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Series GSE46316 Query DataSets for GSE46316
Status Public on Oct 28, 2013
Title Transcription-dependent positioning of Structural Maintenance of Chromosome complexes across the genome: RNA-Seq
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The Structural Maintenance of Chromosomes (SMC) complexes regulate the chromosome structures essential for proper genome regulation and cell viability. In mammals, the coordinated actions of the SMC complexes condensin I, condensin II and cohesin regulate dynamic chromosome structures throughout the cell cycle, but it is not clear how these complexes are positioned across the genome. We report here that condensin I, condensin II and cohesin occupy active euchromatic regions of the embryonic stem cell genome, but not heterochromatic regions. Like cohesin, we find that condensin II is deposited at active genes by the SMC loading factor Nipbl. The recruitment of Condensin II to active genes is dependent on their transcriptional activation. Subsequent transcriptional elongation by RNA polymerase II distributes condensin II across gene bodies. During mitosis, condensin I occupies the same set of active genes occupied by condensin II during interphase. Thus, SMC complexes are positioned in the genome by transcription-dependent processes, indicating that condensin-dependent condensation mechanisms are preferentially utilized in euchromatic regions.
Overall design RNA-seq in mES cells after known-down of Smc1, CapH2 or Smc2.
Contributor(s) Dowen J, Orlando DA, Young RA
Citation(s) 24286025
Submission date Apr 23, 2013
Last update date May 15, 2019
Contact name Richard A Young
Phone 617-258-5219
Organization name Whitehead Institute for Biomedical Research
Lab Young Lab
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (6)
GSM1128586 RNA_Seq_GFP
GSM1128587 RNA-Seq_Smc1
GSM1128588 RNA-Seq_CapH2_R1
BioProject PRJNA198728
SRA SRP021476

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE46316_RAW.tar 2.6 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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