|
| Status |
Public on Jul 05, 2021 |
| Title |
Induction of a chromatin boundary in vivo upon insertion of a TAD border (ChIP-Seq) |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Mammalian genomes are partitioned into sub-megabase to megabase-sized units of preferential interactions called topologically associating domains or TADs, which are likely important for the proper implementation of gene regulatory processes. These domains provide structural scaffolds for distant cis regulatory elements to interact with their target genes within the three-dimensional nuclear space and architectural proteins such as CTCF as well as the cohesin complex participate in the formation of the boundaries between them. However, the importance of the genomic context in providing a given DNA sequence the capacity to act as a boundary element remains to be fully investigated. To address this question, we randomly relocated a topological boundary functionally associated with the mouse HoxD gene cluster and show that it can indeed act similarly outside its initial genomic context. In particular, the relocated DNA segment recruited the required architectural proteins and induced a significant depletion of contacts between genomic regions located across the integration site. The host chromatin landscape was re-organized, with the splitting of the TAD wherein the boundary had integrated. These results provide evidence that topological boundaries can function independently of their site of origin, under physiological conditions during mouse development.
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| |
|
| Overall design |
Analysis of CTCF and RAD21 binding by ChIP in developing mouse limbs upon ectopic integration of region CS38-40 (TgN(38-40))
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| |
|
| Contributor(s) |
Willemin A, RodrÃguez-Carballo E, Lopez-Delisle L, Duboule D |
| Citation(s) |
34292939 |
| |
| Submission date |
Feb 10, 2021 |
| Last update date |
Jul 29, 2021 |
| Contact name |
Lucille Lopez-Delisle |
| E-mail(s) |
lucille.delisle@epfl.ch
|
| Organization name |
EPFL
|
| Street address |
Station 19
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platforms (1) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
|
| Samples (4)
|
|
| This SubSeries is part of SuperSeries: |
| GSE166584 |
Induction of a chromatin boundary in vivo upon insertion of a TAD border |
|
| Relations |
| Reanalysis of |
GSM2713714 |
| Reanalysis of |
GSM2713703 |
| Reanalysis of |
GSM2713709 |
| Reanalysis of |
GSM2191220 |
| Reanalysis of |
GSM2192207 |
| BioProject |
PRJNA701296 |
| SRA |
SRP305735 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE166574_E12_Limbs_TgN3840_input_1kb_meanRatio.bedgraph.gz |
31.4 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE166574_E12_Limbs_TgN3840_input_1kb_ratio.bedgraph.gz |
48.1 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE166574_E12_Limbs_TgN3840_input_2kb_meanRatio.bedgraph.gz |
16.4 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE166574_E12_Limbs_TgN3840_input_2kb_ratio.bedgraph.gz |
24.8 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE166574_GSM2191220_E12_Liver_H3K27ac_on_mm10.bedgraph.gz |
340.3 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE166574_GSM2192207_E12_Limb_H3K27ac_on_mm10.bedgraph.gz |
309.9 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE166574_GSM2713703_E12_DFL_Wt_H3K27ac_on_mm10.bedgraph.gz |
1.2 Gb |
(ftp)(http) |
BEDGRAPH |
| GSE166574_GSM2713709_E12_Limbs_Wt_CTCF_on_mm10.bedgraph.gz |
144.0 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE166574_GSM2713714_E12_Limbs_Wt_RAD21_on_mm10.bed.gz |
476.1 Kb |
(ftp)(http) |
BED |
| GSE166574_GSM2713714_E12_Limbs_Wt_RAD21_on_mm10.bedgraph.gz |
1.9 Gb |
(ftp)(http) |
BEDGRAPH |
| GSE166574_RAW.tar |
1.5 Gb |
(http)(custom) |
TAR (of BED, BEDGRAPH) |
| GSE166574_mm10_TgN3840.fa.gz |
814.1 Mb |
(ftp)(http) |
FA |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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