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Series GSE118699 Query DataSets for GSE118699
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
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.
 
Overall design ChIP-seq of CP190 in Drosophila melanogaster Kc167 cells in mock treatment and CLAMP knockdown. Two replicates per condition, with paired inputs.
 
Contributor(s) Bag I, Palmer CD, Lei EP
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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
Organization name National Institutes of Health
Department National Institute of Diabetes and Digestive and Kidney Diseases
Lab Laboratory of Cellular and Developmental Biology
Street address 50 South Drive
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platforms (1)
GPL17275 Illumina HiSeq 2500 (Drosophila melanogaster)
Samples (12)
GSM3336804 Input for mock treatment, replicate 1
GSM3336805 Input for mock treatment, replicate 2
GSM3336806 Input for dsCP190 treatment, replicate 1
This SubSeries is part of SuperSeries:
GSE118700 The zinc-finger protein CLAMP promotes gypsy chromatin insulator function in Drosophila
Relations
BioProject PRJNA486507
SRA SRP158261

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Supplementary file Size Download File type/resource
GSE118699_RAW.tar 264.6 Mb (http)(custom) TAR (of BIGWIG, NARROWPEAK)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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