|
| Status |
Public on Apr 25, 2020 |
| Title |
A complex regulatory landscape involved in the development of external genitals [ATAC-Seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
In vertebrates, developmental genes are often controlled by large regulatory landscapes matching the dimensions of topologically associating domains (TADs). In various ontogenic contexts, the associated constitutive chromatin backbone is modified by fine-tuned specific variations in enhancer-enhancer and enhancer-promoter interaction profiles. In this work, we use a TAD flanking the HoxD gene cluster as a paradigm to address the question of how these complex regulatory architectures are formed and how they are de-constructed once their function has been achieved. We suggest that this TAD can be considered as a coherent functional unit in itself, with several regulatory sequences acting together to elicit a transcriptional response. With one notable exception, the deletion of each of these sequences in isolation did not produce any substantial modification in the global transcriptional outcome of the system, a result at odds with a conventional view of long-range enhancer function. Likewise, both the deletion and inversion of a CTCF site located in a region rich in such sequences did not affect transcription of the target gene. In the latter case, however, slight modifications were observed in interaction profiles in vivo in agreement with the loop extrusion model, despite no apparent functional consequences. We discuss these unexpected results by considering both conventional explanations and an alternative possibility whereby a rather unspecific accumulation of particular factors within the TAD backbone may have a global impact upon transcription.
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| |
|
| Overall design |
ATAC-seq analysis of the cloaca region of wildtype mouse embryos or the genital tubercle of wildtype or mutant mouse embryos
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| |
|
| Contributor(s) |
Lhopitallier AR, Duboule D |
| Citation(s) |
32301703 |
| |
| Submission date |
Oct 07, 2019 |
| Last update date |
May 07, 2020 |
| Contact name |
Ana Rita Amandio Lhopitallier |
| E-mail(s) |
rita.lhopitallier@epfl.ch
|
| Organization name |
EPFL
|
| Department |
SV-ISREC-EPFL
|
| Lab |
Laboratory of Developmental Genomics
|
| Street address |
SV2842, Station 19
|
| City |
Lausanne |
| ZIP/Postal code |
CH-1015 |
| Country |
Switzerland |
| |
|
| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
|
| Samples (15)
|
|
| This SubSeries is part of SuperSeries: |
| GSE138514 |
A complex regulatory landscape involved in the development of external genitals |
|
| Relations |
| BioProject |
PRJNA576225 |
| SRA |
SRP224626 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE138513_CR_E10_5_merge_WT_ATAC_seq.bedgraph.gz |
927.6 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE138513_GT_E13_5_merge_WT_ATAC_seq.bedgraph.gz |
2.5 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE138513_GT_E13_5_merge_delGT2_ATAC_seq.bedgraph.gz |
1.2 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE138513_GT_E13_5_merge_delProx_ATAC_seq.bedgraph.gz |
1.3 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE138513_GT_E13_5_merge_delV_ATAC_seq.bedgraph.gz |
1.4 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE138513_GT_E13_5_merge_invV_ATAC_seq.bedgraph.gz |
2.2 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE138513_GT_E17_5_merge_WT_ATAC_seq.bedgraph.gz |
1.8 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE138513_RAW.tar |
3.6 Gb |
(http)(custom) |
TAR (of BED, BEDGRAPH) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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