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Series GSE101715 Query DataSets for GSE101715
Status Public on Dec 22, 2017
Title A TAD boundary at the HoxD locus segregates opposing limb regulatory landscapes and their target genes [Hi-C]
Organism Mus musculus
Experiment type Other
Third-party reanalysis
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 Hi-C datasets of E12.5 limb tissues (distal or proximal forelimbs and hindlimbs) of Wt or serial HoxD-deleted alleles -delHoxd(1-13d9)lac and delHoxd(attP-Rel5)d9lac as well as the reanalysis of the CH12 dataset from Rao et al. 2014 (GSE63525, GSM15516333 to GSM15516347 = SRR1658716 to SRR1658730) and mESC dataset from Dixon et al. 2012 (GSE35156, GSM862720 = SRR443883 to SRR443885 and GSM862721 = SRR400251 to SRR400256) on mm10.
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
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)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (6)
GSM2713716 DL_HiC_E12_Wt
GSM2713717 PL_HiC_E12_Wt
GSM2713718 DL_HiC_E12_del1-13d9lac
This SubSeries is part of SuperSeries:
GSE101717 A TAD boundary at the HoxD locus segregates opposing limb regulatory landscapes and their target genes
Reanalysis of GSM862720
Reanalysis of GSM862721
Reanalysis of GSM1551633
Reanalysis of GSM1551634
Reanalysis of GSM1551635
Reanalysis of GSM1551636
Reanalysis of GSM1551637
Reanalysis of GSM1551638
Reanalysis of GSM1551639
Reanalysis of GSM1551640
Reanalysis of GSM1551641
Reanalysis of GSM1551642
Reanalysis of GSM1551643
Reanalysis of GSM1551644
Reanalysis of GSM1551645
Reanalysis of GSM1551646
Reanalysis of GSM1551647
BioProject PRJNA395244
SRA SRP113251

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
GSE101715_GSE35156_mESC_mm10.validPair.txt.gz 4.8 Gb (ftp)(http) TXT
GSE101715_GSE35156_mESC_mm10_txt.tar.gz 382.4 Mb (ftp)(http) TAR
GSE101715_GSE63525_CH12_mm10.validPair.txt.gz 11.1 Gb (ftp)(http) TXT
GSE101715_GSE63525_CH12_mm10_txt.tar.gz 416.0 Mb (ftp)(http) TAR
GSE101715_RAW.tar 12.8 Gb (http)(custom) TAR (of MATRIX, TAR, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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