Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

DNA binding factors shape the mouse methylome at distal regulatory regions.

ABSTRACT: This SuperSeries is composed of the following subset Series: GSE30202: DNA binding factors shape the mouse methylome at distal regulatory regions [BIS_seq] GSE30203: DNA binding factors shape the mouse methylome at distal regulatory regions [ChIP-seq] GSE30204: DNA binding factors shape the mouse methylome at distal regulatory regions [ChIP_chip] GSE30280: DNA binding factors shape the mouse methylome at distal regulatory regions [RNA_seq] Refer to individual Series

ORGANISM(S): Mus musculus

SUBMITTER: Dirk Schuebeler

PROVIDER: E-GEOD-30206 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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DNA-binding factors shape the mouse methylome at distal regulatory regions.

Stadler Michael B MB Murr Rabih R Burger Lukas L Ivanek Robert R Lienert Florian F Schöler Anne A van Nimwegen Erik E Wirbelauer Christiane C Oakeley Edward J EJ Gaidatzis Dimos D Tiwari Vijay K VK Schübeler Dirk D

Nature 20111214 7378

Methylation of cytosines is an essential epigenetic modification in mammalian genomes, yet the rules that govern methylation patterns remain largely elusive. To gain insights into this process, we generated base-pair-resolution mouse methylomes in stem cells and neuronal progenitors. Advanced quantitative analysis identified low-methylated regions (LMRs) with an average methylation of 30%. These represent CpG-poor distal regulatory regions as evidenced by location, DNase I hypersensitivity, pres ...[more]

PMID: 22170606

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Project description:To advance understanding of mechanisms leading to biological and transcriptional endpoints related to estrogen action in the mouse uterus, we have mapped ERM-NM-1 and RNA polymerase II binding sites using chromatin immunoprecipitation (ChIP) followed by sequencing of enriched chromatin fragments (ChIP-seq). In the absence of hormone, 5184 ERM-NM-1 binding sites were apparent in the vehicle treated ovariectomized uterine chromatin, while 17240 were seen one hour after estrogen (E2) treatment, indicating that some sites are occupied by unliganded ERM-NM-1, and that ERM-NM-1 binding is increased by E2. Approximately 15% of the uterine ERM-NM-1 binding sites were adjacent to (<10 KB) annotated transcription start sites and many sites are found within genes or are found more than 100 KB distal from mapped genes; however, the density (sites per bp) of ERM-NM-1 binding sites is significantly greater adjacent to promoters. An increase in quantity of sites but no significant positional differences were seen between vehicle and E2 treated samples in the overall locations of ERM-NM-1 binding sites either distal from, adjacent to or within genes. Analysis of the PolII data revealed the presence of poised promoter proximal PolII on some highly upregulated genes. Additionally, co-recruitment of PolII and ERM-NM-1 to some distal enhancer regions was observed. A de novo motif analysis of sequences in the ERM-NM-1 bound chromatin confirmed that estrogen response elements (EREs) were significantly enriched. Interestingly, in areas of ERM-NM-1 binding without predicted ERE motifs, homeodomain transcription factor (Hox) binding motifs were significantly enriched. The integration of the ERM-NM-1 and PolII binding sites from our uterine ChIP-seq data with transcriptional responses revealed in our uterine microarrays has the potential to greatly enhance our understanding of mechanisms governing estrogen response in uterine and other estrogen target tissues. one sample each, vehicle ER-alpha ChIP seq,1 hour estradiol ER-alpha ChIP seq, vehicle RNA polymerase II ChIP seq,1 hour estradiol RNA polymerase II ChIP seq, input DNA

Dataset Information

DNA binding factors shape the mouse methylome at distal regulatory regions.

Publications

DNA-binding factors shape the mouse methylome at distal regulatory regions.

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