Transcriptomics,Genomics

Dataset Information

296

Complex patterns of accessibility discriminate sites of PcG repression, H4K16 acetylation and replication initiation


ABSTRACT: Full title: Complex patterns of genome accessibility discriminate sites of PcG repression, H4K16 acetylation and replication initiation Histone modifications have been proposed to regulate gene expression in part by modulating DNA accessibility and higher-order chromatin structure. However, there is limited direct evidence to support structural differences between euchromatic and heterochromatic fibers in the nucleus. To ask how histone modifications relate to chromatin compaction, we measured DNA accessibility throughout the genome by combining M.SssI methylase footprinting with methylated DNA immunoprecipitation (MeDIP-footprint). In the Drosophila genome, we find that accessibility to DNA methylase is variable in a manner that relates to the differential distribution of active and repressive histone modifications. Active promoters are highly permissive to M.SssI activity, yet inactive chromosomal domains decorated with H3 lysine 27 trimethylation are least accessible providing in vivo evidence for Polycomb-mediated chromatin compaction. Conversely, DNA accessibility is increased at active chromosomal regions marked with H4 lysine 16 acetylation and at the dosage-compensated male X chromosome suggesting that Drosophila transcriptional dosage compensation is facilitated by more permissive chromatin structure. Interestingly early replicating chromosomal regions and sites of replication initiation show also higher accessibility linking temporal and spatial control of genome duplication to the structural organization of chromatin. In conclusion, using a novel protocol we generated a comprehensive view of DNA accessibility and uncover different levels of chromatin organization, which are delineated by distinct patterns of posttranslational histone modifications and replication. Keywords: cell type comparison, ChIP-chip, MeDIP-footprint, RNA-seq, ChIP-seq MeDIP-footprint and ChIP-chip: ChIP-chip was performed for H3K4me3, H3K36me2, H3K36me3, H3K27me3, and H3K9me2 in Kc cells. We measured DNA accessibility throughout the genome by combining M.SssI methylase footprinting with methylated DNA immunoprecipitation (MeDIP-footprint) in Kc and S2 cells. RNA-seq: cDNA from RNA from Drosophila Kc cells was sequenced using Illumina deep sequencing. Reads were mapped and the abundance of all transcripts was determined. ChIP-seq: PSC ChIP from Drosophila Kc cells was sequenced using Illumina deep sequencing in three lanes. Reads were mapped and the binding profile of PSC was determined.

ORGANISM(S): Drosophila melanogaster  

SUBMITTER: Michael B Stadler   Michaela Schwaiger  Oliver Bell  Florian Lienert  Dirk Schübeler  Christian Beisel  Edward J Oakeley 

PROVIDER: E-GEOD-17697 | ArrayExpress | 2010-03-16

SECONDARY ACCESSION(S): GSE17697SRP002154SRP002153PRJNA118401

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Accessibility of the Drosophila genome discriminates PcG repression, H4K16 acetylation and replication timing.

Bell Oliver O   Schwaiger Michaela M   Oakeley Edward J EJ   Lienert Florian F   Beisel Christian C   Stadler Michael B MB   Schübeler Dirk D  

Nature structural & molecular biology 20100620 7


Histone modifications are thought to regulate gene expression in part by modulating DNA accessibility. Here, we measured genome-wide DNA accessibility in Drosophila melanogaster by combining M.SssI methylation footprinting with methylated DNA immunoprecipitation. We show that methylase accessibility demarcates differential distribution of active and repressive histone modifications as well as sites of transcription and replication initiation. DNA accessibility is increased at active promoters an  ...[more]

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