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Series GSE130545 Query DataSets for GSE130545
Status Public on Dec 01, 2019
Title The zinc finger protein CLAMP promotes long-range chromatin interactions that mediate dosage compensation of the Drosophila male X-chromosome [Hi-C seq]
Organism Drosophila melanogaster
Experiment type Other
Summary Hi-C and 4C-seq anlaysis of Drosophila S2 cells
Drosophila dosage compensation is an important model system for defining how active chromatin domains are formed. The Male-specific lethal dosage compensation complex (MSLc) increases transcript levels of genes along the length of the single male X-chromosome to equalize with that on the two female X-chromosomes. The strongest binding sites for MSLc cluster together in three-dimensional space independent of MSLc because clustering occurs in both sexes. CLAMP, a non-sex specific, ubiquitous zinc finger protein, binds synergistically with MSLc to enrich the occupancy of both factors on the male X-chromosome. Here, we demonstrate that CLAMP promotes the observed clustering of MSLc bindings sites. Genome-wide, CLAMP promotes interactions between active chromatin regions and represses interactions between inactive chromatin regions. Moreover, the X-enriched CLAMP protein promotes longer-range interactions on the active X-chromosome than autosomes. Overall, we define how long-range interactions, mediated by a locally-enriched ubiquitous transcription factor, generate a three-dimensional active chromatin domain.
 
Overall design Biological duplicated Hi-C experiments of Drosophila S2 cells after RNAi of gfp (control) or clamp.
 
Contributor(s) Jordan W, Larschan E
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Submission date May 01, 2019
Last update date Dec 03, 2019
Contact name Erica Larschan
E-mail(s) Erica_Larschan@brown.edu
Organization name Brown University
Street address 185 Meeting St.
City Providence
ZIP/Postal code 02912
Country USA
 
Platforms (1)
GPL17275 Illumina HiSeq 2500 (Drosophila melanogaster)
Samples (4)
GSM3742044 Hi-C: gfp RNAi rep1
GSM3742045 Hi-C: gfp RNAi rep2
GSM3742046 Hi-C: clamp RNAi rep1
This SubSeries is part of SuperSeries:
GSE130546 The zinc finger protein CLAMP promotes long-range chromatin interactions that mediate dosage compensation of the Drosophila male X-chromosome
Relations
BioProject PRJNA540595
SRA SRP194366

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE130545_RAW.tar 287.4 Mb (http)(custom) TAR (of HIC)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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