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| Status |
Public on Dec 31, 2016 |
| Title |
Genome-wide binding of posterior HOXA/D transcription factors reveals subgrouping and association with CTCF [RNA-Seq] |
| Organism |
Gallus gallus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The homeotic genes (Hox genes) encode transcription factors (HOX-TFs) that are key regulators of animal development. Single and compound deletion of Hox genes in mice revealed that they act in a partially redundant manner to pattern the vertebrate limb. Biochemical screens probing the sequence specificity of the DNA-binding domains showed that HOX-TFs recognize largely similar DNA sequences, but also emphasized the important role of co-factors in HOX DNA-binding. However, due to their high sequence homology and overlapping expression patterns, little is known about the genome-wide binding of these transcription factors Here, we set out to systematically compare the effects of the nine limb-bud expressed HOX-TFs on cell differentiation and gene regulation, and compare their genome-wide binding characteristics. We find that HOX-TFs induce distinct regulatory programs in transduced cells. Through genome-wide DNA binding profiling we find that the posterior HOX-TFs can be separated into two groups with distinct binding motifs and association with co-factors. Through this unexpected grouping, we characterize the CCCTC-binding factor (CTCF) as a novel co-factor of HOX-TFs and show that one, but not the other group of HOX-TFs binds to thousands of CTCF-occupied sites in the chicken genome.
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| Overall design |
Examination of the binding of 10 different transcription factors, a Cohesin subunit and an expression analysis (RNAseq analysis) in the chicken primary cell culture overexpression system.
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| Contributor(s) |
Jerković I, Ibrahim DM, Andrey G, Hecht J, Mundlos S |
| Citation missing |
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| |
| Submission date |
Aug 17, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel Murad Ibrahim |
| E-mail(s) |
ibrahim@molgen.mpg.de, daniel.ibrahim@bih-charite.de
|
| Phone |
030 84131516
|
| Organization name |
Berlin Institute of Health
|
| Department |
Center for Regenerative Therapies
|
| Street address |
Augustenburger Platz 1
|
| City |
Berlin |
| State/province |
Berlin |
| ZIP/Postal code |
13353 |
| Country |
Germany |
| |
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| Platforms (1) |
| GPL21476 |
Illumina HiSeq 1500 (Gallus gallus) |
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| Samples (20)
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| This SubSeries is part of SuperSeries: |
| GSE86089 |
Genome-wide binding of posterior HOXA/D transcription factors reveals subgrouping and association with CTCF |
|
| Relations |
| BioProject |
PRJNA339275 |
| SRA |
SRP082371 |
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