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Series GSE191207 Query DataSets for GSE191207
Status Public on Jun 15, 2022
Title Cohesin-dependent chromosome loop extrusion is limited by transcription and stalled replication forks [RNA-seq]
Organism Saccharomyces cerevisiae
Experiment type Expression profiling by high throughput sequencing
Summary Genome function depends on regulated chromosome folding, and loop extrusion by the protein complex cohesin is essential for this multilayered organization. The chromosomal positioning of cohesin is controlled by transcription, and the complex also localizes to stalled replication forks. However, the role of transcription and replication in chromosome looping remains unclear. Here, we show that reduction of chromosome-bound RNA polymerase weakens normal cohesin loop extrusion boundaries, allowing cohesin to form new long-range chromosome cis interactions. Stress response genes activated by transcription inhibition are also shown to act as new loop extrusion boundaries. Furthermore, cohesin loop extrusion during early S-phase is jointly controlled by transcription and replication units. Together, the results reveal that replication and transcription machineries are chromosome folding regulators that block the progression of loop-extruding cohesin, opening for new perspectives on cohesin’s roles in genome function and stability.
Overall design Spike-in RNA-seq of G2/M-arrested, untreated and thiolutin-treated wild type Saccharomyces cerevisiae cells.
Contributor(s) Jeppsson K, Sakata T, Nakato R, Milanova S, Shirahige K, Björkegren C
Citation(s) 35687682
Submission date Dec 18, 2021
Last update date Jun 16, 2022
Contact name Ryuichiro Nakato
Phone +81-3-5841-1471
Organization name The University of Tokyo
Department Institute for Quantitative Biosciences
Lab Laboratory of Computational Genomics
Street address 1-1-1 Yayoi
City Bunkyo-ku
State/province Tokyo
ZIP/Postal code 113-0032
Country Japan
Platforms (1)
GPL31112 NextSeq 2000 (Saccharomyces cerevisiae)
Samples (4)
GSM5741640 A_DMSO_S62
GSM5741641 A_Thiolutin_S63
GSM5741642 B_DMSO_S64
This SubSeries is part of SuperSeries:
GSE162194 Cohesin-dependent chromosome loop extrusion is limited by transcription and stalled replication forks
BioProject PRJNA790450

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Supplementary file Size Download File type/resource
GSE191207_RAW.tar 400.0 Kb (http)(custom) TAR (of RESULTS)
GSE191207_RNA-seq.S_cerevisiae.xlsx 687.8 Kb (ftp)(http) XLSX
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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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