Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species

17 pages, 6 figures, 1 table, supplementary material https://doi.org/10.1186/s13072-018-0205-1

Detalles Bibliográficos
Autores: Anastasiadi, Dafni, Esteve-Codina, Anna, Piferrer, Francesc
Tipo de recurso: artículo
Fecha de publicación:2018
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/172802
Acceso en línea:http://hdl.handle.net/10261/172802
Access Level:acceso abierto
Palabra clave:Gene expression
DNA methylation
Regulation
Gene features
First intron
id ES_9f044e30c0ca9dea8154ae97efb45014
oai_identifier_str oai:digital.csic.es:10261/172802
network_acronym_str ES
network_name_str España
repository_id_str
spelling Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and speciesAnastasiadi, DafniEsteve-Codina, AnnaPiferrer, FrancescGene expressionDNA methylationRegulationGene featuresFirst intron17 pages, 6 figures, 1 table, supplementary material https://doi.org/10.1186/s13072-018-0205-1Abstract Background DNA methylation is one of the main epigenetic mechanisms for the regulation of gene expression in eukaryotes. In the standard model, methylation in gene promoters has received the most attention since it is generally associated with transcriptional silencing. Nevertheless, recent studies in human tissues reveal that methylation of the region downstream of the transcription start site is highly informative of gene expression. Also, in some cell types and specific genes it has been found that methylation of the first intron, a gene feature typically rich in enhancers, is linked with gene expression. However, a genome-wide, tissue-independent, systematic comparative analysis of the relationship between DNA methylation in the first intron and gene expression across vertebrates has not been explored yet. Results The most important findings of this study are: (1) using different tissues from a modern fish, we show a clear genome-wide, tissue-independent quasi-linear inverse relationship between DNA methylation of the first intron and gene expression. (2) This relationship is conserved across vertebrates, since it is also present in the genomes of a model pufferfish, a model frog and different human tissues. Among the gene features, tissues and species interrogated, the first intron’s negative correlation with the gene expression was most consistent. (3) We identified more tissue-specific differentially methylated regions (tDMRs) in the first intron than in any other gene feature. These tDMRs have positive or negative correlation with gene expression, indicative of distinct mechanisms of tissue-specific regulation. (4) Lastly, we identified CpGs in transcription factor binding motifs, enriched in the first intron, the methylation of which tended to increase with the distance from the first exon–first intron boundary, with a concomitant decrease in gene expression. Conclusions Our integrative analysis clearly reveals the important and conserved role of the methylation level of the first intron and its inverse association with gene expression regardless of tissue and species. These findings not only contribute to our basic understanding of the epigenetic regulation of gene expression but also identify the first intron as an informative gene feature regarding the relationship between DNA methylation and gene expression where future studies should be focusedDA was supported by a Ph.D. scholarship from the Spanish Government (BES-2011-044860). AEC is funded by the RED-BIO project of the Spanish National Bioinformatics Institute (INB) under grant number PT13/0001/0044. The INB is funded by the Spanish National Health Institute Carlos III (ISCIII) and the Spanish Ministry of Economy and Competitiveness (MINECO). Research supported by MINECO grant “Epifarm” (ref. AGL2013-41047-R) to FP. We acknowledge support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI)Peer ReviewedBioMed CentralConsejo Superior de Investigaciones Científicas (España)Ministerio de Economía y Competitividad (España)Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2018201820182018info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501http://hdl.handle.net/10261/172802reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/AGL2013-41047-Rhttps://doi.org/10.1186/s13072-018-0205-1Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/1728022026-05-22T06:33:51Z
dc.title.none.fl_str_mv Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species
title Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species
spellingShingle Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species
Anastasiadi, Dafni
Gene expression
DNA methylation
Regulation
Gene features
First intron
title_short Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species
title_full Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species
title_fullStr Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species
title_full_unstemmed Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species
title_sort Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species
dc.creator.none.fl_str_mv Anastasiadi, Dafni
Esteve-Codina, Anna
Piferrer, Francesc
author Anastasiadi, Dafni
author_facet Anastasiadi, Dafni
Esteve-Codina, Anna
Piferrer, Francesc
author_role author
author2 Esteve-Codina, Anna
Piferrer, Francesc
author2_role author
author
dc.contributor.none.fl_str_mv Consejo Superior de Investigaciones Científicas (España)
Ministerio de Economía y Competitividad (España)
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Gene expression
DNA methylation
Regulation
Gene features
First intron
topic Gene expression
DNA methylation
Regulation
Gene features
First intron
description 17 pages, 6 figures, 1 table, supplementary material https://doi.org/10.1186/s13072-018-0205-1
publishDate 2018
dc.date.none.fl_str_mv 2018
2018
2018
2018
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
format article
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/172802
url http://hdl.handle.net/10261/172802
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/AGL2013-41047-R
https://doi.org/10.1186/s13072-018-0205-1
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
_version_ 1869414874448134144
score 15,811543

Similares en LA Referencia