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| 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
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| 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.
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| 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 |
| |
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| Platforms (1) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE101717 |
A TAD boundary at the HoxD locus segregates opposing limb regulatory landscapes and their target genes |
|
| Relations |
| 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 |
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