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| 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
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| 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.
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| Overall design |
Analysis of chromosome conformation by Hi-C in Saccharomyces cerevisiae cells.
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| Contributor(s) |
Jeppsson K, Sakata T, Nakato R, Milanova S, Shirahige K, Björkegren C |
| Citation(s) |
35687682 |
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| Submission date |
Nov 25, 2020 |
| Last update date |
Jun 16, 2022 |
| Contact name |
Ryuichiro Nakato |
| E-mail(s) |
rnakato@iqb.u-tokyo.ac.jp
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| Phone |
+81-3-5841-1471
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| Organization name |
The University of Tokyo
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| Department |
Institute for Quantitative Biosciences
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| Lab |
Laboratory of Computational Genomics
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| Street address |
1-1-1 Yayoi
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| City |
Bunkyo-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
113-0032 |
| Country |
Japan |
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| Platforms (1) |
| GPL26171 |
HiSeq X Ten (Saccharomyces cerevisiae) |
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| Samples (28)
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| GSM4946269 |
WT, DMSO [KJ4] |
| GSM4946270 |
Wpl1-AID, thiolutin [KJ5] |
| GSM4946271 |
WT, aux/dox, DMSO [KJ12] |
| GSM4946272 |
WT, aux/dox, thiolutin [KJ13] |
| GSM4946273 |
Scc2-AID, aux/dox, DMSO [KJ14] |
| GSM4946274 |
Scc2-AID, aux/dox, thiolutin [KJ15] |
| GSM4946275 |
Wpl1-AID, aux/dox, DMSO [KJ16] |
| GSM4946276 |
Wpl1-AID, aux/dox, thiolutin [KJ17] |
| GSM4946277 |
Scc2-AID, aux/dox, DMSO [KJ18] |
| GSM4946278 |
Scc2-AID, aux/dox, thiolutin [KJ19] |
| GSM4946279 |
WT, HU [KJ20] |
| GSM4946280 |
Scc2-AID, HU, aux/dox [KJ22] |
| GSM4946281 |
Wpl1-AID, HU, aux/dox [KJ23] |
| GSM5746898 |
WT, aux/dox, DMSO [KJ24] |
| GSM5746899 |
WT, aux/dox, thiolutin [KJ25] |
| GSM5746900 |
WT, aux/dox, DMSO [KJ26] |
| GSM5746901 |
WT, aux/dox, thiolutin [KJ27] |
| GSM5746902 |
Scc2-AID, aux/dox, thiolutin [KJ28] |
| GSM5746903 |
Scc2-AID, aux/dox, thiolutin [KJ29] |
| GSM5746904 |
WT, HU, aux/dox [KJ30] |
| GSM5746905 |
WT, HU, aux/dox [KJ31] |
| GSM5746906 |
WT, 37°C [KJ36] |
| GSM5746907 |
WT, 37°C [KJ37] |
| GSM5746908 |
rpb1-1, 37°C [KJ38] |
| GSM5746909 |
rpb1-1, 37°C [KJ39] |
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| This SubSeries is part of SuperSeries: |
| GSE162194 |
Cohesin-dependent chromosome loop extrusion is limited by transcription and stalled replication forks |
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| Relations |
| BioProject |
PRJNA680815 |
| SRA |
SRP294207 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE162193_RAW.tar |
344.6 Mb |
(http)(custom) |
TAR (of HIC) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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