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Series GSE205779 Query DataSets for GSE205779
Status Public on Apr 28, 2023
Title Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos [ChIP-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary During development, Hox genes are activated in a time sequence following their relative positions on their clusters, leading to the proper identities of structures along the rostral to caudal axis. To understand the mechanism operating this Hox timer, we used ES-cells derived stembryos and show that the core of the process involves the start of transcription at the anterior part of the cluster, following Wnt signaling, and a concomitant loading of cohesin complexes enriched on the transcribed DNA segments, i.e., with an asymmetric distribution in favor of the anterior part the gene cluster. Chromatin extrusion then occurs with, along with time, successively more posterior CTCF sites acting as transient insulators, thus generating a progressive time-delay in the activation of more posterior-located genes due to long-range contacts with a flanking TAD. Mutant stembryos support this model and reveal that the iterated presence of evolutionary conserved and regularly spaced intergenic CTCF sites control the precision and the pace of this temporal mechanism.
 
Overall design ChIP and ChIPmentation data of wt and mutant stembryos
 
Contributor(s) Rekaik H, Lopez-Delisle L, Mascrez B, Bochaton C, Mayran A, Duboule D
Citation(s) 37322110
Submission date Jun 09, 2022
Last update date Aug 08, 2023
Contact name Lucille Lopez-Delisle
E-mail(s) lucille.delisle@epfl.ch
Organization name EPFL
Street address Station 19
City Lausanne
ZIP/Postal code 1015
Country Switzerland
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (82)
GSM6226233 CTCF ChIP-M of Del(CBS1-2) stembryos at 96h
GSM6226234 CTCF ChIP-M of Del(CBS1-5) stembryos at 96h
GSM6226235 CTCF ChIP-M of Del(CBS1) stembryos at 96h
This SubSeries is part of SuperSeries:
GSE205783 Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos
Relations
BioProject PRJNA847583

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
GSE205779_RAW.tar 22.0 Gb (http)(custom) TAR (of BEDGRAPH, BIGWIG, NARROWPEAK)
GSE205779_wt_144h_pSer2PolII.narrowPeak.gz 232.7 Kb (ftp)(http) NARROWPEAK
GSE205779_wt_144h_pSer2PolII_Normalized.bigwig 560.3 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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