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Series GSE14653 Query DataSets for GSE14653
Status Public on Mar 01, 2009
Title DCC binding and function (ChIP-chip: SDC-3, DPY-27, Mock)
Organism Caenorhabditis elegans
Experiment type Genome binding/occupancy profiling by genome tiling array
Summary In many species, a dosage compensation complex (DCC) is targeted to X chromosomes of one sex to equalize levels of X gene products between males (1X) and females (2X). Here we identify cis-acting regulatory elements that target the C. elegans X chromosome for repression by the DCC. The DCC binds to discrete, dispersed sites on X of two types. rex sites recruit the DCC in an autonomous, DNA sequence-dependent manner using a 12 bp consensus motif that is enriched on X. This motif is critical for DCC binding, is clustered in rex sites, and confers much of X-chromosome specificity. Motif variants enriched on X by 3.8-fold or more are highly predictive (95%) for rex sites. In contrast, dox sites lack the X-enriched variants and cannot bind the DCC when detached from X. dox sites are more prevalent than rex sites and, unlike rex sites, reside preferentially in promoters of some expressed genes. These findings fulfill predictions for a targeting model in which the DCC binds to recruitment sites on X and disperses to discrete sites lacking autonomous recruitment ability. To relate DCC binding to function, we identified dosage-compensated and non-compensated genes on X. Unexpectedly, many genes of both types have bound DCC, but many do not, suggesting the DCC acts over long distances to repress X gene expression. Remarkably, the DCC binds to autosomes, but at far fewer sites and rarely at consensus motifs. DCC disruption causes opposite effects on expression of X and autosomal genes. The DCC thus acts at a distance to impact expression throughout the genome.

Keywords: dosage compensation, condensin, X chromosome, gene expression, epigenetics, C. elegans
 
Overall design ChIP-chip experiments included: biological duplicates of SDC-3, a single DPY-27 IP, and a mock IP.
 
Contributor(s) Jans J, Gladden JM, Ralston EJ, Pickle CS, Michel AH, Pferdehirt RR, Eisen MB, Meyer BJ
Citation(s) 19270160
Submission date Jan 30, 2009
Last update date Mar 20, 2012
Contact name Barbara J. Meyer
E-mail(s) bjmeyer@berkeley.edu
Phone 510 643 5583
Organization name HHMI/UCB
Department MCB
Lab Meyer
Street address 16 Barker Hall #3204
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
 
Platforms (1)
GPL8135 NimbleGen 080319_C_elegans_ChIP_03_design_ID-7348
Samples (5)
GSM365609 N2 SDC-3 HD-IP2
GSM365610 N2 DPY-27 HD-IP2
GSM365611 N2 mock HD-IP2
This SubSeries is part of SuperSeries:
GSE14640 A condensin-like dosage compensation complex acts at a distance to control expression throughout the genome
Relations
BioProject PRJNA114419

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
GSE14653_RAW.tar 523.5 Mb (http)(custom) TAR (of GFF, PAIR)
Processed data included within Sample table
Processed data provided as supplementary file

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