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Series GSE138507 Query DataSets for GSE138507
Status Public on Apr 25, 2020
Title A complex regulatory landscape involved in the development of external genitals [4C-seq]
Organism Mus musculus
Experiment type Other
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.
 
Overall design 4C-seq analysis of 3D chromatin interactions in different wild type and mutant mouse embryonic tissues
 
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)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (34)
GSM4110040 CR_E10_5_WT_Hoxd13VP
GSM4110041 FB_E12_5_WT_GT2VP
GSM4110042 FB_E12_5_WT_Hoxd13VP
This SubSeries is part of SuperSeries:
GSE138514 A complex regulatory landscape involved in the development of external genitals
Relations
BioProject PRJNA576226
SRA SRP224625

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
GSE138507_RAW.tar 50.2 Mb (http)(custom) TAR (of BEDGRAPH)
GSE138507_average_GT_E13_5_InvV_Hoxd13VP.bedGraph.gz 2.7 Mb (ftp)(http) BEDGRAPH
GSE138507_average_GT_E13_5_InvV_islandVVP.bedGraph.gz 1.9 Mb (ftp)(http) BEDGRAPH
GSE138507_average_GT_E13_5_InvV_island_IVVP.bedGraph.gz 1.4 Mb (ftp)(http) BEDGRAPH
GSE138507_average_GT_E13_5_WT_Hoxd13VP.bedGraph.gz 4.1 Mb (ftp)(http) BEDGRAPH
GSE138507_average_GT_E13_5_WT_island_IVVP.bedGraph.gz 3.2 Mb (ftp)(http) BEDGRAPH
GSE138507_average_GT_E13_5_delGT2_Hoxd13VP.bedGraph.gz 3.1 Mb (ftp)(http) BEDGRAPH
GSE138507_average_GT_E13_5_delProx_Hoxd13VP.bedGraph.gz 3.6 Mb (ftp)(http) BEDGRAPH
GSE138507_average_GT_E13_5_delV_Hoxd13VP.bedGraph.gz 3.8 Mb (ftp)(http) BEDGRAPH
GSE138507_average_GT_E13_5_delV_island_IVVP.bedGraph.gz 2.4 Mb (ftp)(http) BEDGRAPH
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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