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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 20, 2022 |
| Title |
Developmental and evolutionary comparative analysis of a HoxD regulatory landscape in mammals and birds [ChIP-seq] |
| Organisms |
Gallus gallus; Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Modifications in gene regulation during development are considered to be a driving force in the evolution of organisms. Part of these changes involve rapidly evolving cis-regulatory elements (CREs), which interact with their target genes through higher-order 3D chromatin structures. How such 3D architectures and variations in CREs contribute to transcriptional evolvability nevertheless remains elusive. During vertebrate evolution, Hox genes were redeployed in different organs in a class-specific manner, while maintaining the same basic function in organizing the primary body axis. Since a large part of the relevant enhancers are located in a conserved regulatory landscape, this gene cluster represents an interesting paradigm to study the emergence of regulatory innovations. In this work, we analyzed Hoxd gene regulation in both murine vibrissae and chicken feather primordia, two mammalian- and avian-specific skin appendages which express different subsets of Hoxd genes, and compared their regulatory modalities with the regulations at work during the elongation of the posterior trunk, a mechanism highly conserved in amniotes. We show that in the former two structures, distinct subsets of Hoxd genes are contacted by different lineage-specific enhancers, likely as a result of using an ancestral chromatin topology as an evolutionary playground, whereas the regulations implemented in the mouse and chicken embryonic trunk partially rely on conserved CREs. Nevertheless, a high proportion of these non-coding sequences active in the trunk appear to have functionally diverged between the two species, suggesting that transcriptional robustness is maintained despite a considerable divergence in CREs’ sequence, an observation supported by a genome-wide comparative approach.
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| Overall design |
ChIP-seq analysis of CTCF in mouse and chicken embryonic posterior trunks. ChIP-seq analysis of H3K27ac in mouse and chicken posterior trunk, skin and brain samples.
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| Contributor(s) |
Hintermann A, Guerreiro I, Bolt CC, Lopez-Delisle L, Gitto S, Duboule D, Beccari L |
| Citation(s) |
35770682 |
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| Submission date |
Jan 25, 2022 |
| Last update date |
Dec 15, 2023 |
| Contact name |
Aurelie Hintermann |
| E-mail(s) |
aur.hin@gmail.com
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| Organization name |
University of Geneva
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| Department |
Genetics and Evolution
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| Street address |
30 quai Ernest-Ansermet
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| City |
Geneva |
| ZIP/Postal code |
1205 |
| Country |
Switzerland |
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| Platforms (3) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL19005 |
Illumina HiSeq 2500 (Gallus gallus) |
| GPL23499 |
Illumina HiSeq 4000 (Gallus gallus) |
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| Samples (15)
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| This SubSeries is part of SuperSeries: |
| GSE195592 |
Developmental and evolutionary comparative analysis of a HoxD regulatory landscape in mammals and birds |
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| Relations |
| BioProject |
PRJNA800459 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE194418_ChIP_H3K27ac_E85_PT_rep1rep2.bigwig |
399.6 Mb |
(ftp)(http) |
BIGWIG |
| GSE194418_ChIP_H3K27ac_E85_PT_rep1rep2.narrowPeak.gz |
1.4 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE194418_ChIP_H3K27ac_E85_PT_rep1rep2_OL_ATAC_E95_PT.narrowPeak.gz |
1.1 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE194418_ChIP_H3K27ac_E85_PT_rep1rep2_OL_ATAC_E95_PT_OL_CNEs.bed.gz |
76 b |
(ftp)(http) |
BED |
| GSE194418_ChIP_H3K27ac_E85_PT_rep1rep2_overlapCNEs.narrowPeak.gz |
232.1 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE194418_ChIP_H3K27ac_HH18_PT_rep1rep2.bigwig |
216.2 Mb |
(ftp)(http) |
BIGWIG |
| GSE194418_ChIP_H3K27ac_HH18_PT_rep1rep2.narrowPeak.gz |
1.1 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE194418_ChIP_H3K27ac_HH18_PT_rep1rep2_OL_ATAC_HH19_PT.narrowPeak.gz |
1.0 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE194418_ChIP_H3K27ac_HH18_PT_rep1rep2_OL_ATAC_HH19_PT_OL_CNEs.bed.gz |
78 b |
(ftp)(http) |
BED |
| GSE194418_ChIP_H3K27ac_HH18_PT_rep1rep2_overlapCNEs.narrowPeak.gz |
282.7 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE194418_ChIP_H3K27ac_HH35_DS_rep1rep2.bigwig |
223.0 Mb |
(ftp)(http) |
BIGWIG |
| GSE194418_ChIP_H3K27ac_HH35_DS_rep1rep2.narrowPeak.gz |
271.6 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE194418_ChIP_H3K27ac_HH35_DS_rep1rep2_OL_ATAC_HH35_DS.narrowPeak.gz |
242.9 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE194418_ChIP_H3K27ac_HH35_DS_rep1rep2_OL_ATAC_HH35_DS_OL_CNEs.bed.gz |
78 b |
(ftp)(http) |
BED |
| GSE194418_ChIP_H3K27ac_HH35_DS_rep1rep2_overlapCNEs.narrowPeak.gz |
46.8 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE194418_RAW.tar |
4.5 Gb |
(http)(custom) |
TAR (of BED, BIGWIG, NARROWPEAK) |
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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