Integration of DNA methylation and gene transcription across nineteen cell types reveals cell type-specific and genomic region-dependent regulatory patterns

Abstract Despite numerous studies done on understanding the role of DNA methylation, limited work has focused on systems integration of cell type-specific interplay between DNA methylation and gene transcription. Through a genome-wide analysis of DNA methylation across 19 cell types with T-47D as re...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Binhua Tang, Yufan Zhou, Chiou-Miin Wang, Tim H.-M. Huang, Victor X. Jin
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b597d3a6847f4b45bc16c451c33629b7
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:b597d3a6847f4b45bc16c451c33629b7
record_format	dspace
spelling	oai:doaj.org-article:b597d3a6847f4b45bc16c451c33629b72021-12-02T11:53:01ZIntegration of DNA methylation and gene transcription across nineteen cell types reveals cell type-specific and genomic region-dependent regulatory patterns10.1038/s41598-017-03837-z2045-2322https://doaj.org/article/b597d3a6847f4b45bc16c451c33629b72017-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-03837-zhttps://doaj.org/toc/2045-2322Abstract Despite numerous studies done on understanding the role of DNA methylation, limited work has focused on systems integration of cell type-specific interplay between DNA methylation and gene transcription. Through a genome-wide analysis of DNA methylation across 19 cell types with T-47D as reference, we identified 106,252 cell type-specific differentially-methylated CpGs categorized into 7,537 differentially (46.6% hyper- and 53.4% hypo-) methylated regions. We found 44% promoter regions and 75% CpG islands were T-47D cell type-specific methylated. Pyrosequencing experiments validated the cell type-specific methylation across three benchmark cell lines. Interestingly, these DMRs overlapped with 1,145 known tumor suppressor genes. We then developed a Bayesian Gaussian Regression model to measure the relationship among DNA methylation, genomic segment distribution, differential gene expression and tumor suppressor gene status. The model uncovered that 3′UTR methylation has much less impact on transcriptional activity than other regions. Integration of DNA methylation and 82 transcription factor binding information across the 19 cell types suggested diverse interplay patterns between the two regulators. Our integrative analysis reveals cell type-specific and genomic region-dependent regulatory patterns and provides a perspective for integrating hundreds of various omics-seq data together.Binhua TangYufan ZhouChiou-Miin WangTim H.-M. HuangVictor X. JinNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-11 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Binhua Tang Yufan Zhou Chiou-Miin Wang Tim H.-M. Huang Victor X. Jin Integration of DNA methylation and gene transcription across nineteen cell types reveals cell type-specific and genomic region-dependent regulatory patterns
description	Abstract Despite numerous studies done on understanding the role of DNA methylation, limited work has focused on systems integration of cell type-specific interplay between DNA methylation and gene transcription. Through a genome-wide analysis of DNA methylation across 19 cell types with T-47D as reference, we identified 106,252 cell type-specific differentially-methylated CpGs categorized into 7,537 differentially (46.6% hyper- and 53.4% hypo-) methylated regions. We found 44% promoter regions and 75% CpG islands were T-47D cell type-specific methylated. Pyrosequencing experiments validated the cell type-specific methylation across three benchmark cell lines. Interestingly, these DMRs overlapped with 1,145 known tumor suppressor genes. We then developed a Bayesian Gaussian Regression model to measure the relationship among DNA methylation, genomic segment distribution, differential gene expression and tumor suppressor gene status. The model uncovered that 3′UTR methylation has much less impact on transcriptional activity than other regions. Integration of DNA methylation and 82 transcription factor binding information across the 19 cell types suggested diverse interplay patterns between the two regulators. Our integrative analysis reveals cell type-specific and genomic region-dependent regulatory patterns and provides a perspective for integrating hundreds of various omics-seq data together.
format	article
author	Binhua Tang Yufan Zhou Chiou-Miin Wang Tim H.-M. Huang Victor X. Jin
author_facet	Binhua Tang Yufan Zhou Chiou-Miin Wang Tim H.-M. Huang Victor X. Jin
author_sort	Binhua Tang
title	Integration of DNA methylation and gene transcription across nineteen cell types reveals cell type-specific and genomic region-dependent regulatory patterns
title_short	Integration of DNA methylation and gene transcription across nineteen cell types reveals cell type-specific and genomic region-dependent regulatory patterns
title_full	Integration of DNA methylation and gene transcription across nineteen cell types reveals cell type-specific and genomic region-dependent regulatory patterns
title_fullStr	Integration of DNA methylation and gene transcription across nineteen cell types reveals cell type-specific and genomic region-dependent regulatory patterns
title_full_unstemmed	Integration of DNA methylation and gene transcription across nineteen cell types reveals cell type-specific and genomic region-dependent regulatory patterns
title_sort	integration of dna methylation and gene transcription across nineteen cell types reveals cell type-specific and genomic region-dependent regulatory patterns
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/b597d3a6847f4b45bc16c451c33629b7
work_keys_str_mv	AT binhuatang integrationofdnamethylationandgenetranscriptionacrossnineteencelltypesrevealscelltypespecificandgenomicregiondependentregulatorypatterns AT yufanzhou integrationofdnamethylationandgenetranscriptionacrossnineteencelltypesrevealscelltypespecificandgenomicregiondependentregulatorypatterns AT chioumiinwang integrationofdnamethylationandgenetranscriptionacrossnineteencelltypesrevealscelltypespecificandgenomicregiondependentregulatorypatterns AT timhmhuang integrationofdnamethylationandgenetranscriptionacrossnineteencelltypesrevealscelltypespecificandgenomicregiondependentregulatorypatterns AT victorxjin integrationofdnamethylationandgenetranscriptionacrossnineteencelltypesrevealscelltypespecificandgenomicregiondependentregulatorypatterns
_version_	1718394947991764992

Integration of DNA methylation and gene transcription across nineteen cell types reveals cell type-specific and genomic region-dependent regulatory patterns

Ejemplares similares