DNA sequence at CpG islands directly influences chromatin structure via the CpG binding protein Cfp1

ABSTRACT: CpG islands (CGIs) are prominent in the mammalian genome due to their G+C rich base composition and high density of CpG dinucleotides. Most mammalian gene promoters are embedded within CGIs that lack DNA methylation and coincide with sites of histone H3 lysine 4 trimethylation (H3K4me3),irrespective of transcriptional activity. In spite of these intriguing correlations, the functional significance of non-methylated CGI sequences with respect to chromatin structure and transcription is unknown. High throughput sequencing of Cfp1-bound chromatin identified a striking concordance with non-methylated CGIs and sites of H3K4me3 in the mouse brain. Protocol: Brains were manually homogenised to a single cells suspension and crosslinked using 1% formaldehyde. Chromatin was sheared using a combination of Micrococcal nuclease and sonication (Skene et al, Mol Cell, 2010). Cells were crosslinked using 1% formaldehyde and chromatin sheared using sonication.Protein-DNA complexes were immunoprecipitated with the appropriate antibody and DNA was subsequently extracted. Adaptors were ligated to purified DNA which was then amplified by PCR. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols Sequencing was performed at the Wellcome Trust Sanger Institute; Hinxton, Cambridge, UK.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

INSTRUMENT(S): Illumina Genome Analyzer II

ORGANISM(S): mus musculus

SUBMITTER:  

PROVIDER: E-ERAD-79 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress