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Series GSE94115 Query DataSets for GSE94115
Status Public on Jul 01, 2017
Title The Drosophila Dosage Compensation Complex activates target genes via chromosome looping within the active compartment
Organism Drosophila melanogaster
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary X chromosome dosage compensation in Drosophila requires chromosome-wide coordination of gene activation. The male-specific-lethal dosage compensation complex (DCC) identifies X chromosomal High Affinity Sites (HAS) from which it reaches out to boost transcription. A recently discovered sub-class of HAS, PionX sites, represent first contacts on the X. We explored the chromosomal interactions of representative PionX sites by high-resolution 4C methodology and determined the overall chromosome conformation by Hi-C in sex-sorted embryos. X chromosomes from male and female cells display similar nuclear architecture, concordant with clustered, constitutively active genes. PionX sites, like HAS, are evenly distributed in the active compartment and engage in short- and long-range interactions beyond compartment boundaries. De novo induction of DCC in female cells allowed monitoring the reach of activation surrounding PionX sites. Remarkably, DCC not only activates genes in linear proximity, but also at megabase distance if close in space, suggesting that dosage compensation profits from chromosome folding.
 
Overall design Hi-C: female and male embryos (2 biological replicates).
4C-seq: S2 (male) cells GFP or MSL2 RNAi; Kc (female) cells GFP or SXL RNAi (2 biological replicates) at various viewpoints.
ChIP-seq (Covaris): S2 cells: Input, H4K16ac (replicate: GSM929157) or MSL2 (4 biological replicates); Kc cells: Input and H4K16ac (2 biological replicates). ChIP-seq (MNase): S2 and Kc cells: Input and H3K36me3 (2 biological replicates).
RNA-seq: S2 cells: GFP RNAi (2 biological replicates); Kc cells: GFP, SXL #1 (DRSC21490), SXL#2 (DRSC28896) RNAi after 3, 6 and 9 days.
 
Contributor(s) Schauer T, Ghavi-Helm Y, Sexton T, Albig C, Regnard C, Cavalli G, Furlong EE, Becker PB
Citation(s) 28794204, 31767855
Submission date Jan 26, 2017
Last update date Dec 04, 2019
Contact name Tamas Schauer
E-mail(s) tamas.schauer@helmholtz-munich.de
Organization name Helmholtz Zentrum München
Department Institute of Epigenetics and Stem Cells
Street address Feodor-Lynen-Straße 21
City Munich
ZIP/Postal code 81377
Country Germany
 
Platforms (3)
GPL13304 Illumina HiSeq 2000 (Drosophila melanogaster)
GPL19132 Illumina NextSeq 500 (Drosophila melanogaster)
GPL19951 Illumina HiSeq 1500 (Drosophila melanogaster)
Samples (116)
GSM2469422 Hi-C female 1 [Sample 1]
GSM2469423 Hi-C female 2 [Sample 2]
GSM2469424 Hi-C male 1 [Sample 3]
Relations
BioProject PRJNA368961
SRA SRP097891

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Supplementary file Size Download File type/resource
GSE94115_RAW.tar 929.2 Mb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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