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Series GSE36927 Query DataSets for GSE36927
Status Public on Mar 30, 2012
Title Topoisomerase II is required for proper dosage compensation in Drosophila
Organism Drosophila melanogaster
Experiment type Expression profiling by array
Genome binding/occupancy profiling by genome tiling array
Summary Investigate Topo II levels in dosage compensated and non-dosage compensated genes
Dosage compensation refers to the equalization of most X-linked gene products between males and females. In Drosophila, it is mediated by the MSL complex that preferentially associates with numerous sites on the X chromosome in somatic cells of males, and is responsible for an enhancement of the transcriptional rate of a substantial number of X-linked genes. Here we show that topoisomerase II (Topo II) is an integral part of the mechanistic basis of dosage compensation and we highlight a novel function for this enzyme. A widely accepted model of transcription postulates that the moving bubble generated by an RNA polymerase elongating complex induces positive DNA supercoiling in the region ahead of the complex and negative supercoiling in its wake. These transitory changes in supercoiling are resolved by the action of topoisomerases. We have investigated the role of Topo II in dosage compensation by RNAi-mediated depletion, and we have used chromatin immunoprecipitation to determine its genomic distribution and relative abundance on X-linked genes. Topo II is enriched on dosage compensated genes and this enrichment is independent from the approximate two-fold enhancement in transcription of these genes. We have demonstrated an RNA-dependent association of Topo II with MLE, the ATPase-helicase subunit of the MSL complex. Our results indicate a role for Topo II that is additional to and different from its function in restoring normal DNA superhelicity during the transcription process. We suggest that the enhanced level of Topo II alters the DNA supercoiling of compensated gene units to facilitate transcription and could provide a basis for the recent report that the MSL complex enhances transcription by increasing the rate of elongation of RNA polymerase II.
 
Overall design Investigation of dosage compensated gene expression levels in S2 and S2 Topo II RNAi knockdown cells. mRNA was isolated from S2 cells and S2 cells with RNAi knockdown of Topo II. The mRNA was then converted to cDNA and hybridized to a NimbleGen D. melanogaster gene expression array. 2 replicates each.
S2 cells were ChIP with anti-Topo II antibody
 
Contributor(s) Ramos E, Lucchesi J, Cugusi S
Citation(s) 23989663
Submission date Mar 29, 2012
Last update date Mar 20, 2024
Contact name Edward Ramos
Organization name Emory University
Department Biology
Street address 1510 Clifton Rd NE
City Atlanta
State/province GA
ZIP/Postal code 30322
Country USA
 
Platforms (2)
GPL15057 NimbleGen Drosophila melanogaster Whole Genome 2.1M tiling array [DM_5_Catalog_tiling_HX1; DesignID 6725]
GPL15387 NimbleGen Drosophila melanogaster gene expression 12X135K array
Samples (6)
GSM906433 Dmel_S2_gfp_rep1
GSM906434 Dmel_S2_gfp_rep2
GSM906435 Dmel_S2_TopoIIRNAi_rep1
Relations
BioProject PRJNA157311

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
GSE36927_RAW.tar 355.2 Mb (http)(custom) TAR (of GFF, PAIR)
Processed data included within Sample table
Processed data provided as supplementary file

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