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| Status |
Public on Jan 23, 2021 |
| Title |
DBX2 REGULATION IN LIMBS SUGGESTS INTER-TAD SHARING OF ENHANCERS [HiC reanalysis] |
| Sample organisms |
Gallus gallus; Mus musculus |
| Experiment type |
Other
Third-party reanalysis
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| Summary |
During tetrapod limb development, the HOXA13 and HOXD13 transcription factors are critical for the emergence and organization of the autopods, the most distal aspect where digits will develop. Since previous work had suggested that the Dbx2 gene is a target of these factors, we set up to analyze in detail this potential regulatory interaction. We used a chromatin conformation capture approach (4Cseq) to characterize the regulatory domain and interactions of the transcription factor Dbx2 and of its neighboring genes Nell2 and Ano6 in distal and/ or proximal forelimbs of E12 mouse embryos. In particular, we analyzed their interaction with distal limb specific regulatory elements (DLE1 and DLE2) by the analysis of H2K27ac coverages (Beccari et al 2016) and Hoxa13/Hoxd13 binding (Sheth R et al 2016). We report that Dbx2, Nell2 and Ano6 are expressed in distal limb buds and are controlled by the same enhancers located close to Dbx2. As the Nell2 and Ano6 genes are localized into two different topologically associating domains (TADs) flanking the Dbx2 locus, we conclude that these enhancers can overcome TAD boundaries in either direction, to co-regulate a set of genes located in distinct chromatin domains.
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| Overall design |
HiC reanalysis of GSM2713716 from Rodriguez-Carballo et al. 2017, GSM2533818 to GSM2533821 and GSM2533839 to GSM2533842 from Bonev et al. 2017 and GSE115562 from Yakushiji-Kaminatsui et al.
Data Processing:
For capture Hi-C on chicken, data were processed independently using HiCUP v0.8.0 (https://doi.org/10.1126/science.1181369) on galGal6. Valid pairs were obtained using a custom python script.
For downstream analysis FL and HL valid pair files were concatenated.
For data from Bonev et al. 2017, valid pairs were downloaded from GSEXXXXX.
For all, the valid pairs of all studies were loaded in cool file using cooler version 0.8.10 (https://doi.org/10.1093/bioinformatics/btz540) using resolution of 5Kb, 20Kb or 40Kb. Matrices were balanced using cooler balance –cis-only. The TAD-separation score and the domains were obtained using hicFindTADs version 3.5.2 ( https://doi.org/10.1093/nar/gkaa220, https://doi.org/10.1093/nar/gky504, https://doi.org/10.1038/s41467-017-02525-w) with --minBoundaryDistance 100000 and either default parameters for the choice of window size or a fixed window size of 120Kb.
all scripts are available at at https://github.com/lldelisle/scriptsForBeccariEtAl2021
Genome build: mm10, galGal6
Files: *validPairs*: valid pairs in juicebox format (<readname> <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2><frag2> <mapq1> <mapq2> with str = strand (0 for forward, anything else for reverse), pos = middle of the fragment.) *.cool: matrices in cool format balanced using cooler *domains.bed.gz: TAD coordinates (default were obtained with default parameters, 120kb were obtained with fixed window size of 120kb)
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| Contributor(s) |
Lopez-Delisle L, Beccari L, Duboule D |
| Citation(s) |
33497014 |
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| Submission date |
Nov 12, 2020 |
| Last update date |
Feb 01, 2021 |
| Contact name |
Lucille Lopez-Delisle |
| E-mail(s) |
lucille.delisle@epfl.ch
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| Organization name |
EPFL
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| Street address |
Station 19
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| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
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| This SubSeries is part of SuperSeries: |
| GSE161386 |
DBX2 REGULATION IN LIMBS SUGGESTS INTER-TAD SHARING OF ENHANCERS |
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| Relations |
| Reanalysis of |
GSM2533818 |
| Reanalysis of |
GSM2533819 |
| Reanalysis of |
GSM2533820 |
| Reanalysis of |
GSM2533821 |
| Reanalysis of |
GSM2533839 |
| Reanalysis of |
GSM2533840 |
| Reanalysis of |
GSM2533841 |
| Reanalysis of |
GSM2533842 |
| Reanalysis of |
GSM2713716 |
| Reanalysis of |
GSM3182470 |
| Reanalysis of |
GSM3182471 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE161378_E12_DL_40kb.120kb_domains.bed.gz |
57.1 Kb |
(ftp)(http) |
BED |
| GSE161378_E12_DL_40kb.cool.gz |
39.6 Mb |
(ftp)(http) |
COOL |
| GSE161378_E12_DL_40kb.default_domains.bed.gz |
67.9 Kb |
(ftp)(http) |
BED |
| GSE161378_E14_Cortex_chr15_5kb.120kb_domains.bed.gz |
5.7 Kb |
(ftp)(http) |
BED |
| GSE161378_E14_Cortex_chr15_5kb.cool.gz |
36.5 Mb |
(ftp)(http) |
COOL |
| GSE161378_E14_Cortex_chr15_5kb.default_domains.bed.gz |
5.7 Kb |
(ftp)(http) |
BED |
| GSE161378_ES_chr15_5kb.120kb_domains.bed.gz |
6.4 Kb |
(ftp)(http) |
BED |
| GSE161378_ES_chr15_5kb.cool.gz |
36.5 Mb |
(ftp)(http) |
COOL |
| GSE161378_ES_chr15_5kb.default_domains.bed.gz |
6.4 Kb |
(ftp)(http) |
BED |
| GSE161378_HH20_FL_WT_CHi-C.validPairs.csort.txt.gz |
649.6 Mb |
(ftp)(http) |
TXT |
| GSE161378_HH20_HL_FL_20kb.120kb_domains.bed.gz |
54.9 Kb |
(ftp)(http) |
BED |
| GSE161378_HH20_HL_FL_20kb.cool.gz |
54.6 Mb |
(ftp)(http) |
COOL |
| GSE161378_HH20_HL_FL_20kb.default_domains.bed.gz |
55.0 Kb |
(ftp)(http) |
BED |
| GSE161378_HH20_HL_WT_CHi-C.validPairs.csort.txt.gz |
722.3 Mb |
(ftp)(http) |
TXT |
| GSE161378_README.txt |
30.5 Kb |
(ftp)(http) |
TXT |
| Processed data are available on Series record |
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