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Series GSE235557 Query DataSets for GSE235557
Status Public on Jan 30, 2024
Title Loop-extruding Smc5/6 organizes transcription-induced positive DNA supercoils [ChIP-seq]
Organism Saccharomyces cerevisiae
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The Structural Maintenance of Chromosome (SMC) protein complexes cohesin, condensin and the Smc5/6 complex (Smc5/6) are essential for chromosome function. At the molecular level, these complexes fold DNA by loop extrusion. Accordingly, cohesin creates chromosome loops in interphase, and condensin compacts mitotic chromosomes. However, the role of Smc5/6’s recently discovered DNA loop extrusion activity is unknown. Here, we uncover that Smc5/6 controls the spatial organization of supercoiled chromosomal regions. The results show that Smc5/6 associates with transcription-induced positively supercoiled chromosomal DNA at cohesin-dependent chromosome loop boundaries. Mechanistically, single-molecule imaging reveals that dimers of Smc5/6 specifically recognize the tip of positively supercoiled DNA plectonemes, and efficiently initiates loop extrusion to gather the supercoiled DNA into a large plectonemic loop. Finally, Hi-C analysis shows that Smc5/6 links chromosomal regions containing transcription-induced positive supercoiling in cis. Altogether, our findings indicate that Smc5/6 controls the three-dimensional organization of chromosomes by recognizing and initiating loop extrusion on positively supercoiled DNA.
Overall design Analysis of Smc5/6, cohesin and RNA pol II chromosomal association by ChIP-seq in Saccharomyces cerevisiae
Web link http:// 10.1016/j.molcel.2024.01.005
Contributor(s) Jeppsson K, Pradhan B, Sutani T, Sakata T, Igarashi MU, Berta DG, Kanno T, Nakato R, Yokota N, Shirahige K, Kim E, Björkegren C
Citation(s) 38295804
Submission date Jun 22, 2023
Last update date May 08, 2024
Contact name Kristian Jeppsson
Organization name Krolinska Institute
Department Department of Cell and Molecular Biology
Street address 3-1-1 Koyadai
City Stockholm
ZIP/Postal code 17177
Country Sweden
Platforms (1)
GPL17342 Illumina HiSeq 2500 (Saccharomyces cerevisiae)
Samples (61)
GSM7505191 Smc6-FLAG, IP [2019_030B_3067-1_IP]
GSM7505192 Smc6-FLAG, Input [2019_030B_3067-1_WCE]
GSM7505193 Smc6-FLAG Scc2-AID, IP [2019_030B_3541-1_IP]
This SubSeries is part of SuperSeries:
GSE235560 Loop-extruding Smc5/6 organizes transcription-induced positive DNA supercoils.
BioProject PRJNA986462

Download family Format
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE235557_RAW.tar 44.9 Mb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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