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Series GSE31654 Query DataSets for GSE31654
Status Public on Nov 28, 2011
Title Chromatin landscape at the HoxD locus in developing digits and forebrain
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by genome tiling array
Summary The emergence and evolution of digits was an essential step in the success of the tetrapod lineage. Amongst the key players, Hoxd genes were functionally co-opted in the developing digital plate, where they help organize growth and patterns. To understand both the evolutionary recruitment and transcriptional regulation of this genomic locus, we analyzed its architecture and chromatin status in developing digits, combined with a deletion approach in vivo. We show that the active and inactive parts of the gene cluster adopt opposite spatial configurations, corresponding to different chromatin domains. Active genes are contacted by several regulatory islands, located within a neighboring gene desert, which contribute quantitatively or qualitatively to the global transcriptional readout. We refer to this novel type of control as a ‘regulatory archipelago’ and discuss the value of this concept to understand both the morphological flexibility of tetrapod digits and the robustness of the underlying developmental process.
Distribution of histone marks and RNA Pol2 at the Hoxd locus in developing limbs and brain at E12.5
 
Overall design Array data were quantile normalized within ChIP/input replicate groups and scaled to medial feature intensity of 100 using TAS software (Affymetrix). For each genomic position, a data set was generated consisting of all (PM-MM) pairs mapping within a sliding window of 250 bp. For each tissue, two independent ChIP-chip experiments were performed with all mentionned antibodies.
 
Contributor(s) Montavon T, Duboule D
Citation(s) 22118467
Submission date Aug 25, 2011
Last update date Mar 23, 2012
Contact name Thomas Montavon
Organization name EPFL
Street address SV 2843, Station 19
City Lausanne
ZIP/Postal code 1015
Country Switzerland
 
Platforms (1)
GPL14183 Mus musculus HoxD cluster tiling PRNFGMm2b520462F
Samples (8)
GSM786022 Brain H3K27Ac
GSM786023 Brain H3K4me1
GSM786024 Brain H3K4me3
This SubSeries is part of SuperSeries:
GSE31659 HoxD locus in the developing limb, digit, and brain
Relations
BioProject PRJNA155011

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
GSE31654_RAW.tar 26.1 Mb (http)(custom) TAR (of BAR, CEL)
Processed data provided as supplementary file

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