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| Status |
Public on Apr 18, 2014 |
| Title |
The RNA-binding protein Rumpelstiltskin antagonizes gypsy chromatin insulator function in a tissue-specific manner |
| Organism |
Drosophila melanogaster |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Chromatin insulators are DNA-protein complexes situated throughout the genome that contribute to higher order organization and demarcation into distinct transcriptional domains. Mounting evidence in different species implicates RNA and RNA-binding proteins as regulators of chromatin insulator activities. Here we identify the Drosophila hnRNP M homolog Rumpelstiltskin (Rump) as an antagonist of gypsy chromatin insulator enhancer-blocking and barrier activities. Despite ubiquitous expression of Rump, improvement of barrier activity is detected only in tissue outside of the central nervous system (CNS) when Rump levels are reduced. Furthermore, rump mutants restore insulator complex localization in an otherwise compromised genetic background only in non-CNS tissues. Rump associates physically with core gypsy insulator proteins, and ChIP-Seq analysis of Rump demonstrates extensive colocalization with a subset of gypsy insulator sites across the genome. The genome-wide binding profile and tissue-specificity of Rump contrast with that of Shep, a recently identified RNA-binding protein that antagonizes gypsy insulator activity exclusively in the CNS. Our findings indicate parallel roles for RNA-binding proteins in mediating tissue-specific regulation of chromatin insulator activity.
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| |
|
| Overall design |
ChIP-seq of Rump, Mod(mdg4)2.2, Shep, Su(Hw), and CP190 in Drosophila Kc167 cells
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| |
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| Contributor(s) |
Dale RK, Lei EP |
| Citation(s) |
24706949, 25063299 |
| Submission date |
Oct 21, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Ryan Dale |
| E-mail(s) |
dalerr@nih.gov
|
| Organization name |
National Institutes of Health
|
| Department |
National Institute of Child Health and Human Development
|
| Lab |
Bioinformatics and Scientific Programming Core
|
| Street address |
Rm 10D39, 10 Center Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL9061 |
Illumina Genome Analyzer II (Drosophila melanogaster) |
| GPL13304 |
Illumina HiSeq 2000 (Drosophila melanogaster) |
|
| Samples (10)
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| Relations |
| BioProject |
PRJNA223239 |
| SRA |
SRP031622 |
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