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| Status |
Public on Apr 15, 2021 |
| Title |
Occupancies of tissue-specific cis-regulatory modules by Spemann-Mangold organizer-specific transcription factors for embryonic head specification |
| Organism |
Xenopus tropicalis |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Spemann-Mangold organizer-specific transcription factors (TFs), Otx2, Lim1/Lhx1, and Gsc, are essential for embryonic head specification. However, the molecular mechanisms by which those TFs interact with the genome to direct head formation are largely unknown. Here we employed ChIP-seq and RNA-seq approaches in Xenopus tropicalis gastrulae and found that occupancy of the corepressor, TLE/Groucho, is a better indicator of tissue-specific cis-regulatory modules (CRMs) than the coactivator p300, during early embryonic stages. On the basis of TLE binding and comprehensive CRM profiling, we defined two distinct types of Otx2- and TLE-occupied CRMs. Using these devices, Otx2 and Lim1/Lhx1 (activator) or Goosecoid (repressor) are able to upregulate or downregulate a large battery of target genes in the head organizer. An underlying principle is that Otx marks target genes for head specification to be regulated positively or negatively by partner TFs through specific types of CRMs.
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| Overall design |
ChIP-seq analyses using Xenopus tropicalis embryos.
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| Contributor(s) |
Yasuoka Y, Suzuki Y, Takahashi S, Sudou N, Haramoto Y, Cho KW, Asashima M, Sugano S, Taira M |
| Citation(s) |
25005894 |
| BioProject |
PRJDB2596 |
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| Submission date |
Apr 14, 2021 |
| Last update date |
Apr 20, 2021 |
| Contact name |
Aaron Zorn |
| E-mail(s) |
ZornLab1@gmail.com, Aaron.Zorn@cchmc.org
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| Organization name |
Cincinnati Children's Hospital and Medical Center
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| Department |
Developmental Biology
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| Lab |
Zorn Lab
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| Street address |
240 Albert Sabin Way, Bld S
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| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
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| Platforms (1) |
| GPL24898 |
Illumina Genome Analyzer IIx (Xenopus tropicalis) |
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| Samples (11)
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| Supplementary file |
Size |
Download |
File type/resource |
| GSE172076_RAW.tar |
2.7 Gb |
(http)(custom) |
TAR (of BROADPEAK, BW, NARROWPEAK) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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