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Series GSE11335 Query DataSets for GSE11335
Status Public on Nov 24, 2008
Title Chip-chip from MEF cells with H3ac, H4ac, H4K20me1, H3K27me3, H3K9me3, H4K20me3, H3K4me2, H3K4me3 and H3K9ac
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by genome tiling array
Summary Genome wide chromatin maps have shown that spreading repressive histone modifications such as H3K9me3 and H4K20me3 are present on pericentromeric and telomeric repeats and on the inactive X chromosome where H3K27me3 or H3K9me3 alternately modify megabasepair sized domains. However, only a few regions along an autosome of which Homeobox gene clusters are notable examples, have been shown to display spreading of repressive histone modifications. Here we present a ChIP-Chip map of repressive and active histone modifications along mouse Chr.17 in embryonic, fibroblast cells. Our results show that the majority of H3K27me3 modifications form BLOCs rather than focal peaks. H3K27me3 BLOCs modify silent genes of all types and their flanking intergenic regions, indicating a negative correlation between H3K27me3 and transcription. However, non-transcribed gene-poor regions also lacked H3K27me3. We therefore performed a low resolution analysis of whole mouse Chr.17 which revealed that H3K27me3 specifically marks megabasepair sized domains that are enriched for genes, SINEs and active histone modifications. These genic H3K27me3 domains alternate with similar sized gene-poor domains that are deficient in active histone modifications, but enriched for LINE and LTR transposons as well as H3K9me3 and H4K20me3. Thus, a mouse autosome can be seen to contain alternating chromatin bands that predominantly separate genes from one retrotransposons class, which could offer unique chromatin compartments for the specific regulation of genes or the silencing of transposons.
Keywords: Chip-chip, chromosome 17 wide unbiased mapping
 
Overall design unbiased mapping of several histone modifications on chromosome 17 in two independent MEF cell lines
 
Contributor(s) Pauler FM, Sloane MA, Barlow DP
Citation(s) 19047520
Submission date May 05, 2008
Last update date Mar 19, 2012
Contact name Florian M Pauler
E-mail florian.pauler@univie.ac.at
Phone +43 1 4277 54323
Fax +43 1 42770 9546
Organization name CeMM
Lab Denise P Barlow
Street address Dr Bohrgasse 9/4
City Vienna
State/province Vienna
ZIP/Postal code A1030
Country Austria
 
Platforms (3)
GPL6813 GenAu mouse chr17 1734
GPL6814 GenAu mouse chr17 2356
GPL6815 GenAu mouse chr17 2588
Samples (34)
GSM286012 MEFB H3K27me3 MS35
GSM286013 MEFF H3K27me3 MS39
GSM286014 MEFF H3K27me3 MS40
This SubSeries is part of SuperSeries:
GSE11389 Mouse Chromosome 17 Mapping in Two MEF Cell Lines
Relations
BioProject PRJNA109205

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE11335_RAW.tar 503.4 Mb (http)(custom) TAR (of TXT)
Raw data provided as supplementary file
Processed data included within Sample table
Raw data included within Sample table

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