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| Status |
Public on Jan 28, 2019 |
| Title |
The zinc-finger protein CLAMP promotes gypsy chromatin insulator function in Drosophila: differential ChIP-seq of CP190 and CLAMP under CP190 knockdown |
| Organism |
Drosophila melanogaster |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Chromatin insulators are DNA-protein complexes that establish higher order independent DNA domains to influence transcriptional regulation. Insulators are defined by two different functions: they can block communication between an enhancer and a promoter and also act as a barrier between heterochromatin and euchromatin. In Drosophila, the gypsy-insulator complex contains three core components: Su(Hw), CP190 and Mod(mdg4)67.2. Here we identify a novel role for Chromatin-linked adaptor for MSL proteins (CLAMP) in promoting gypsy chromatin insulator function. When Clamp is depleted by RNAi, gypsy-dependent enhancer blocking activity decreases and barrier activity is reduced in all tissues. Furthermore, Clamp RNAi knockdowns and mutation result in disorganized insulator complex localization in the nucleus. Co-immunoprecipitation experiments showed that CLAMP physically associates with core gypsy-insulator proteins. Co-localization of CLAMP with gypsy components on polytene chromosomes and ChIP-seq analysis demonstrates co-localization of CLAMP with a subset of insulator sites across the genome. Thus, our findings suggest a ubiquitous, genome-wide role for CLAMP in promoting gypsy-dependent chromatin insulator activity.
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| Overall design |
ChIP-seq of CP190 in Drosophila melanogaster Kc167 cells in mock treatment and CLAMP knockdown. Two replicates per condition, with paired inputs.
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| Contributor(s) |
Bag I, Palmer CD, Lei EP |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Aug 17, 2018 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Cameron Palmer |
| E-mail(s) |
palmercd@nih.gov
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| Organization name |
National Institutes of Health
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| Department |
National Institute of Diabetes and Digestive and Kidney Diseases
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| Lab |
Laboratory of Cellular and Developmental Biology
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| Street address |
50 South Drive
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platforms (1) |
| GPL17275 |
Illumina HiSeq 2500 (Drosophila melanogaster) |
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| Samples (12)
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| GSM3336807 |
Input for dsCP190 treatment, replicate 2 |
| GSM3336808 |
CLAMP IP, mock treatment, replicate 1 |
| GSM3336809 |
CP190 IP, mock treatment, replicate 1 |
| GSM3336810 |
CLAMP IP, mock treatment, replicate 2 |
| GSM3336811 |
CP190 IP, mock treatment, replicate 2 |
| GSM3336812 |
CLAMP IP, dsCP190 treatment, replicate 1 |
| GSM3336813 |
CP190 IP, dsCP190 treatment, replicate 1 |
| GSM3336814 |
CLAMP IP, dsCP190 treatment, replicate 2 |
| GSM3336815 |
CP190 IP, dsCP190 treatment, replicate 2 |
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| This SubSeries is part of SuperSeries: |
| GSE118700 |
The zinc-finger protein CLAMP promotes gypsy chromatin insulator function in Drosophila |
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| Relations |
| BioProject |
PRJNA486507 |
| SRA |
SRP158261 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE118699_RAW.tar |
264.6 Mb |
(http)(custom) |
TAR (of BIGWIG, NARROWPEAK) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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