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Series GSE59119 Query DataSets for GSE59119
Status Public on Apr 07, 2015
Title The contribution of cohesin-SA1 to chromatin architecture and gene expression in two murine tissues
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Cohesin, which consists of SMC1, SMC3, Rad21 and either SA1 or SA2, topologically embraces the chromatin fibers to hold sister chromatids together and to stabilize chromatin loops. Increasing evidence indicates that these loops are the organizing principle of higher-order chromatin architecture, which in turn is critical for gene expression. To determine how cohesin contributes to the establishment of tissue-specific transcriptional programs, we compared genome-wide cohesin distribution, gene expression and chromatin architecture in cerebral cortex and pancreas from adult mice. More than one third of cohesin binding sites differ between the two tissues and these are enriched at the regulatory regions of tissue-specific genes. Cohesin colocalizes extensively with the CCCTC-binding factor (CTCF). Cohesin/CTCF sites at active enhancers and promoters contain, at least, cohesin-SA1 whereas either cohesin-SA1 or cohesin-SA2 are present at active promoters independently of CTCF. Analyses of chromatin contacts at the Protocadherin gene cluster and the Regenerating islet-derived (Reg) gene cluster, mostly expressed in brain and pancreas respectively, revealed remarkable differences in the architecture of these loci in the two tissues that correlate with the presence of cohesin. Moreover, we found decreased binding of cohesin and reduced transcription of the Reg genes in the pancreas of SA1 heterozygous mice. Given that Reg proteins are involved in the control of inflammation in pancreas, such reduction may contribute to the increased incidence of pancreatic cancer reported in these animals.
Overall design Examination of the relationship between gene expression, genome wide cohesin distribution and chromatin structure
Contributor(s) Cuadrado A, Losada A, Remeseiro S, Graña O, Pisano DG
Citation(s) 25735743
Submission date Jul 07, 2014
Last update date May 15, 2019
Contact name Ana Losada
Phone +34 - 917 328 000
Organization name Centro Nacional de Investigaciones Oncológicas (CNIO)
Department Molecular Oncology Programme
Lab Chromosome Dynamics Group
Street address C/ Melchor Fernández Almagro, 3.
City Madrid
State/province Madrid
ZIP/Postal code 28029
Country Spain
Platforms (2)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (51)
GSM1428903 Adult brain rep 1_RNA-seq
GSM1428904 Adult brain rep 2_RNA-seq
GSM1428905 SA1 knock out embrionary brain rep 1_RNA-seq
BioProject PRJNA254460
SRA SRP044099

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MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource 540.4 Mb (ftp)(http) ZIP 396.7 Mb (ftp)(http) ZIP
GSE59119_AC_4C_1214_HT_VP1_raw.txt.gz 1.4 Gb (ftp)(http) TXT
GSE59119_AC_4C_1214_WT_VP1_raw.txt.gz 1.5 Gb (ftp)(http) TXT 766.5 Mb (ftp)(http) ZIP 348.8 Mb (ftp)(http) ZIP
GSE59119_ChIP_bedfiles.tar.gz 2.3 Mb (ftp)(http) TAR 314.6 Mb (ftp)(http) ZIP 274.2 Mb (ftp)(http) ZIP 768.3 Mb (ftp)(http) ZIP 518.4 Mb (ftp)(http) ZIP
GSE59119_RAW.tar 8.3 Mb (http)(custom) TAR (of FPKM_TRACKING)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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