Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

FAIRE-seq in Rex1GFPd2 mouse embryonic stem cell line

ABSTRACT: Formaldehyde-assisted isolation of regulatory elements (FAIRE) in Rex1GFPd2 mouse ES cells (parental line; E14Tg2a)

INSTRUMENT(S): Illumina Genome Analyzer IIx

ORGANISM(S): Mus musculus

SUBMITTER: Ian Donaldson

PROVIDER: E-MTAB-2283 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Otx2 and Oct4 drive early enhancer activation during embryonic stem cell transition from naive pluripotency.

Yang Shen-Hsi SH Kalkan Tüzer T Morissroe Claire C Marks Hendrik H Stunnenberg Hendrik H Smith Austin A Sharrocks Andrew D AD

Cell reports 20140612 6

Embryonic stem cells (ESCs) are unique in that they have the capacity to differentiate into all of the cell types in the body. We know a lot about the complex transcriptional control circuits that maintain the naive pluripotent state under self-renewing conditions but comparatively less about how cells exit from this state in response to differentiation stimuli. Here, we examined the role of Otx2 in this process in mouse ESCs and demonstrate that it plays a leading role in remodeling the gene re ...[more]

PMID: 24931607

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Project description:Chromatin accessibility is an important functional genomics phenotype that influences transcription factor binding and gene expression. Genome-scale technologies allow chromatin accessibility to be mapped with high-resolution, facilitating detailed analyses into the genetic architecture and evolution of chromatin structure within and between species. We performed Formaldehyde-Assisted Isolation of Regulatory Elements sequencing (FAIRE-Seq) to map chromatin accessibility in two parental haploid yeast species, Saccharomyces cerevisiae and Saccharomyces paradoxus and their diploid hybrid. We show that although broad-scale characteristics of the chromatin landscape are well conserved between these species, accessibility is significantly different for 947 regions upstream of genes that are enriched for GO terms such as intracellular transport and protein localization exhibit. We also develop new statistical methods to investigate the genetic architecture of variation in chromatin accessibility between species, and find that cis effects are more common and of greater magnitude than trans effects. Interestingly, we find that cis and trans effects at individual genes are often negatively correlated, suggesting widespread compensatory evolution to stabilize levels of chromatin accessibility. Finally, we demonstrate that the relationship between chromatin accessibility and gene expression levels is complex, and a significant proportion of differences in chromatin accessibility might be functionally benign. There are 20 samples in total. These consist of 10 FAIRE-seq samples, specifically 6 haploid samples, S. cerevisiae strain UWOPS05_217_3 replicates 1 and 2, S. cerevisiae strain DBVPG1373 replicates 1 and 2, and S. paradoxus strain CBS432 replicates 1 and 2. There are also 4 diploid hybrid samples, hybrid between S. cerevisiae strain UWOPS05_217_3 and S. paradoxus strain CBS432 replicates 1 and 2, and the hybrid between S. cerevisiae strain DBVPG1373 and S. paradoxus strain CBS432 replicates 1 and 2. There are also RNA-seq samples for each of these 10 samples.

Dataset Information

FAIRE-seq in Rex1GFPd2 mouse embryonic stem cell line

Publications

Otx2 and Oct4 drive early enhancer activation during embryonic stem cell transition from naive pluripotency.

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