NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE185775 Query DataSets for GSE185775
Status Public on Sep 29, 2022
Title Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes
Organisms Gallus gallus; Mus musculus; Monodelphis domestica
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Other
Summary Regulatory landscapes drive complex developmental gene expression but it remains unclear how their integrity is maintained when incorporating novel genes and functions during evolution. Here, we investigated how a placental mammal-specific gene, Zfp42, emerged in an ancient vertebrate topologically-associated domain (TAD) without adopting or disrupting the conserved expression of its gene, Fat1. In ESCs, physical TAD-partitioning separates Zfp42 and Fat1 with distinct local enhancers that drive their independent expression. This separation is driven by chromatin activity and not CTCF/cohesin. In contrast, in embryonic limbs, inactive Zfp42 shares Fat1’s intact TAD without responding to active Fat1 enhancers. However, neither Fat1 enhancer-incompatibility nor nuclear envelope-attachment account for Zfp42’s unresponsiveness. Rather, Zfp42’s promoter is rendered inert to enhancers by context-dependent DNA methylation. Thus, diverse mechanisms enabled the integration of independent Zfp42 regulation in the Fat1 locus. Critically, such regulatory complexity appears common in evolution as, genome-wide, most TADs contain multiple independently-expressed genes.
 
Overall design Refer to individual Series
Web link https://doi.org/10.1016/j.cell.2022.09.006
 
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Oct 12, 2021
Last update date Oct 02, 2022
Contact name Michael I Robson
E-mail(s) robson@molgen.mpg.de
Organization name Max Planck Institute for Molecular Genetics
Street address Max Planck Institut für molekulare Genet, Ihnestrasse 63-73
City Berlin
ZIP/Postal code 14195
Country Germany
 
Platforms (5)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (88)
GSM5623336 WGBS__limb_E115_wt_mouse_Rep-1
GSM5623337 WGBS__limb_E115_wt_mouse_Rep-2
GSM5623338 WGBS__limb_E115_deltaDNMT3B_mouse_Rep-1
This SuperSeries is composed of the following SubSeries:
GSE185765 Promoter repression and 3D-restructuring resolves divergent developmental gene expression in TADs [WGBS]
GSE185766 Promoter repression and 3D-restructuring resolves divergent developmental gene expression in TADs [RNA-Seq]
GSE185768 Promoter repression and 3D-restructuring resolves divergent developmental gene expression in TADs [Hi-C]
Relations
BioProject PRJNA770724

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
GSE185775_RAW.tar 13.1 Gb (http)(custom) TAR (of BW, HIC)
SRA Run SelectorHelp
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap