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Series GSE101713 Query DataSets for GSE101713
Status Public on Dec 22, 2017
Title A TAD boundary at the HoxD locus segregates opposing limb regulatory landscapes and their target genes [4C-Seq]
Organism Mus musculus
Experiment type Other
Summary The mammalian HoxD cluster is positioned at the boundary between two topologically associating domains (TADs), each of them matching a distinct, enhancer-rich regulatory landscape. During limb development, the telomeric TAD controls the early phase of Hoxd gene transcription in future forearm cells, whereas the centromeric TAD subsequently regulates transcription of more posterior Hoxd genes in presumptive digit cells. The TAD boundary is essential as it prevents the terminal Hoxd13 gene to respond to potent forearm enhancers, thereby allowing the formation of proper proximal limb structures. Here we apply chromosome conformation capture onto embryonic proximal and distal limb bud cells micro-dissected from a set of nested deletions involving part- or all- of this boundary region to try to understand the nature and function of this CTCF- and cohesin-rich DNA region. We document a progressive release of the boundary effect, allowing for inter-TAD contacts to be established, which were favoured by the functional status of the newly accessed enhancers. However, the boundary was highly resilient and only a 400kb large deletion including the whole gene cluster was eventually able to merge the two neighbouring TADs into a single structure. We propose that the whole HoxD cluster is a dynamic transcriptional boundary, showing slight variations depending on both the transcriptional status and the ontogenetic context
 
Overall design 4C-seq analysis of Hoxd4, Hoxd13, Evx2, CS38, Island-4, Island-2, Cs65, LacZ 3D interactions in proximal and distal limbs from E12.5 wt or serial HoxD-deleted alleles
 
Contributor(s) Rodriguez-Carballo E, Lopez-Delisle L, Beccari L, Duboule D
Citation(s) 29273679, 31299961
Submission date Jul 20, 2017
Last update date Jul 25, 2021
Contact name Eddie Rodríguez-Carballo
E-mail(s) edgardo.rodriguez@unige.ch
Organization name Université de Genève
Department Department of Genetics and Evolution
Street address 4, Boulevard d'Yvoy
City Geneva
ZIP/Postal code 1205
Country Switzerland
 
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (72)
GSM2713631 DFL_E12_Wt_Island2
GSM2713632 PFL_E12_Wt_Island2
GSM2713633 DFL_E12_attp-rel5_Island2
This SubSeries is part of SuperSeries:
GSE101717 A TAD boundary at the HoxD locus segregates opposing limb regulatory landscapes and their target genes
Relations
BioProject PRJNA395247
SRA SRP113252

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
GSE101713_RAW.tar 212.2 Mb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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