GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE162193 Query DataSets for GSE162193
Status Public on Jun 15, 2022
Title Cohesin-dependent chromosome loop extrusion is limited by transcription and stalled replication forks [Hi-C]
Organism Saccharomyces cerevisiae
Experiment type Other
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 Analysis of chromosome conformation by Hi-C in Saccharomyces cerevisiae cells.
Contributor(s) Jeppsson K, Sakata T, Nakato R, Milanova S, Shirahige K, Björkegren C
Citation(s) 35687682
Submission date Nov 25, 2020
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)
GPL26171 HiSeq X Ten (Saccharomyces cerevisiae)
Samples (28)
GSM4946266 WT, aux/dox [KJ1]
GSM4946267 Scc2-AID, aux/dox [KJ2]
GSM4946268 Wpl1-AID, aux/dox [KJ3]
This SubSeries is part of SuperSeries:
GSE162194 Cohesin-dependent chromosome loop extrusion is limited by transcription and stalled replication forks
BioProject PRJNA680815
SRA SRP294207

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
GSE162193_RAW.tar 344.6 Mb (http)(custom) TAR (of HIC)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap