Genome-wide profiling of transcribed enhancers during macrophage activation

Bibliographic Details
Main Author: Denisenko, Elena
Publication Date: 2017
Other Authors: Guler, Reto, Mhlanga, Musa, Suzuki, Harukazu, Brombacher, Frank, Schmeier, Sebastian
Format: Article
Language: eng
Source: Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
Download full: http://hdl.handle.net/10451/51575
Summary: © The Author(s) 2017. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/ publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
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network_name_str Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
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spelling Genome-wide profiling of transcribed enhancers during macrophage activationMacrophage activationTranscriptional enhancersTranscriptional regulationeRNA© The Author(s) 2017. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/ publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.Background: Macrophages are sentinel cells essential for tissue homeostasis and host defence. Owing to their plasticity, macrophages acquire a range of functional phenotypes in response to microenvironmental stimuli, of which M(IFN-γ) and M(IL-4/IL-13) are well known for their opposing pro- and anti-inflammatory roles. Enhancers have emerged as regulatory DNA elements crucial for transcriptional activation of gene expression. Results: Using cap analysis of gene expression and epigenetic data, we identify on large-scale transcribed enhancers in bone marrow-derived mouse macrophages, their time kinetics, and target protein-coding genes. We observe an increase in target gene expression, concomitant with increasing numbers of associated enhancers, and find that genes associated with many enhancers show a shift towards stronger enrichment for macrophage-specific biological processes. We infer enhancers that drive transcriptional responses of genes upon M(IFN-γ) and M(IL-4/IL-13) macrophage activation and demonstrate stimuli specificity of regulatory associations. Finally, we show that enhancer regions are enriched for binding sites of inflammation-related transcription factors, suggesting a link between stimuli response and enhancer transcriptional control. Conclusions: Our study provides new insights into genome-wide enhancer-mediated transcriptional control of macrophage genes, including those implicated in macrophage activation, and offers a detailed genome-wide catalogue of transcribed enhancers in bone marrow-derived mouse macrophages.This work was supported by grants from the South African National Research Foundation (NRF) and from the Department of Science and Technology, South African Research Chair Initiative (SARCHi) and South Africa Medical Research Council (SAMRC) to FB, grant from the Japan Society for the Promotion of Science (JSPS) and National Research Foundation of South Africa to FB and HS, and grants from the South African National Research Foundation (NRF) Competitive Programme for Unrated Researchers (CSUR) to RG.Springer NatureRepositório da Universidade de LisboaDenisenko, ElenaGuler, RetoMhlanga, MusaSuzuki, HarukazuBrombacher, FrankSchmeier, Sebastian2022-03-02T16:56:34Z20172017-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10451/51575engEpigenetics & Chromatin (2017) 10:5010.1186/s13072-017-0158-91756-8935info:eu-repo/semantics/openAccessreponame:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiainstacron:RCAAP2025-03-17T14:42:06Zoai:repositorio.ulisboa.pt:10451/51575Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireinfo@rcaap.ptopendoar:https://opendoar.ac.uk/repository/71602025-05-29T03:22:31.782282Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiafalse
dc.title.none.fl_str_mv Genome-wide profiling of transcribed enhancers during macrophage activation
title Genome-wide profiling of transcribed enhancers during macrophage activation
spellingShingle Genome-wide profiling of transcribed enhancers during macrophage activation
Denisenko, Elena
Macrophage activation
Transcriptional enhancers
Transcriptional regulation
eRNA
title_short Genome-wide profiling of transcribed enhancers during macrophage activation
title_full Genome-wide profiling of transcribed enhancers during macrophage activation
title_fullStr Genome-wide profiling of transcribed enhancers during macrophage activation
title_full_unstemmed Genome-wide profiling of transcribed enhancers during macrophage activation
title_sort Genome-wide profiling of transcribed enhancers during macrophage activation
author Denisenko, Elena
author_facet Denisenko, Elena
Guler, Reto
Mhlanga, Musa
Suzuki, Harukazu
Brombacher, Frank
Schmeier, Sebastian
author_role author
author2 Guler, Reto
Mhlanga, Musa
Suzuki, Harukazu
Brombacher, Frank
Schmeier, Sebastian
author2_role author
author
author
author
author
dc.contributor.none.fl_str_mv Repositório da Universidade de Lisboa
dc.contributor.author.fl_str_mv Denisenko, Elena
Guler, Reto
Mhlanga, Musa
Suzuki, Harukazu
Brombacher, Frank
Schmeier, Sebastian
dc.subject.por.fl_str_mv Macrophage activation
Transcriptional enhancers
Transcriptional regulation
eRNA
topic Macrophage activation
Transcriptional enhancers
Transcriptional regulation
eRNA
description © The Author(s) 2017. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/ publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
publishDate 2017
dc.date.none.fl_str_mv 2017
2017-01-01T00:00:00Z
2022-03-02T16:56:34Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10451/51575
url http://hdl.handle.net/10451/51575
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Epigenetics & Chromatin (2017) 10:50
10.1186/s13072-017-0158-9
1756-8935
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Springer Nature
publisher.none.fl_str_mv Springer Nature
dc.source.none.fl_str_mv reponame:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
instacron:RCAAP
instname_str FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
instacron_str RCAAP
institution RCAAP
reponame_str Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
collection Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
repository.name.fl_str_mv Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
repository.mail.fl_str_mv info@rcaap.pt
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