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GEO help: Mouse over screen elements for information. |
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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
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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.
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Overall design |
Analysis of Smc5/6, cohesin and RNA pol II chromosomal association by ChIP-seq in Saccharomyces cerevisiae
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Web link |
http:// 10.1016/j.molcel.2024.01.005
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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 |
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Submission date |
Jun 22, 2023 |
Last update date |
May 08, 2024 |
Contact name |
Kristian Jeppsson |
E-mail(s) |
kristian.jeppsson@ki.se
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Organization name |
Krolinska Institute
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Department |
Department of Cell and Molecular Biology
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Street address |
3-1-1 Koyadai
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City |
Stockholm |
ZIP/Postal code |
17177 |
Country |
Sweden |
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Platforms (1) |
GPL17342 |
Illumina HiSeq 2500 (Saccharomyces cerevisiae) |
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Samples (61)
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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] |
GSM7505194 |
Smc6-FLAG Wpl1-AID, IP [2019_030B_3594-1_IP] |
GSM7505195 |
Smc6-FLAG, IP [2019_030B_3067-2_IP] |
GSM7505196 |
Smc6-FLAG, Input [2019_030B_3067-2_WCE] |
GSM7505197 |
Smc6-FLAG Scc2-AID, IP [2019_030B_3541-2_IP] |
GSM7505198 |
Smc6-FLAG Wpl1-AID, IP [2019_030B_3594-2_IP] |
GSM7505199 |
Smc6-FLAG top2-4, IP [2019_030B_3069-2_IP] |
GSM7505200 |
Smc6-FLAG top2-4 Scc2-AID, IP [2019_030B_3543-2_IP] |
GSM7505201 |
Smc6-FLAG top2-4 Wpl1-AID, IP [2019_030B_3595-2_IP] |
GSM7505202 |
Smc6-FLAG, 0 min thiolutin, IP [2017_032B_173-2_0_IP] |
GSM7505203 |
Smc6-FLAG, 0 min thiolutin, input [2017_032B_173-2_0_Input] |
GSM7505204 |
Smc6-FLAG, 3 min thiolutin, IP [2017_032B_173-2_3+_IP] |
GSM7505205 |
Smc6-FLAG, 3 min thiolutin, input [2017_032B_173-2_3+_Input] |
GSM7505206 |
Smc6-FLAG, 15 min thiolutin, IP [2017_032B_173-2_15+_IP] |
GSM7505207 |
Smc6-FLAG, 15 min thiolutin, input [2017_032B_173-2_15+_Input] |
GSM7505208 |
Smc6-FLAG, 30 min thiolutin, IP [2017_032B_173-2_30+_IP] |
GSM7505209 |
Smc6-FLAG, 30 min thiolutin, input [2017_032B_173-2_30+_Input] |
GSM7505210 |
Smc6-FLAG, 30 min DMSO, IP [2017_032B_173-2_30-_IP] |
GSM7505211 |
Smc6-FLAG, 30 min DMSO, input [2017_032B_173-2_30-_Input] |
GSM7505212 |
Smc6-FLAG top2-4, 0 min thiolutin, IP [2017_032B_1367-2_0+_IP] |
GSM7505213 |
Smc6-FLAG top2-4, 0 min thiolutin, input [2017_032B_1367-2_0+_Input] |
GSM7505214 |
Smc6-FLAG top2-4, 3 min thiolutin, IP [2017_032B_1367-2_3+_IP] |
GSM7505215 |
Smc6-FLAG top2-4, 3 min thiolutin, input [2017_032B_1367-2_3+_Input] |
GSM7505216 |
Smc6-FLAG top2-4, 15 min thiolutin, IP [2017_032B_1367-2_15+_IP] |
GSM7505217 |
Smc6-FLAG top2-4, 15 min thiolutin, input [2017_032B_1367-2_15+_Input] |
GSM7505218 |
Smc6-FLAG top2-4, 30 min thiolutin, IP [2017_032B_1367-2_30+_IP] |
GSM7505219 |
Smc6-FLAG top2-4, 30 min thiolutin, input [2017_032B_1367-2_30+_Input] |
GSM7505220 |
Smc6-FLAG top2-4, 30 min DMSO, IP [2017_032B_1367-2_30-_IP] |
GSM7505221 |
Smc6-FLAG top2-4, 30 min DMSO, input [2017_032B_1367-2_30-_Input] |
GSM7505222 |
Scc1-FLAG, 0 min thiolutin, IP [2017_032B_234-2_0_IP] |
GSM7505223 |
Scc1-FLAG, 3 min thiolutin, IP [2017_034B_234-2_3+_IP] |
GSM7505224 |
Scc1-FLAG, 15 min thiolutin, IP [2017_034B_234-2_15+_IP] |
GSM7505225 |
Scc1-FLAG, 30 min thiolutin, IP [2017_034B_234-2_30+_IP] |
GSM7505226 |
Scc1-FLAG, 30 min DMSO, IP [2017_032B_234-2_30-_IP] |
GSM7505227 |
Scc1-FLAG top2-4, 0 min thiolutin, IP [2017_032B_383-2_0_IP] |
GSM7505228 |
Scc1-FLAG top2-4, 3 min thiolutin, IP [2017_032B_383-2_3+_IP] |
GSM7505229 |
Scc1-FLAG top2-4, 15 min thiolutin, IP [2017_032B_383-2_15+_IP] |
GSM7505230 |
Scc1-FLAG top2-4, 30 min thiolutin, IP [2017_032B_383-2_30+_IP] |
GSM7505231 |
Scc1-FLAG top2-4, 30 min DMSO, IP [2017_032B_383-2_30-_IP] |
GSM7505232 |
Rpo21-FLAG, 0 min thiolutin, IP [2017_035A_1958-2_0_IP] |
GSM7505233 |
Rpo21-FLAG, 3 min thiolutin, IP [2017_034B_1958-2_3+_IP] |
GSM7505234 |
Rpo21-FLAG, 15 min thiolutin, IP [2017_034B_1958-2_15+_IP] |
GSM7505235 |
Rpo21-FLAG, 30 min thiolutin, IP [2017_035A_1958-2_30+_IP] |
GSM7505236 |
Rpo21-FLAG, 30 min DMSO, IP [2017_036B_1958-2_30-_IP] |
GSM7505237 |
Rpo21-FLAG top2-4, 0 min thiolutin, IP [2017_036B_1959-2_0_IP] |
GSM7505238 |
Rpo21-FLAG top2-4, 3 min thiolutin, IP [2017_036B_1959-2_3+_IP] |
GSM7505239 |
Rpo21-FLAG top2-4, 15 min thiolutin, IP [2017_036B_1959-2_15+_IP] |
GSM7505240 |
Rpo21-FLAG top2-4, 30 min thiolutin, IP [2017_036B_1959-2_30+_IP] |
GSM7505241 |
Rpo21-FLAG top2-4, 30 min DMSO, IP [2017_036B_1959-2_30-_IP] |
GSM7505242 |
Smc6-FLAG, IP [2019_030B_3067-3_IP] |
GSM7505243 |
Smc6-FLAG, Input [2019_030B_3067-3_WCE] |
GSM7505244 |
Smc6-FLAG Top1-AID, IP [2019_030B_3318-3_IP] |
GSM7505245 |
Smc6-FLAG top2-4, IP [2019_030B_3069-3_IP] |
GSM7505246 |
Smc6-FLAG Top1-AID top2-4, IP [2019_030B_3341-3_IP] |
GSM7505247 |
Smc6-FLAG, IP [2017_035A_173-X_IP] |
GSM7505248 |
Smc6-FLAG, Input [2017_035A_173-X_Input] |
GSM7505249 |
Smc6-FLAG top2-4, IP [2017_036B_1367-X_IP] |
GSM7505250 |
Scc1-FLAG, IP [2017_034B_234-X_IP] |
GSM7505251 |
Scc1-FLAG top2-4, IP [2017_034B_383-X_IP] |
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This SubSeries is part of SuperSeries: |
GSE235560 |
Loop-extruding Smc5/6 organizes transcription-induced positive DNA supercoils. |
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Relations |
BioProject |
PRJNA986462 |
Supplementary file |
Size |
Download |
File type/resource |
GSE235557_RAW.tar |
44.9 Mb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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