the core promoter, such as the initiator (Inr), direct transcription initiation by RNA polymerase II. Here we show that the human Inr has the consensus of BBCA+1BW at focused promoters in which transcription initiates at a single site or a narrow cluster of sites. The analysis of 7678 focused transcription start sites revealed 40% with a perfect match to the Inr and 16% with a single mismatch outside of the CA+1 core. TATA-like sequences are underrepresented in Inr promoters. This consensus is a key component of the DNA sequence rules that specify transcription initiation in humans.
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366
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Zacher B, Michel M, Schwalb B, Cramer P, Tresch A, Gagneur J. Accurate Promoter and Enhancer Identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN. PLoS One 2017; 12:e0169249. [PMID: 28056037 PMCID: PMC5215863 DOI: 10.1371/journal.pone.0169249] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 12/14/2016] [Indexed: 12/22/2022] Open
Abstract
Accurate maps of promoters and enhancers are required for understanding transcriptional regulation. Promoters and enhancers are usually mapped by integration of chromatin assays charting histone modifications, DNA accessibility, and transcription factor binding. However, current algorithms are limited by unrealistic data distribution assumptions. Here we propose GenoSTAN (Genomic STate ANnotation), a hidden Markov model overcoming these limitations. We map promoters and enhancers for 127 cell types and tissues from the ENCODE and Roadmap Epigenomics projects, today’s largest compendium of chromatin assays. Extensive benchmarks demonstrate that GenoSTAN generally identifies promoters and enhancers with significantly higher accuracy than previous methods. Moreover, GenoSTAN-derived promoters and enhancers showed significantly higher enrichment of complex trait-associated genetic variants than current annotations. Altogether, GenoSTAN provides an easy-to-use tool to define promoters and enhancers in any system, and our annotation of human transcriptional cis-regulatory elements constitutes a rich resource for future research in biology and medicine.
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Affiliation(s)
- Benedikt Zacher
- Gene Center and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität Munich, Germany
- * E-mail: (BZ); (AT); (JG)
| | - Margaux Michel
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Björn Schwalb
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Achim Tresch
- Department of Biology, University of Cologne, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- * E-mail: (BZ); (AT); (JG)
| | - Julien Gagneur
- Gene Center and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität Munich, Germany
- * E-mail: (BZ); (AT); (JG)
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367
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Blumberg A, Rice EJ, Kundaje A, Danko CG, Mishmar D. Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution. Genome Res 2017; 27:362-373. [PMID: 28049628 PMCID: PMC5340964 DOI: 10.1101/gr.209924.116] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 12/29/2016] [Indexed: 12/13/2022]
Abstract
Mitochondrial DNA (mtDNA) genes are long known to be cotranscribed in polycistrones, yet it remains impossible to study nascent mtDNA transcripts quantitatively in vivo using existing tools. To this end, we used deep sequencing (GRO-seq and PRO-seq) and analyzed nascent mtDNA-encoded RNA transcripts in diverse human cell lines and metazoan organisms. Surprisingly, accurate detection of human mtDNA transcription initiation sites (TISs) in the heavy and light strands revealed a novel conserved transcription pausing site near the light-strand TIS. This pausing site correlated with the presence of a bacterial pausing sequence motif, with reduced SNP density, and with a DNase footprinting signal in all tested cells. Its location within conserved sequence block 3 (CSBIII), just upstream of the known transcription–replication transition point, suggests involvement in such transition. Analysis of nonhuman organisms enabled de novo mtDNA sequence assembly, as well as detection of previously unknown mtDNA TIS, pausing, and transcription termination sites with unprecedented accuracy. Whereas mammals (Pan troglodytes, Macaca mulatta, Rattus norvegicus, and Mus musculus) showed a human-like mtDNA transcription pattern, the invertebrate pattern (Drosophila melanogaster and Caenorhabditis elegans) profoundly diverged. Our approach paves the path toward in vivo, quantitative, reference sequence-free analysis of mtDNA transcription in all eukaryotes.
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Affiliation(s)
- Amit Blumberg
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, 84105 Israel
| | - Edward J Rice
- Baker Institute for Animal Health, Cornell University, Ithaca, New York 14853, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, California 94305-5120, USA
| | - Charles G Danko
- Baker Institute for Animal Health, Cornell University, Ithaca, New York 14853, USA
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, 84105 Israel
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368
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Nagari A, Murakami S, Malladi VS, Kraus WL. Computational Approaches for Mining GRO-Seq Data to Identify and Characterize Active Enhancers. Methods Mol Biol 2017; 1468:121-138. [PMID: 27662874 PMCID: PMC5522910 DOI: 10.1007/978-1-4939-4035-6_10] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Transcriptional enhancers are DNA regulatory elements that are bound by transcription factors and act to positively regulate the expression of nearby or distally located target genes. Enhancers have many features that have been discovered using genomic analyses. Recent studies have shown that active enhancers recruit RNA polymerase II (Pol II) and are transcribed, producing enhancer RNAs (eRNAs). GRO-seq, a method for identifying the location and orientation of all actively transcribing RNA polymerases across the genome, is a powerful approach for monitoring nascent enhancer transcription. Furthermore, the unique pattern of enhancer transcription can be used to identify enhancers in the absence of any information about the underlying transcription factors. Here, we describe the computational approaches required to identify and analyze active enhancers using GRO-seq data, including data pre-processing, alignment, and transcript calling. In addition, we describe protocols and computational pipelines for mining GRO-seq data to identify active enhancers, as well as known transcription factor binding sites that are transcribed. Furthermore, we discuss approaches for integrating GRO-seq-based enhancer data with other genomic data, including target gene expression and function. Finally, we describe molecular biology assays that can be used to confirm and explore further the function of enhancers that have been identified using genomic assays. Together, these approaches should allow the user to identify and explore the features and biological functions of new cell type-specific enhancers.
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Affiliation(s)
- Anusha Nagari
- The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-8511, USA
- The Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8511, USA
| | - Shino Murakami
- The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-8511, USA
- The Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8511, USA
- Program in Genetics, Development and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Venkat S Malladi
- The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-8511, USA
- The Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8511, USA
| | - W Lee Kraus
- The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-8511, USA.
- The Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8511, USA.
- Program in Genetics, Development and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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369
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España AP, Santiago-Algarra D, Pradel L, Spicuglia S. [High-throughput approaches to study cis-regulating elements]. Biol Aujourdhui 2017; 211:271-280. [PMID: 29956654 DOI: 10.1051/jbio/2018015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Indexed: 12/22/2022]
Abstract
Gene expression in higher eukaryotes is regulated through the involvement of transcription start site (TSS)-proximal (promoters) and -distal (enhancers) regulatory elements. Enhancer elements play an essential role during development and cell differentiation, while genetic alterations in these elements are a major cause of human disease. Here, we discuss recent advances in high-throughput approaches to identify and characterize enhancer elements, from the well-established massively parallel reporter assays to the recent clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-based technologies. We discuss how these approaches contribute toward a better understanding of enhancer function in normal and pathological conditions.
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Affiliation(s)
- Alexandre P España
- Aix-Marseille Université, INSERM, TAGC, UMR 1090, 13288 Marseille, France - Équipe Labellisée Ligue Contre le Cancer, Laboratoire TAGC, INSERM U1090, Aix-Marseille Université, Parc Scientifique de Luminy, 163 avenue de Luminy, 13288 Marseille Cedex 09, France
| | - David Santiago-Algarra
- Aix-Marseille Université, INSERM, TAGC, UMR 1090, 13288 Marseille, France - Équipe Labellisée Ligue Contre le Cancer, Laboratoire TAGC, INSERM U1090, Aix-Marseille Université, Parc Scientifique de Luminy, 163 avenue de Luminy, 13288 Marseille Cedex 09, France
| | - Lydie Pradel
- Aix-Marseille Université, INSERM, TAGC, UMR 1090, 13288 Marseille, France - Équipe Labellisée Ligue Contre le Cancer, Laboratoire TAGC, INSERM U1090, Aix-Marseille Université, Parc Scientifique de Luminy, 163 avenue de Luminy, 13288 Marseille Cedex 09, France
| | - Salvatore Spicuglia
- Aix-Marseille Université, INSERM, TAGC, UMR 1090, 13288 Marseille, France - Équipe Labellisée Ligue Contre le Cancer, Laboratoire TAGC, INSERM U1090, Aix-Marseille Université, Parc Scientifique de Luminy, 163 avenue de Luminy, 13288 Marseille Cedex 09, France
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370
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Abstract
Recent years have seen a burst in the number of studies investigating tRNA biology. With the transition from a gene-centred to a genome-centred perspective, tRNAs and other RNA polymerase III transcripts surfaced as active regulators of normal cell physiology and disease. Novel strategies removing some of the hurdles that prevent quantitative tRNA profiling revealed that the differential exploitation of the tRNA pool critically affects the ability of the cell to balance protein homeostasis during normal and stress conditions. Furthermore, growing evidence indicates that the adaptation of tRNA synthesis to cellular dynamics can influence translation and mRNA stability to drive carcinogenesis and other pathological disorders. This review explores the contribution given by genomics, transcriptomics and epitranscriptomics to the discovery of emerging tRNA functions, and gives insights into some of the technical challenges that still limit our understanding of the RNA polymerase III transcriptional machinery.
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Affiliation(s)
- Andrea Orioli
- Center for Integrative Genomics, Université de Lausanne, Lausanne, VD 1015, Switzerland
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371
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van Arensbergen J, FitzPatrick VD, de Haas M, Pagie L, Sluimer J, Bussemaker HJ, van Steensel B. Genome-wide mapping of autonomous promoter activity in human cells. Nat Biotechnol 2016; 35:145-153. [PMID: 28024146 DOI: 10.1038/nbt.3754] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 12/01/2016] [Indexed: 12/20/2022]
Abstract
Previous methods to systematically characterize sequence-intrinsic activity of promoters have been limited by relatively low throughput and the length of the sequences that could be tested. Here we present 'survey of regulatory elements' (SuRE), a method that assays more than 108 DNA fragments, each 0.2-2 kb in size, for their ability to drive transcription autonomously. In SuRE, a plasmid library of random genomic fragments upstream of a 20-bp barcode is constructed, and decoded by paired-end sequencing. This library is used to transfect cells, and barcodes in transcribed RNA are quantified by high-throughput sequencing. When applied to the human genome, we achieve 55-fold genome coverage, allowing us to map autonomous promoter activity genome-wide in K562 cells. By computational modeling we delineate subregions within promoters that are relevant for their activity. We show that antisense promoter transcription is generally dependent on the sense core promoter sequences, and that most enhancers and several families of repetitive elements act as autonomous transcription initiation sites.
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Affiliation(s)
- Joris van Arensbergen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Vincent D FitzPatrick
- Department of Biological Sciences, Columbia University, New York, New York, USA.,Department of Systems Biology, Columbia University Medical Center, New York, New York, USA
| | - Marcel de Haas
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ludo Pagie
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jasper Sluimer
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, New York, USA.,Department of Systems Biology, Columbia University Medical Center, New York, New York, USA
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands
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372
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Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolution. Nat Biotechnol 2016; 35:136-144. [PMID: 28024147 DOI: 10.1038/nbt.3739] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 11/08/2016] [Indexed: 01/13/2023]
Abstract
Gene expression is controlled by enhancers that activate transcription from the core promoters of their target genes. Although a key function of core promoters is to convert enhancer activities into gene transcription, whether and how strongly they activate transcription in response to enhancers has not been systematically assessed on a genome-wide level. Here we describe self-transcribing active core promoter sequencing (STAP-seq), a method to determine the responsiveness of genomic sequences to enhancers, and apply it to the Drosophila melanogaster genome. We cloned candidate fragments at the position of the core promoter (also called minimal promoter) in reporter plasmids with or without a strong enhancer, transfected the resulting library into cells, and quantified the transcripts that initiated from each candidate for each setup by deep sequencing. In the presence of a single strong enhancer, the enhancer responsiveness of different sequences differs by several orders of magnitude, and different levels of responsiveness are associated with genes of different functions. We also identify sequence features that predict enhancer responsiveness and discuss how different core promoters are employed for the regulation of gene expression.
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373
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Epstein-Barr virus super-enhancer eRNAs are essential for MYC oncogene expression and lymphoblast proliferation. Proc Natl Acad Sci U S A 2016; 113:14121-14126. [PMID: 27864512 DOI: 10.1073/pnas.1616697113] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Epstein-Barr virus (EBV) super-enhancers (ESEs) are essential for lymphoblastoid cell (LCL) growth and survival. Reanalyses of LCL global run-on sequencing (Gro-seq) data found abundant enhancer RNAs (eRNAs) being transcribed at ESEs. Inactivation of ESE components, EBV nuclear antigen 2 (EBNA2) and bromodomain-containing protein 4 (BRD4), significantly decreased eRNAs at ESEs -428 and -525 kb upstream of the MYC oncogene transcription start site (TSS). shRNA knockdown of the MYC -428 and -525 ESE eRNA caused LCL growth arrest and reduced cell growth. Furthermore, MYC ESE eRNA knockdown also significantly reduced MYC expression, ESE H3K27ac signals, and MYC ESEs looping to MYC TSS. These data indicate that ESE eRNAs strongly affect cell gene expression and enable LCL growth.
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374
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Chen CY, Shi W, Balaton BP, Matthews AM, Li Y, Arenillas DJ, Mathelier A, Itoh M, Kawaji H, Lassmann T, Hayashizaki Y, Carninci P, Forrest ARR, Brown CJ, Wasserman WW. YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses. Sci Rep 2016; 6:37324. [PMID: 27857184 PMCID: PMC5114649 DOI: 10.1038/srep37324] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 10/24/2016] [Indexed: 12/27/2022] Open
Abstract
Sex differences in susceptibility and progression have been reported in numerous diseases. Female cells have two copies of the X chromosome with X-chromosome inactivation imparting mono-allelic gene silencing for dosage compensation. However, a subset of genes, named escapees, escape silencing and are transcribed bi-allelically resulting in sexual dimorphism. Here we conducted in silico analyses of the sexes using human datasets to gain perspectives into such regulation. We identified transcription start sites of escapees (escTSSs) based on higher transcription levels in female cells using FANTOM5 CAGE data. Significant over-representations of YY1 transcription factor binding motif and ChIP-seq peaks around escTSSs highlighted its positive association with escapees. Furthermore, YY1 occupancy is significantly biased towards the inactive X (Xi) at long non-coding RNA loci that are frequent contacts of Xi-specific superloops. Our study suggests a role for YY1 in transcriptional activity on Xi in general through sequence-specific binding, and its involvement at superloop anchors.
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Affiliation(s)
- Chih-Yu Chen
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.,Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wenqiang Shi
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.,Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bradley P Balaton
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Allison M Matthews
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yifeng Li
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - David J Arenillas
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anthony Mathelier
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Masayoshi Itoh
- RIKEN Omics Science Center, Yokohama, Japan.,RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama, Japan
| | - Hideya Kawaji
- RIKEN Omics Science Center, Yokohama, Japan.,RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama, Japan
| | - Timo Lassmann
- RIKEN Omics Science Center, Yokohama, Japan.,RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Japan
| | - Yoshihide Hayashizaki
- RIKEN Omics Science Center, Yokohama, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama, Japan
| | - Piero Carninci
- RIKEN Omics Science Center, Yokohama, Japan.,RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Japan
| | - Alistair R R Forrest
- RIKEN Omics Science Center, Yokohama, Japan.,RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Japan.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, Nedlands, Western Australia, Australia
| | - Carolyn J Brown
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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375
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Lai WKM, Pugh BF. Genome-wide uniformity of human 'open' pre-initiation complexes. Genome Res 2016; 27:15-26. [PMID: 27927716 PMCID: PMC5204339 DOI: 10.1101/gr.210955.116] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 11/03/2016] [Indexed: 01/05/2023]
Abstract
Transcription of protein-coding and noncoding DNA occurs pervasively throughout the mammalian genome. Their sites of initiation are generally inferred from transcript 5' ends and are thought to be either locally dispersed or focused. How these two modes of initiation relate is unclear. Here, we apply permanganate treatment and chromatin immunoprecipitation (PIP-seq) of initiation factors to identify the precise location of melted DNA separately associated with the preinitiation complex (PIC) and the adjacent paused complex (PC). This approach revealed the two known modes of transcription initiation. However, in contrast to prevailing views, they co-occurred within the same promoter region: initiation originating from a focused PIC, and broad nucleosome-linked initiation. PIP-seq allowed transcriptional orientation of Pol II to be determined, which may be useful near promoters where sufficient sense/anti-sense transcript mapping information is lacking. PIP-seq detected divergently oriented Pol II at both coding and noncoding promoters, as well as at enhancers. Their occupancy levels were not necessarily coupled in the two orientations. DNA sequence and shape analysis of initiation complex sites suggest that both sequence and shape contribute to specificity, but in a context-restricted manner. That is, initiation sites have the locally "best" initiator (INR) sequence and/or shape. These findings reveal a common core to pervasive Pol II initiation throughout the human genome.
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Affiliation(s)
- William K M Lai
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - B Franklin Pugh
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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376
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Duttke SHC. 12th Conference on Transcription and Chromatin - August 27-30, 2016 - Heidelberg, Germany. Epigenetics 2016; 11:839-843. [PMID: 27801613 DOI: 10.1080/15592294.2016.1238556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
A pleasant atmosphere and outstanding science certainly made the 12th EMBL Conference on Transcription and Chromatin an event to remember. With 62 talks and over 200 posters, there was no shortage of cutting edge research to catch on.
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Affiliation(s)
- Sascha H C Duttke
- a Department of Cellular & Molecular Medicine , University of California , San Diego , CA , USA
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377
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Zabidi MA, Stark A. Regulatory Enhancer-Core-Promoter Communication via Transcription Factors and Cofactors. Trends Genet 2016; 32:801-814. [PMID: 27816209 DOI: 10.1016/j.tig.2016.10.003] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/08/2016] [Accepted: 10/10/2016] [Indexed: 01/20/2023]
Abstract
Gene expression is regulated by genomic enhancers that recruit transcription factors and cofactors to activate transcription from target core promoters. Over the past years, thousands of enhancers and core promoters in animal genomes have been annotated, and we have learned much about the domain structure in which regulatory genomes are organized in animals. Enhancer-core-promoter targeting occurs at several levels, including regulatory domains, DNA accessibility, and sequence-encoded core-promoter specificities that are likely mediated by different regulatory proteins. We review here current knowledge about enhancer-core-promoter targeting, regulatory communication between enhancers and core promoters, and the protein factors involved. We conclude with an outlook on open questions that we find particularly interesting and that will likely lead to additional insights in the upcoming years.
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Affiliation(s)
- Muhammad A Zabidi
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria.
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378
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Weber B, Zicola J, Oka R, Stam M. Plant Enhancers: A Call for Discovery. TRENDS IN PLANT SCIENCE 2016; 21:974-987. [PMID: 27593567 DOI: 10.1016/j.tplants.2016.07.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/18/2016] [Accepted: 07/28/2016] [Indexed: 05/12/2023]
Abstract
Higher eukaryotes typically contain many different cell types, displaying different cellular functions that are influenced by biotic and abiotic cues. The different functions are characterized by specific gene expression patterns mediated by regulatory sequences such as transcriptional enhancers. Recent genome-wide approaches have identified thousands of enhancers in animals, reviving interest in enhancers in gene regulation. Although the regulatory roles of plant enhancers are as crucial as those in animals, genome-wide approaches have only very recently been applied to plants. Here we review characteristics of enhancers at the DNA and chromatin level in plants and other species, their similarities and differences, and techniques widely used for genome-wide discovery of enhancers in animal systems that can be implemented in plants.
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Affiliation(s)
- Blaise Weber
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Johan Zicola
- Max Planck Institute for Plant Breeding Research, Department Plant Developmental Biology, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Rurika Oka
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Maike Stam
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
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379
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Brent MR. Past Roadblocks and New Opportunities in Transcription Factor Network Mapping. Trends Genet 2016; 32:736-750. [PMID: 27720190 DOI: 10.1016/j.tig.2016.08.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 08/12/2016] [Accepted: 08/16/2016] [Indexed: 12/11/2022]
Abstract
One of the principal mechanisms by which cells differentiate and respond to changes in external signals or conditions is by changing the activity levels of transcription factors (TFs). This changes the transcription rates of target genes via the cell's TF network, which ultimately contributes to reconfiguring cellular state. Since microarrays provided our first window into global cellular state, computational biologists have eagerly attacked the problem of mapping TF networks, a key part of the cell's control circuitry. In retrospect, however, steady-state mRNA abundance levels were a poor substitute for TF activity levels and gene transcription rates. Likewise, mapping TF binding through chromatin immunoprecipitation proved less predictive of functional regulation and less amenable to systematic elucidation of complete networks than originally hoped. This review explains these roadblocks and the current, unprecedented blossoming of new experimental techniques built on second-generation sequencing, which hold out the promise of rapid progress in TF network mapping.
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Affiliation(s)
- Michael R Brent
- Departments of Computer Science and Genetics and Center for Genome Sciences and Systems Biology, Washington University, , Saint Louis, MO, USA.
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380
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Bell CG. Insights in human epigenomic dynamics through comparative primate analysis. Genomics 2016; 108:115-125. [DOI: 10.1016/j.ygeno.2016.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Revised: 08/03/2016] [Accepted: 09/29/2016] [Indexed: 12/11/2022]
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381
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Azofeifa JG, Dowell RD. A generative model for the behavior of RNA polymerase. Bioinformatics 2016; 33:227-234. [PMID: 27663494 PMCID: PMC5942361 DOI: 10.1093/bioinformatics/btw599] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 08/31/2016] [Accepted: 09/12/2016] [Indexed: 12/30/2022] Open
Abstract
MOTIVATION Transcription by RNA polymerase is a highly dynamic process involving multiple distinct points of regulation. Nascent transcription assays are a relatively new set of high throughput techniques that measure the location of actively engaged RNA polymerase genome wide. Hence, nascent transcription is a rich source of information on the regulation of RNA polymerase activity. To fully dissect this data requires the development of stochastic models that can both deconvolve the stages of polymerase activity and identify significant changes in activity between experiments. RESULTS We present a generative, probabilistic model of RNA polymerase that fully describes loading, initiation, elongation and termination. We fit this model genome wide and profile the enzymatic activity of RNA polymerase across various loci and following experimental perturbation. We observe striking correlation of predicted loading events and regulatory chromatin marks. We provide principled statistics that compute probabilities reminiscent of traveler's and divergent ratios. We finish with a systematic comparison of RNA Polymerase activity at promoter versus non-promoter associated loci. AVAILABILITY AND IMPLEMENTATION Transcription Fit (Tfit) is a freely available, open source software package written in C/C ++ that requires GNU compilers 4.7.3 or greater. Tfit is available from GitHub (https://github.com/azofeifa/Tfit). CONTACT robin.dowell@colorado.eduSupplementary information: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Joseph G Azofeifa
- Department of Computer Science, University of Colorado, Boulder, CO, USA
| | - Robin D Dowell
- Department of Computer Science, University of Colorado, Boulder, CO, USA.,Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA.,BioFrontiers Institute, University of Colorado, Boulder, CO, USA
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382
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Lewis J, van der Burg K, Mazo-Vargas A, Reed R. ChIP-Seq-Annotated Heliconius erato Genome Highlights Patterns of cis -Regulatory Evolution in Lepidoptera. Cell Rep 2016; 16:2855-2863. [DOI: 10.1016/j.celrep.2016.08.042] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 07/14/2016] [Accepted: 08/12/2016] [Indexed: 12/11/2022] Open
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383
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Zhao Y, Liu Q, Acharya P, Stengel KR, Sheng Q, Zhou X, Kwak H, Fischer MA, Bradner JE, Strickland SA, Mohan SR, Savona MR, Venters BJ, Zhou MM, Lis JT, Hiebert SW. High-Resolution Mapping of RNA Polymerases Identifies Mechanisms of Sensitivity and Resistance to BET Inhibitors in t(8;21) AML. Cell Rep 2016; 16:2003-16. [PMID: 27498870 PMCID: PMC4996374 DOI: 10.1016/j.celrep.2016.07.032] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 12/17/2015] [Accepted: 07/13/2016] [Indexed: 02/07/2023] Open
Abstract
Bromodomain and extra-terminal domain (BET) family inhibitors offer an approach to treating hematological malignancies. We used precision nuclear run-on transcription sequencing (PRO-seq) to create high-resolution maps of active RNA polymerases across the genome in t(8;21) acute myeloid leukemia (AML), as these polymerases are exceptionally sensitive to BET inhibitors. PRO-seq identified over 1,400 genes showing impaired release of promoter-proximal paused RNA polymerases, including the stem cell factor receptor tyrosine kinase KIT that is mutated in t(8;21) AML. PRO-seq also identified an enhancer 3' to KIT. Chromosome conformation capture confirmed contacts between this enhancer and the KIT promoter, while CRISPRi-mediated repression of this enhancer impaired cell growth. PRO-seq also identified microRNAs, including MIR29C and MIR29B2, that target the anti-apoptotic factor MCL1 and were repressed by BET inhibitors. MCL1 protein was upregulated, and inhibition of BET proteins sensitized t(8:21)-containing cells to MCL1 inhibition, suggesting a potential mechanism of resistance to BET-inhibitor-induced cell death.
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MESH Headings
- Antineoplastic Agents/pharmacology
- Azepines/pharmacology
- Cell Line, Tumor
- Chromosomes, Human, Pair 21
- Chromosomes, Human, Pair 8
- Clustered Regularly Interspaced Short Palindromic Repeats
- DNA-Directed RNA Polymerases/genetics
- DNA-Directed RNA Polymerases/metabolism
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Enhancer Elements, Genetic
- Gene Expression Regulation, Leukemic
- High-Throughput Nucleotide Sequencing/methods
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Multigene Family
- Myeloid Cell Leukemia Sequence 1 Protein/genetics
- Myeloid Cell Leukemia Sequence 1 Protein/metabolism
- Promoter Regions, Genetic
- Protein Isoforms/antagonists & inhibitors
- Protein Isoforms/genetics
- Protein Isoforms/metabolism
- Proteins/antagonists & inhibitors
- Proteins/genetics
- Proteins/metabolism
- Proto-Oncogene Proteins c-kit/genetics
- Proto-Oncogene Proteins c-kit/metabolism
- Transcription, Genetic
- Translocation, Genetic
- Triazoles/pharmacology
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Affiliation(s)
- Yue Zhao
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Qi Liu
- Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Pankaj Acharya
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Kristy R Stengel
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Quanhu Sheng
- Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37212, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Melissa A Fischer
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Stephen A Strickland
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Sanjay R Mohan
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Michael R Savona
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Bryan J Venters
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Ming-Ming Zhou
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Scott W Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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384
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Lavender CA, Cannady KR, Hoffman JA, Trotter KW, Gilchrist DA, Bennett BD, Burkholder AB, Burd CJ, Fargo DC, Archer TK. Downstream Antisense Transcription Predicts Genomic Features That Define the Specific Chromatin Environment at Mammalian Promoters. PLoS Genet 2016; 12:e1006224. [PMID: 27487356 PMCID: PMC4972320 DOI: 10.1371/journal.pgen.1006224] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 07/06/2016] [Indexed: 01/23/2023] Open
Abstract
Antisense transcription is a prevalent feature at mammalian promoters. Previous studies have primarily focused on antisense transcription initiating upstream of genes. Here, we characterize promoter-proximal antisense transcription downstream of gene transcription starts sites in human breast cancer cells, investigating the genomic context of downstream antisense transcription. We find extensive correlations between antisense transcription and features associated with the chromatin environment at gene promoters. Antisense transcription downstream of promoters is widespread, with antisense transcription initiation observed within 2 kb of 28% of gene transcription start sites. Antisense transcription initiates between nucleosomes regularly positioned downstream of these promoters. The nucleosomes between gene and downstream antisense transcription start sites carry histone modifications associated with active promoters, such as H3K4me3 and H3K27ac. This region is bound by chromatin remodeling and histone modifying complexes including SWI/SNF subunits and HDACs, suggesting that antisense transcription or resulting RNA transcripts contribute to the creation and maintenance of a promoter-associated chromatin environment. Downstream antisense transcription overlays additional regulatory features, such as transcription factor binding, DNA accessibility, and the downstream edge of promoter-associated CpG islands. These features suggest an important role for antisense transcription in the regulation of gene expression and the maintenance of a promoter-associated chromatin environment. Gene transcription is regulated by the coordinated interaction of genetic, epigenetic and trans-acting factors. The chromatin environment at gene promoters, including positioned nucleosomes that may display functional histone modifications, is a key regulator of gene expression, contributing to transcriptional activation and repression. In addition to sense-strand transcription of gene sequences, antisense transcription is prevalent at gene promoters. Often resulting in a short-lived non-coding RNA transcript, the function of antisense transcription is poorly understood. Using next-generation sequencing techniques, we characterized transcription in human breast cancer cells and found extensive correlations between antisense transcription and the chromatin environment at promoters. We found that downstream antisense transcription initiates from between regularly positioned nucleosomes and that those nucleosomes between sense and downstream antisense transcription start sites display histone modifications associated with active gene promoters. Chromatin remodelers and other protein complexes responsible for creation and maintenance of the promoter chromatin environment associate with this same region, suggesting an important role of antisense transcription in the regulation of gene expression.
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Affiliation(s)
- Christopher A Lavender
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America.,Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Kimberly R Cannady
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Jackson A Hoffman
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Kevin W Trotter
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Daniel A Gilchrist
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Brian D Bennett
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Adam B Burkholder
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Craig J Burd
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America.,Wexner Medical Center, The Ohio State University, Columbus, Ohio, United States of America
| | - David C Fargo
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Trevor K Archer
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
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385
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Mahat DB, Kwak H, Booth GT, Jonkers IH, Danko CG, Patel RK, Waters CT, Munson K, Core LJ, Lis JT. Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nat Protoc 2016; 11:1455-76. [PMID: 27442863 PMCID: PMC5502525 DOI: 10.1038/nprot.2016.086] [Citation(s) in RCA: 304] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We provide a protocol for precision nuclear run-on sequencing (PRO-seq) and its variant, PRO-cap, which map the location of active RNA polymerases (PRO-seq) or transcription start sites (TSSs) (PRO-cap) genome-wide at high resolution. The density of RNA polymerases at a particular genomic locus directly reflects the level of nascent transcription at that region. Nuclei are isolated from cells and, under nuclear run-on conditions, transcriptionally engaged RNA polymerases incorporate one or, at most, a few biotin-labeled nucleotide triphosphates (biotin-NTPs) into the 3' end of nascent RNA. The biotin-labeled nascent RNA is used to prepare sequencing libraries, which are sequenced from the 3' end to provide high-resolution positional information for the RNA polymerases. PRO-seq provides much higher sensitivity than ChIP-seq, and it generates a much larger fraction of usable sequence reads than ChIP-seq or NET-seq (native elongating transcript sequencing). Similarly to NET-seq, PRO-seq maps the RNA polymerase at up to base-pair resolution with strand specificity, but unlike NET-seq it does not require immunoprecipitation. With the protocol provided here, PRO-seq (or PRO-cap) libraries for high-throughput sequencing can be generated in 4-5 working days. The method has been applied to human, mouse, Drosophila melanogaster and Caenorhabditis elegans cells and, with slight modifications, to yeast.
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Affiliation(s)
- Dig Bijay Mahat
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Gregory T Booth
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Iris H Jonkers
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Charles G Danko
- The Baker Institute of Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Ravi K Patel
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Colin T Waters
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Katie Munson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - Leighton J Core
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA
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386
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García-González E, Escamilla-Del-Arenal M, Arzate-Mejía R, Recillas-Targa F. Chromatin remodeling effects on enhancer activity. Cell Mol Life Sci 2016; 73:2897-910. [PMID: 27026300 PMCID: PMC11108574 DOI: 10.1007/s00018-016-2184-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 03/04/2016] [Accepted: 03/14/2016] [Indexed: 01/02/2023]
Abstract
During organism development, a diversity of cell types emerges with disparate, yet stable profiles of gene expression with distinctive cellular functions. In addition to gene promoters, the genome contains enhancer regulatory sequences, which are implicated in cellular specialization by facilitating cell-type and tissue-specific gene expression. Enhancers are DNA binding elements characterized by highly sophisticated and various mechanisms of action allowing for the specific interaction of general and tissue-specific transcription factors (TFs). However, eukaryotic organisms package their genetic material into chromatin, generating a physical barrier for TFs to interact with their cognate sequences. The ability of TFs to bind DNA regulatory elements is also modulated by changes in the chromatin structure, including histone modifications, histone variants, ATP-dependent chromatin remodeling, and the methylation status of DNA. Furthermore, it has recently been revealed that enhancer sequences are also transcribed into a set of enhancer RNAs with regulatory potential. These interdependent processes act in the context of a complex network of chromatin interactions, which together contributes to a renewed vision of how gene activation is coordinated in a cell-type-dependent manner. In this review, we describe the interplay between genetic and epigenetic aspects associated with enhancers and discuss their possible roles on enhancer function.
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Affiliation(s)
- Estela García-González
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, C.P. 04510, Mexico City, México
| | - Martín Escamilla-Del-Arenal
- Department of Biochemistry and Molecular Biophysics, Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York City, NY, 10027, USA
| | - Rodrigo Arzate-Mejía
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, C.P. 04510, Mexico City, México
| | - Félix Recillas-Targa
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Circuito Exterior S/N, Ciudad Universitaria, C.P. 04510, Mexico City, México.
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387
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Chen Y, Pai AA, Herudek J, Lubas M, Meola N, Järvelin AI, Andersson R, Pelechano V, Steinmetz LM, Jensen TH, Sandelin A. Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters. Nat Genet 2016; 48:984-94. [PMID: 27455346 PMCID: PMC5008441 DOI: 10.1038/ng.3616] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 06/14/2016] [Indexed: 12/11/2022]
Abstract
Mammalian transcriptomes are complex and formed by extensive promoter activity. In addition, gene promoters are largely divergent and initiate transcription of reverse-oriented promoter upstream transcripts (PROMPTs). Although PROMPTs are commonly terminated early, influenced by polyadenylation sites, promoters often cluster so that the divergent activity of one might impact another. Here we found that the distance between promoters strongly correlates with the expression, stability and length of their associated PROMPTs. Adjacent promoters driving divergent mRNA transcription support PROMPT formation, but owing to polyadenylation site constraints, these transcripts tend to spread into the neighboring mRNA on the same strand. This mechanism to derive new alternative mRNA transcription start sites (TSSs) is also evident at closely spaced promoters supporting convergent mRNA transcription. We suggest that basic building blocks of divergently transcribed core promoter pairs, in combination with the wealth of TSSs in mammalian genomes, provide a framework with which evolution shapes transcriptomes.
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Affiliation(s)
- Yun Chen
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Athma A Pai
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jan Herudek
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Michal Lubas
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.,Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Nicola Meola
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Aino I Järvelin
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Robin Andersson
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Vicent Pelechano
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Lars M Steinmetz
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.,Stanford Genome Technology Center, Palo Alto, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Torben Heick Jensen
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
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388
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Nguyen Q, Carninci P. Expression Specificity of Disease-Associated lncRNAs: Toward Personalized Medicine. Curr Top Microbiol Immunol 2016; 394:237-58. [PMID: 26318140 DOI: 10.1007/82_2015_464] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Long noncoding RNAs (lncRNAs) perform diverse regulatory functions in transcription, translation' chromatin modification, and cellular organization. Misregulation of lncRNAs is found linked to various human diseases. Compared to protein-coding RNAs' lncRNAs are more specific to organs, tissues, cell types, developmental stages, and disease conditions' making them promising candidates as diagnostic and prognostic biomarkers and as gene therapy targets. The functional annotation of mammalian genome (FANTOM) consortium utilizes cap analysis of gene expression (CAGE) method to quantify genome-wide activities of promoters and enhancers of coding and noncoding RNAs across a large collection of human and mouse tissues' cell types' diseases, and time-courses. The project discovered widespread transcription of major lncRNA classes, including lncRNAs derived from enhancers' bidirectional promoters' antisense lncRNAs' and repetitive elements. Results from FANTOM project enable assessment of lncRNA expression specificity across tissue and disease conditions' based on differential promoter and enhancer usage. More than 85 % of disease-related SNPs are within noncoding regions and are strikingly overrepresented in enhancer and promoter regions, suggestive of the importance of lncRNA loci at these SNP harboring regions to human diseases. In this chapter' we discuss lncRNA expression specificity' review diverse functions of disease-associated lncRNAs' and present perspectives on their potential therapeutic applications for personalized medicine. The future development of lncRNA applications relies on technologies to identify and validate their functions' structures' and mechanisms. Comprehensive understanding of genome-wide interaction networks of lncRNAs with proteins, chromatins, and other RNAs in regulating cellular processes will allow personalized medicine to use lncRNAs as highly specific biomarkers in diagnosis' prognosis, and therapeutic targets.
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Affiliation(s)
- Quan Nguyen
- Division of Genomic Technologies, RIKEN Yokohama Campus, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-Cho, Tsurumi-Ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Piero Carninci
- Division of Genomic Technologies, RIKEN Yokohama Campus, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-Cho, Tsurumi-Ku, Yokohama City, Kanagawa, 230-0045, Japan.
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389
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Vernimmen D, Bickmore WA. The Hierarchy of Transcriptional Activation: From Enhancer to Promoter. Trends Genet 2016; 31:696-708. [PMID: 26599498 DOI: 10.1016/j.tig.2015.10.004] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/18/2015] [Accepted: 10/15/2015] [Indexed: 12/20/2022]
Abstract
Regulatory elements (enhancers) that are remote from promoters play a critical role in the spatial, temporal, and physiological control of gene expression. Studies on specific loci, together with genome-wide approaches, suggest that there may be many common mechanisms involved in enhancer-promoter communication. Here, we discuss the multiprotein complexes that are recruited to enhancers and the hierarchy of events taking place between regulatory elements and promoters.
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Affiliation(s)
- Douglas Vernimmen
- The Roslin Institute, Developmental Biology Division, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
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390
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Selectivity of ORC binding sites and the relation to replication timing, fragile sites, and deletions in cancers. Proc Natl Acad Sci U S A 2016; 113:E4810-9. [PMID: 27436900 DOI: 10.1073/pnas.1609060113] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The origin recognition complex (ORC) binds sites from which DNA replication is initiated. We address ORC binding selectivity in vivo by mapping ∼52,000 ORC2 binding sites throughout the human genome. The ORC binding profile is broader than those of sequence-specific transcription factors, suggesting that ORC is not bound or recruited to specific DNA sequences. Instead, ORC binds nonspecifically to open (DNase I-hypersensitive) regions containing active chromatin marks such as H3 acetylation and H3K4 methylation. ORC sites in early and late replicating regions have similar properties, but there are far more ORC sites in early replicating regions. This suggests that replication timing is due primarily to ORC density and stochastic firing of origins. Computational simulation of stochastic firing from identified ORC sites is in accord with replication timing data. Large genomic regions with a paucity of ORC sites are strongly associated with common fragile sites and recurrent deletions in cancers. We suggest that replication origins, replication timing, and replication-dependent chromosome breaks are determined primarily by the genomic distribution of activator proteins at enhancers and promoters. These activators recruit nucleosome-modifying complexes to create the appropriate chromatin structure that allows ORC binding and subsequent origin firing.
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391
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Heinäniemi M, Vuorenmaa T, Teppo S, Kaikkonen MU, Bouvy-Liivrand M, Mehtonen J, Niskanen H, Zachariadis V, Laukkanen S, Liuksiala T, Teittinen K, Lohi O. Transcription-coupled genetic instability marks acute lymphoblastic leukemia structural variation hotspots. eLife 2016; 5. [PMID: 27431763 PMCID: PMC4951197 DOI: 10.7554/elife.13087] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 06/09/2016] [Indexed: 12/11/2022] Open
Abstract
Progression of malignancy to overt disease requires multiple genetic hits. Activation-induced deaminase (AID) can drive lymphomagenesis by generating off-target DNA breaks at loci that harbor highly active enhancers and display convergent transcription. The first active transcriptional profiles from acute lymphoblastic leukemia (ALL) patients acquired here reveal striking similarity at structural variation (SV) sites. Specific transcriptional features, namely convergent transcription and Pol2 stalling, were detected at breakpoints. The overlap was most prominent at SV with recognition motifs for the recombination activating genes (RAG). We present signal feature analysis to detect vulnerable regions and quantified from human cells how convergent transcription contributes to R-loop generation and RNA polymerase stalling. Wide stalling regions were characterized by high DNAse hypersensitivity and unusually broad H3K4me3 signal. Based on 1382 pre-B-ALL patients, the ETV6-RUNX1 fusion positive patients had over ten-fold elevation in RAG1 while high expression of AID marked pre-B-ALL lacking common cytogenetic changes.
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Affiliation(s)
- Merja Heinäniemi
- School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Tapio Vuorenmaa
- School of Medicine, University of Eastern Finland, Kuopio, Finland.,A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Susanna Teppo
- School of Medicine, University of Tampere, Tampere, Finland
| | - Minna U Kaikkonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | | | - Juha Mehtonen
- School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Henri Niskanen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Vasilios Zachariadis
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | | | | | | | - Olli Lohi
- School of Medicine, University of Tampere, Tampere, Finland.,Tampere University Hospital, Tampere, Finland
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392
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RNA polymerase II promoter-proximal pausing in mammalian long non-coding genes. Genomics 2016; 108:64-77. [PMID: 27432546 DOI: 10.1016/j.ygeno.2016.07.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 07/11/2016] [Accepted: 07/14/2016] [Indexed: 01/13/2023]
Abstract
Mammalian genomes encode a large number of non-coding RNAs (ncRNAs) that greatly exceed mRNA genes. While the physiological and pathological roles of ncRNAs have been increasingly understood, the mechanisms of regulation of ncRNA expression are less clear. Here, our genomic study has shown that a significant number of long non-coding RNAs (lncRNAs, >1000 nucleotides) harbor RNA polymerase II (Pol II) engaged with the transcriptional start site. A pausing and transcriptional elongation factor for protein-coding genes, tripartite motif-containing 28 (TRIM28) regulates the transcription of a subset of lncRNAs in mammalian cells. In addition, the majority of lncRNAs in human and murine cells regulated by Pol II promoter-proximal pausing appear to function in stimulus-inducible biological pathways. Our findings suggest an important role of Pol II pausing for the transcription of mammalian lncRNA genes.
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393
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Nguyen TA, Jones RD, Snavely AR, Pfenning AR, Kirchner R, Hemberg M, Gray JM. High-throughput functional comparison of promoter and enhancer activities. Genome Res 2016; 26:1023-33. [PMID: 27311442 PMCID: PMC4971761 DOI: 10.1101/gr.204834.116] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 06/14/2016] [Indexed: 01/26/2023]
Abstract
Promoters initiate RNA synthesis, and enhancers stimulate promoter activity. Whether promoter and enhancer activities are encoded distinctly in DNA sequences is unknown. We measured the enhancer and promoter activities of thousands of DNA fragments transduced into mouse neurons. We focused on genomic loci bound by the neuronal activity-regulated coactivator CREBBP, and we measured enhancer and promoter activities both before and after neuronal activation. We find that the same sequences typically encode both enhancer and promoter activities. However, gene promoters generate more promoter activity than distal enhancers, despite generating similar enhancer activity. Surprisingly, the greater promoter activity of gene promoters is not due to conventional core promoter elements or splicing signals. Instead, we find that particular transcription factor binding motifs are intrinsically biased toward the generation of promoter activity, whereas others are not. Although the specific biases we observe may be dependent on experimental or cellular context, our results suggest that gene promoters are distinguished from distal enhancers by specific complements of transcriptional activators.
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Affiliation(s)
- Thomas A Nguyen
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Richard D Jones
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Andrew R Snavely
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Andreas R Pfenning
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Rory Kirchner
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Martin Hemberg
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, United Kingdom
| | - Jesse M Gray
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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394
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Schwalb B, Michel M, Zacher B, Frühauf K, Demel C, Tresch A, Gagneur J, Cramer P. TT-seq maps the human transient transcriptome. Science 2016; 352:1225-8. [DOI: 10.1126/science.aad9841] [Citation(s) in RCA: 294] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 05/06/2016] [Indexed: 12/14/2022]
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395
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Skvortsova YV, Kondratieva SA, Zinovyeva MV, Nikolaev LG, Azhikina TL, Gainetdinov IV. Intragenic Locus in Human PIWIL2 Gene Shares Promoter and Enhancer Functions. PLoS One 2016; 11:e0156454. [PMID: 27248499 PMCID: PMC4889060 DOI: 10.1371/journal.pone.0156454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/13/2016] [Indexed: 01/18/2023] Open
Abstract
Recently, more evidence supporting common nature of promoters and enhancers has been accumulated. In this work, we present data on chromatin modifications and non-polyadenylated transcription characteristic for enhancers as well as results of in vitro luciferase reporter assays suggesting that PIWIL2 alternative promoter in exon 7 also functions as an enhancer for gene PHYHIP located 60Kb upstream. This finding of an intragenic enhancer serving as a promoter for a shorter protein isoform implies broader impact on understanding enhancer-promoter networks in regulation of gene expression.
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Affiliation(s)
- Yulia V Skvortsova
- Department of Genomics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Sofia A Kondratieva
- Department of Genomics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Marina V Zinovyeva
- Department of Genomics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Lev G Nikolaev
- Department of Genomics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Tatyana L Azhikina
- Department of Genomics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ildar V Gainetdinov
- Department of Genomics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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396
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Lacadie SA, Ibrahim MM, Gokhale SA, Ohler U. Divergent transcription and epigenetic directionality of human promoters. FEBS J 2016; 283:4214-4222. [DOI: 10.1111/febs.13747] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 02/08/2016] [Accepted: 04/25/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Scott A. Lacadie
- Berlin Institute for Medical Systems Biology; Max Delbrück Center for Molecular Medicine; Berlin Germany
- Berlin Institute of Health (BIH); Germany
| | - Mahmoud M. Ibrahim
- Berlin Institute for Medical Systems Biology; Max Delbrück Center for Molecular Medicine; Berlin Germany
- Department of Biology; Humboldt University Berlin; Germany
| | - Sucheta A. Gokhale
- Berlin Institute for Medical Systems Biology; Max Delbrück Center for Molecular Medicine; Berlin Germany
| | - Uwe Ohler
- Berlin Institute for Medical Systems Biology; Max Delbrück Center for Molecular Medicine; Berlin Germany
- Berlin Institute of Health (BIH); Germany
- Department of Biology; Humboldt University Berlin; Germany
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397
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Pundhir S, Bagger FO, Lauridsen FB, Rapin N, Porse BT. Peak-valley-peak pattern of histone modifications delineates active regulatory elements and their directionality. Nucleic Acids Res 2016; 44:4037-51. [PMID: 27095194 PMCID: PMC4872112 DOI: 10.1093/nar/gkw250] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/03/2016] [Indexed: 12/20/2022] Open
Abstract
Formation of nucleosome free region (NFR) accompanied by specific histone modifications at flanking nucleosomes is an important prerequisite for enhancer and promoter activity. Due to this process, active regulatory elements often exhibit a distinct shape of histone signal in the form of a peak-valley-peak (PVP) pattern. However, different features of PVP patterns and their robustness in predicting active regulatory elements have never been systematically analyzed. Here, we present PARE, a novel computational method that systematically analyzes the H3K4me1 or H3K4me3 PVP patterns to predict NFRs. We show that NFRs predicted by H3K4me1 and me3 patterns are associated with active enhancers and promoters, respectively. Furthermore, asymmetry in the height of peaks flanking the central valley can predict the directionality of stable transcription at promoters. Using PARE on ChIP-seq histone modifications from four ENCODE cell lines and four hematopoietic differentiation stages, we identified several enhancers whose regulatory activity is stage specific and correlates positively with the expression of proximal genes in a particular stage. In conclusion, our results demonstrate that PVP patterns delineate both the histone modification landscape and the transcriptional activities governed by active enhancers and promoters, and therefore can be used for their prediction. PARE is freely available at http://servers.binf.ku.dk/pare.
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Affiliation(s)
- Sachin Pundhir
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, 2200 Copenhagen, Denmark Danish Stem Cell Centre (DanStem), Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Frederik O Bagger
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, 2200 Copenhagen, Denmark Danish Stem Cell Centre (DanStem), Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Felicia B Lauridsen
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, 2200 Copenhagen, Denmark Danish Stem Cell Centre (DanStem), Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Nicolas Rapin
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, 2200 Copenhagen, Denmark Danish Stem Cell Centre (DanStem), Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Bo T Porse
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, 2200 Copenhagen, Denmark Danish Stem Cell Centre (DanStem), Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
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398
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The Determinants of Directionality in Transcriptional Initiation. Trends Genet 2016; 32:322-333. [PMID: 27066865 DOI: 10.1016/j.tig.2016.03.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 03/11/2016] [Accepted: 03/16/2016] [Indexed: 01/20/2023]
Abstract
A new paradigm has emerged in recent years characterizing transcription initiation as a bidirectional process encompassing a larger proportion of the genome than previously thought. Past concepts of coding genes thinly scattered among a vast background of transcriptionally inert noncoding DNA have been abandoned. A richer picture has taken shape, integrating transcription of coding genes, enhancer RNAs (eRNAs), and various other noncoding transcriptional events. In this review we give an overview of recent studies detailing the mechanisms of RNA polymerase II (RNA Pol II)-based transcriptional initiation and discuss the ways in which transcriptional direction is established as well as its functional implications.
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399
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Bunch H. Role of genome guardian proteins in transcriptional elongation. FEBS Lett 2016; 590:1064-75. [PMID: 27010360 DOI: 10.1002/1873-3468.12152] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 03/18/2016] [Accepted: 03/21/2016] [Indexed: 12/17/2022]
Abstract
Maintaining genomic integrity is vital for cell survival and homeostasis. Mutations in critical genes in germ-line and somatic cells are often implicated with the onset or progression of diseases. DNA repair enzymes thus take important roles as guardians of the genome in the cell. Besides the known function to repair DNA damage, recent findings indicate that DNA repair enzymes regulate the transcription of protein-coding and noncoding RNA genes. In particular, a novel role of DNA damage response signaling has been identified in the regulation of transcriptional elongation. Topoisomerases-mediated DNA breaks appear important for the regulation. In this review, recent findings of these DNA break- and repair-associated enzymes in transcription and potential roles of transcriptional activation-coupled DNA breaks are discussed.
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Affiliation(s)
- Heeyoun Bunch
- Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, MA, USA
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400
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Mahat DB, Salamanca HH, Duarte FM, Danko CG, Lis JT. Mammalian Heat Shock Response and Mechanisms Underlying Its Genome-wide Transcriptional Regulation. Mol Cell 2016; 62:63-78. [PMID: 27052732 DOI: 10.1016/j.molcel.2016.02.025] [Citation(s) in RCA: 270] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 02/01/2016] [Accepted: 02/18/2016] [Indexed: 12/25/2022]
Abstract
The heat shock response (HSR) is critical for survival of all organisms. However, its scope, extent, and the molecular mechanism of regulation are poorly understood. Here we show that the genome-wide transcriptional response to heat shock in mammals is rapid and dynamic and results in induction of several hundred and repression of several thousand genes. Heat shock factor 1 (HSF1), the "master regulator" of the HSR, controls only a fraction of heat shock-induced genes and does so by increasing RNA polymerase II release from promoter-proximal pause. Notably, HSF2 does not compensate for the lack of HSF1. However, serum response factor appears to transiently induce cytoskeletal genes independently of HSF1. The pervasive repression of transcription is predominantly HSF1-independent and is mediated through reduction of RNA polymerase II pause release. Overall, mammalian cells orchestrate rapid, dynamic, and extensive changes in transcription upon heat shock that are largely modulated at pause release, and HSF1 plays a limited and specialized role.
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Affiliation(s)
- Dig B Mahat
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - H Hans Salamanca
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - Fabiana M Duarte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - Charles G Danko
- Baker Institute for Animal Health, Cornell University, Ithaca, New York 14850, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA.
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