Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition
Summary: Transcriptional enhancers, including super-enhancers (SEs), form physical interactions with promoters to regulate cell-type-specific gene expression. SEs are characterized by high transcription factor occupancy and large domains of active chromatin, and they are commonly assigned to target...
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doaj-a9fe24befd3e4a119da1557f07e1eacc2020-11-24T21:36:17ZengElsevierCell Reports2211-12472018-03-01221026152627Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State TransitionClara Lopes Novo0Biola-Maria Javierre1Jonathan Cairns2Anne Segonds-Pichon3Steven W. Wingett4Paula Freire-Pritchett5Mayra Furlan-Magaril6Stefan Schoenfelder7Peter Fraser8Peter J. Rugg-Gunn9Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UKNuclear Dynamics Programme, Babraham Institute, Cambridge CB22 3AT, UKNuclear Dynamics Programme, Babraham Institute, Cambridge CB22 3AT, UKBioinformatics Group, Babraham Institute, Cambridge CB22 3AT, UKBioinformatics Group, Babraham Institute, Cambridge CB22 3AT, UKNuclear Dynamics Programme, Babraham Institute, Cambridge CB22 3AT, UKNuclear Dynamics Programme, Babraham Institute, Cambridge CB22 3AT, UKNuclear Dynamics Programme, Babraham Institute, Cambridge CB22 3AT, UKNuclear Dynamics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Department of Biological Science, Florida State University, Tallahassee, FL 32306, USAEpigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK; Corresponding authorSummary: Transcriptional enhancers, including super-enhancers (SEs), form physical interactions with promoters to regulate cell-type-specific gene expression. SEs are characterized by high transcription factor occupancy and large domains of active chromatin, and they are commonly assigned to target promoters using computational predictions. How promoter-SE interactions change upon cell state transitions, and whether transcription factors maintain SE interactions, have not been reported. Here, we used promoter-capture Hi-C to identify promoters that interact with SEs in mouse embryonic stem cells (ESCs). We found that SEs form complex, spatial networks in which individual SEs contact multiple promoters, and a rewiring of promoter-SE interactions occurs between pluripotent states. We also show that long-range promoter-SE interactions are more prevalent in ESCs than in epiblast stem cells (EpiSCs) or Nanog-deficient ESCs. We conclude that SEs form cell-type-specific interaction networks that are partly dependent on core transcription factors, thereby providing insights into the gene regulatory organization of pluripotent cells. : Novo et al. use promoter-capture Hi-C to map the target promoters of super-enhancers (SEs) in mouse pluripotent cells. SEs form complex networks, and a subset of promoter-SE interactions was rewired between ESCs and EpiSCs. In ESCs, many SEs form long-range contacts that are not detected in EpiSC or Nanog-deficient ESCs. Keywords: epigenetics, genome organization, chromatin looping, gene regulation, pluripotency, differentiation, promoter capture Hi-Chttp://www.sciencedirect.com/science/article/pii/S2211124718302213 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Clara Lopes Novo Biola-Maria Javierre Jonathan Cairns Anne Segonds-Pichon Steven W. Wingett Paula Freire-Pritchett Mayra Furlan-Magaril Stefan Schoenfelder Peter Fraser Peter J. Rugg-Gunn |
spellingShingle |
Clara Lopes Novo Biola-Maria Javierre Jonathan Cairns Anne Segonds-Pichon Steven W. Wingett Paula Freire-Pritchett Mayra Furlan-Magaril Stefan Schoenfelder Peter Fraser Peter J. Rugg-Gunn Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition Cell Reports |
author_facet |
Clara Lopes Novo Biola-Maria Javierre Jonathan Cairns Anne Segonds-Pichon Steven W. Wingett Paula Freire-Pritchett Mayra Furlan-Magaril Stefan Schoenfelder Peter Fraser Peter J. Rugg-Gunn |
author_sort |
Clara Lopes Novo |
title |
Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition |
title_short |
Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition |
title_full |
Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition |
title_fullStr |
Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition |
title_full_unstemmed |
Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition |
title_sort |
long-range enhancer interactions are prevalent in mouse embryonic stem cells and are reorganized upon pluripotent state transition |
publisher |
Elsevier |
series |
Cell Reports |
issn |
2211-1247 |
publishDate |
2018-03-01 |
description |
Summary: Transcriptional enhancers, including super-enhancers (SEs), form physical interactions with promoters to regulate cell-type-specific gene expression. SEs are characterized by high transcription factor occupancy and large domains of active chromatin, and they are commonly assigned to target promoters using computational predictions. How promoter-SE interactions change upon cell state transitions, and whether transcription factors maintain SE interactions, have not been reported. Here, we used promoter-capture Hi-C to identify promoters that interact with SEs in mouse embryonic stem cells (ESCs). We found that SEs form complex, spatial networks in which individual SEs contact multiple promoters, and a rewiring of promoter-SE interactions occurs between pluripotent states. We also show that long-range promoter-SE interactions are more prevalent in ESCs than in epiblast stem cells (EpiSCs) or Nanog-deficient ESCs. We conclude that SEs form cell-type-specific interaction networks that are partly dependent on core transcription factors, thereby providing insights into the gene regulatory organization of pluripotent cells. : Novo et al. use promoter-capture Hi-C to map the target promoters of super-enhancers (SEs) in mouse pluripotent cells. SEs form complex networks, and a subset of promoter-SE interactions was rewired between ESCs and EpiSCs. In ESCs, many SEs form long-range contacts that are not detected in EpiSC or Nanog-deficient ESCs. Keywords: epigenetics, genome organization, chromatin looping, gene regulation, pluripotency, differentiation, promoter capture Hi-C |
url |
http://www.sciencedirect.com/science/article/pii/S2211124718302213 |
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