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| Status |
Public on Jan 23, 2021 |
| Title |
DBX2 REGULATION IN LIMBS SUGGESTS INTER-TAD SHARING OF ENHANCERS [ChIP-Seq reanalysis] |
| Sample organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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 |
ChIP reanalysis of GSM2151013,GSM2151014 from Sheth et al. 2016 and GSE77900 from Becarri et al. 2016
Data processing
Adapter sequence and bad quality bases were removed with cutadapt (http://dx.doi.org/10.14806/ej.17.1.200) version 1.16 with options -a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -q 30 -m 15 (-A beeing used only in PE datasets).
Reads were mapped with bowtie 2.3.5 (https://doi.org/10.1038/nmeth.1923) with default parameters on mm10. Alignment with a mapping quality below 30 was discarded with samtools view version 1.9 (https://doi.org/10.1093/bioinformatics/btp352, https://doi.org/10.1093/bioinformatics/btr509).
For Hoxa13 and Hoxd13, coverage and peak calling were computed by macs2 version 2.1.1.20160309 with options --call-summits -f BAMPE -B. Coverage was then normalized by the number of million fragments used in macs2 coverage. For histone marks, coverage and peak calling were computed by macs2 with options -f BAM --nomodel --extsize 200 --broad using the BAM of input in -c. The coverage was then normalized by the number of million tags used in macs2 coverage.
For DFL_E12_H3K27ac, the two replicates were averaged.
all scripts are available at at https://github.com/lldelisle/scriptsForBeccariEtAl2021
Genome build: mm10
Files: bigwig: coverage normalized to the million tags/fragments used, narrowPeak/broadPeak: the peaks as called by macs2
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| Contributor(s) |
Lopez-Delisle L, Beccari L, Duboule D |
| Citation(s) |
33497014 |
| 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 |
GSM2061120 |
| Reanalysis of |
GSM2061121 |
| Reanalysis of |
GSM2061122 |
| Reanalysis of |
GSM2061123 |
| Reanalysis of |
GSM2061125 |
| Reanalysis of |
GSM2061132 |
| Reanalysis of |
GSM2061133 |
| Reanalysis of |
GSM2151013 |
| Reanalysis of |
GSM2151014 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE161377_DFL_E11_Hoxa13_macs_default_q30_norm.bw |
447.4 Mb |
(ftp)(http) |
BW |
| GSE161377_DFL_E11_Hoxa13_macs_default_q30_peaks.narrowPeak.gz |
2.8 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE161377_DFL_E11_Hoxd13_macs_default_q30_norm.bw |
669.6 Mb |
(ftp)(http) |
BW |
| GSE161377_DFL_E11_Hoxd13_macs_default_q30_peaks.narrowPeak.gz |
2.4 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE161377_DFL_E12_WT_H3K27ac_neq2.bw |
558.1 Mb |
(ftp)(http) |
BW |
| GSE161377_DFL_E12_WT_H3K27ac_rep1_macs_200_q30_norm.bw |
251.6 Mb |
(ftp)(http) |
BW |
| GSE161377_DFL_E12_WT_H3K27ac_rep1_macs_200_q30_with_input_broad_peaks.broadPeak.gz |
856.4 Kb |
(ftp)(http) |
BROADPEAK |
| GSE161377_DFL_E12_WT_H3K27ac_rep2_macs_200_q30_norm.bw |
268.3 Mb |
(ftp)(http) |
BW |
| GSE161377_DFL_E12_WT_H3K27ac_rep2_macs_200_q30_with_input_broad_peaks.broadPeak.gz |
786.6 Kb |
(ftp)(http) |
BROADPEAK |
| GSE161377_DFL_E12_WT_H3K27me3_rep2_macs_200_q30_norm.bw |
226.0 Mb |
(ftp)(http) |
BW |
| GSE161377_DFL_E12_WT_H3K27me3_rep2_macs_200_q30_with_input_broad_peaks.broadPeak.gz |
411.0 Kb |
(ftp)(http) |
BROADPEAK |
| GSE161377_PFL_E12_WT_H3K27ac_rep1_macs_200_q30_norm.bw |
239.1 Mb |
(ftp)(http) |
BW |
| GSE161377_PFL_E12_WT_H3K27ac_rep1_macs_200_q30_with_input_broad_peaks.broadPeak.gz |
1.8 Mb |
(ftp)(http) |
BROADPEAK |
| GSE161377_PFL_E12_WT_H3K27me3_rep1_macs_200_q30_norm.bw |
368.2 Mb |
(ftp)(http) |
BW |
| GSE161377_PFL_E12_WT_H3K27me3_rep1_macs_200_q30_with_input_broad_peaks.broadPeak.gz |
760.0 Kb |
(ftp)(http) |
BROADPEAK |
| GSE161377_README.txt |
33.4 Kb |
(ftp)(http) |
TXT |
| Processed data are available on Series record |
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