Genomics

Dataset Information

0

Chromatin States in Human ES Cells Reveal Key Regulatory Sequences and Genes Involved in Pluripotency and Self-renewal


ABSTRACT: Human embryonic stem cells (hESCs) are offering a new therapeutic approach because of their unique ability to proliferate indefinitely in vitro and differentiate into multiple cell types. However, our understanding of the molecular mechanisms of pluripotency and self-renewal remain incomplete. To elucidate the key regulatory sequences and genes responsible for these cellular properties, we have determined potential enhancers and insulators in the genome of human ES cells and examined the dynamics of four key chromatin modifications (H3K4me1, H3K4me3, H3K27ac and H3K27me3) at both promoters and enhancers during the differentiation of these cells. We observe that most enhancers gain or lose H3K4me1 and H3K27ac during differentiation in a manner that correlates with expression of their potential target genes. By contrast, chromatin modifications at promoters remain stable and largely invariant during hESC differentiation, with the exception of a small number of promoters where a dynamic switch between acetylation and methylation at H3K27 marks the transition between activation and silencing of gene expression. Our results reveal more than 50,000 potential enhancers for early human development, and identify key genes that are involved in differentiation and maintenance of pluripotency in human ES cells. ChIP-Seq Analysis of SOX2 and NANOG in hESC H1 cells. 36 cycles of sequencing was done on the Illumina Genome Analyzer II platform.

ORGANISM(S): Homo sapiens  

SUBMITTER: Jessica Antosiewicz-Bourget   Lee Edsall  Ron Stewart  Leonard Lee  Joseph R Ecker  A H Millar  Victor Ruotti  Mattia Pelizzola  Julian Tonti-Filippini  Bing Ren  Joseph R Nery  Gary Hon  Que-Minh Ngo  James A Thomson  Robert H Dowen  Zhen Ye  R D Hawkins 

PROVIDER: E-GEOD-18292 | ArrayExpress | 2009-10-14

SECONDARY ACCESSION(S): SRP001264GSE18292PRJNA117929

REPOSITORIES: GEO, ArrayExpress, ENA

altmetric image

Publications


DNA cytosine methylation is a central epigenetic modification that has essential roles in cellular processes including genome regulation, development and disease. Here we present the first genome-wide, single-base-resolution maps of methylated cytosines in a mammalian genome, from both human embryonic stem cells and fetal fibroblasts, along with comparative analysis of messenger RNA and small RNA components of the transcriptome, several histone modifications, and sites of DNA-protein interaction  ...[more]

Similar Datasets

2009-10-14 | GSE18292 | GEO
2012-05-08 | E-GEOD-32483 | ArrayExpress
2016-02-22 | E-GEOD-77267 | ArrayExpress
2012-03-29 | E-GEOD-36374 | ArrayExpress
| GSE95237 | GEO
2011-06-24 | E-GEOD-30173 | ArrayExpress
2013-12-17 | E-GEOD-50455 | ArrayExpress
2013-12-17 | E-GEOD-50417 | ArrayExpress
2013-12-17 | E-GEOD-50465 | ArrayExpress
2015-06-12 | E-GEOD-66896 | ArrayExpress