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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 |
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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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