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Series GSE151553 Query DataSets for GSE151553
Status Public on Nov 04, 2020
Title Cohesin residency determines chromatin loop patterns
Organism Saccharomyces cerevisiae
Experiment type Other
Summary The organization of chromatin into higher-order structures is essential for chromosome segregation, the repair of DNA damage, and the regulation of gene expression. These structures are formed by the evolutionarily conserved SMC (structural maintenance of chromosomes) complexes. By analyzing synchronized populations of budding yeast with Micro-C, we observed that chromatin loops are formed genome-wide, and are dependent upon the SMC complex, cohesin. We correlated the loop signal with the position and intensity of cohesin binding to chromosomes in wild-type and cells depleted for the cohesin regulators Wpl1p and Pds5p. We generate a model to explain how the genomic distribution and frequency of loops are driven by cohesin residency on chromosomes. In this model a dynamic pool of cohesin with loop extrusion activity stops when encounters two regions occupied by stably bound cohesin, forming a loop. Different regions are occupied by cohesin in different cells, defining different patterns of chromatin loops.
Overall design We mapped the 3D genome organization of mitotic chromatin in budding yeast (A364 background) by using Micro-C. We performed two replicates of Micro-C experiments for wild-type, Mcd1-AID, Brn1-AID, Wpl-AID, and one replicate for Pds5-AID cells. Time-course experiments were done in two replicates at 23°C and 30°C, respectively. The Micro-C contact matrices were stored into the formats for HiGlass (.mcool) or Juicer (.hic) 3D genome browsers.
Contributor(s) Hsieh TS, Costantino L, Lamothe R, Darzacq X, Koshland D
Citation(s) 33170773
Submission date Jun 01, 2020
Last update date Nov 16, 2020
Contact name Xavier Darzacq
Phone 510-642-0884
Organization name University of California, Berkeley
Department Molecular and Cell Biology
Lab Darzacq Lab
Street address 475D Li Ka Shing Center
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
Platforms (1)
GPL21656 Illumina HiSeq 4000 (Saccharomyces cerevisiae)
Samples (25)
GSM4585126 A364_rep1
GSM4585127 A364_rep2
GSM4585128 mcd1-AID_rep1
BioProject PRJNA636358
SRA SRP265482

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Supplementary file Size Download File type/resource
GSE151553_A364_merged.hic 224.7 Mb (ftp)(http) HIC
GSE151553_A364_merged.mcool 116.9 Mb (ftp)(http) MCOOL
GSE151553_RAW.tar 7.6 Gb (http)(custom) TAR (of HIC, MCOOL)
GSE151553_brn1-AID_merged.hic 200.4 Mb (ftp)(http) HIC
GSE151553_brn1-AID_merged.mcool 103.6 Mb (ftp)(http) MCOOL
GSE151553_mcd1-AID-brn1-AID_merged.hic 250.0 Mb (ftp)(http) HIC
GSE151553_mcd1-AID_brn1-AID_merged.mcool 122.0 Mb (ftp)(http) MCOOL
GSE151553_mcd1-AID_merged.hic 271.6 Mb (ftp)(http) HIC
GSE151553_mcd1-AID_merged.mcool 134.8 Mb (ftp)(http) MCOOL
GSE151553_pds5-AID.hic 422.2 Mb (ftp)(http) HIC
GSE151553_pds5-AID.mcool 207.6 Mb (ftp)(http) MCOOL
GSE151553_wpl1-AID_merged.hic 619.8 Mb (ftp)(http) HIC
GSE151553_wpl1-AID_merged.mcool 319.5 Mb (ftp)(http) MCOOL
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Processed data are available on Series record

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