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Series GSE198610 Query DataSets for GSE198610
Status Public on Mar 07, 2024
Title Mitotic chromosomes are self-entangled and disentangle through a Topoisomerase II-dependent two stage exit from mitosis
Organism Homo sapiens
Experiment type Other
Summary The topological state of chromosomes determines their mechanical properties, dynamics, and function. Recent work indicated that interphase chromosomes are largely free of entanglements. Here, we use Hi-C, polymer simulations and multi-contact 3C, and propose that, in contrast, mitotic chromosomes are self-entangled. We explore how a mitotic self-entangled state is converted into an unentangled interphase state during mitotic exit. Most mitotic entanglements are removed during anaphase/telophase, with remaining ones removed during early G1, in a Topoisomerase II-dependent process. Polymer models suggest a two-stage disentanglement pathway: first, decondensation of mitotic chromosomes with remaining condensin loops produces entropic forces that bias Topoisomerase II activity towards decatenation. At the second stage, the loops are released, and formation of new entanglements is prevented by lower Topoisomerase II activity, allowing the establishment of unentangled and territorial G1 chromosomes. When mitotic entanglements are not removed, in experiment and models, a normal interphase state cannot be acquired.
 
Overall design Hi-C and MC-3C experiments in HeLa S3 and Hi-C experiments in HCT116 + Rad21-mAC cell lines. Hi-C experiments have 1-3 replicates each, MC-3C experiments have 3 replicates each.
 
Contributor(s) Hildebrand EM, Polovnikov K, Dekker B, Liu Y, Lafontaine DL, Fox A, Li Y, Venev SV, Mirny L, Dekker J
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Submission date Mar 14, 2022
Last update date Mar 08, 2024
Contact name Job Dekker
E-mail(s) job.dekker@umassmed.edu
Organization name University of Massachusetts Medical School/HHMI
Department Program in Systems Biology
Lab Dekker Lab
Street address 368 Plantation Street
City Worcester
State/province MA
ZIP/Postal code 01606
Country USA
 
Platforms (3)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL28352 Sequel II (Homo sapiens)
GPL30173 NextSeq 2000 (Homo sapiens)
Samples (137)
GSM5953515 DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at different times: 4-9hr ICRF-193 R2
GSM5953516 DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at different times: 4-9hr DMSO R2
GSM5953517 DpnII Hi-C on HeLa S3 MR DMSO or ICRF-193 added at different times: 3-8hr ICRF-193 R2
Relations
BioProject PRJNA816145

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
GSE198610_MRICRF_MC3C_FirstXFragmentsPerWalk_Annotated.txt.gz 1.9 Gb (ftp)(http) TXT
GSE198610_RAW.tar 38.0 Gb (http)(custom) TAR (of MCOOL)
GSE198610_TI-HiC-Dpn-HCT116-Rad21AID-G1Sort-DMSO-ETOH-2hr-R1R2R3.sampled.hg38.mapq_30.1000.mcool 581.2 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HCT116-Rad21AID-G1Sort-DMSO-IAA-2hr-R1R2R3.sampled.hg38.mapq_30.1000.mcool 608.1 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HCT116-Rad21AID-G1Sort-ICRF-ETOH-2hr-R1R2R3.sampled.hg38.mapq_30.1000.mcool 590.4 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HCT116-Rad21AID-G1Sort-ICRF-IAA-2hr-R1R2R3.sampled.hg38.mapq_30.1000.mcool 587.3 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-Async-Camp-4hr-CampExp-R1R2.sampled.hg38.mapq_30.1000.mcool 499.0 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-Async-DMSO-4hr-CampExp-R1R2.sampled.hg38.mapq_30.1000.mcool 504.3 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-G1Sort-DMSO-2hr-R1R2.sampled.hg38.mapq_30.1000.mcool 337.9 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-G1Sort-ICRF-2hr-R1R2.sampled.hg38.mapq_30.1000.mcool 338.5 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t0-Ctrl-CampExp-R1R2.sampled.hg38.mapq_30.1000.mcool 520.1 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t0-Ctrl-R1R2.sampled.hg38.mapq_30.1000.mcool 463.6 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t0-Ctrl-TxnInhibExp-R1R2.sampled.hg38.mapq_30.1000.mcool 469.3 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t2hr-Ctrl-CampExp-R1R2.sampled.hg38.mapq_30.1000.mcool 524.6 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t2hr-Ctrl-R1R2.sampled.hg38.mapq_30.1000.mcool 467.1 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t4.5hr-DRB-TPL-4.5hr-ICRF-2hr-TxnInhibExp-R1R2.sampled.hg38.mapq_30.1000.mcool 499.4 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t4.5hr-DRB-TPL-4.5hr-TxnInhibExp-R1R2.sampled.hg38.mapq_30.1000.mcool 502.5 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t4hr-DMSO-2hr-G1Sort-R1R2.sampled.hg38.mapq_30.1000.mcool 349.5 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t4hr-DMSO-2hr-TxnInhibExp-R1R2.sampled.hg38.mapq_30.1000.mcool 504.9 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t4hr-DMSO-2hr-Unsorted-R1R2.sampled.hg38.mapq_30.1000.mcool 480.6 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t4hr-ICRF-2hr-G1Sort-R1R2.sampled.hg38.mapq_30.1000.mcool 351.1 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t4hr-ICRF-2hr-TxnInhibExp-R1R2.sampled.hg38.mapq_30.1000.mcool 500.8 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t4hr-ICRF-2hr-Unsorted-R1R2.sampled.hg38.mapq_30.1000.mcool 468.6 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t6hr-Camp-6hr-CampExp-R1R2.sampled.hg38.mapq_30.1000.mcool 521.2 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t6hr-DMSO-6hr-CampExp-R1R2.sampled.hg38.mapq_30.1000.mcool 515.2 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t7hr-DMSO-5hr-G1Sort-ICRFTiming_R1R2.sampled.hg38.mapq_30.1000.mcool 424.3 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t7hr-ICRF-5hr-G1Sort-ICRFTiming_R1R2.sampled.hg38.mapq_30.1000.mcool 422.8 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t8hr-DMSO-5hr-G1Sort-ICRFTiming_R1R2.sampled.hg38.mapq_30.1000.mcool 430.4 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t8hr-DMSO-6hr-CampExp-R1R2.sampled.hg38.mapq_30.1000.mcool 500.5 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t8hr-DMSO-6hr-G1Sort-R1R2.sampled.hg38.mapq_30.1000.mcool 337.3 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t8hr-DMSO-6hr-Unsorted-R1R2.sampled.hg38.mapq_30.1000.mcool 446.0 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t8hr-DMSO-6hr-readded-R1R2.sampled.hg38.mapq_30.1000.mcool 474.4 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t8hr-DMSO-6hr-readded-R1R2R3.sampled.hg38.mapq_30.1000.mcool 644.7 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t8hr-ICRF-5hr-G1Sort-ICRFTiming_R1R2.sampled.hg38.mapq_30.1000.mcool 429.3 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t8hr-ICRF-6hr-G1Sort-R1R2.sampled.hg38.mapq_30.1000.mcool 339.7 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t8hr-ICRF-6hr-Unsorted-R1R2.sampled.hg38.mapq_30.1000.mcool 468.5 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t8hr-ICRF-6hr-readded-R1R2.sampled.hg38.mapq_30.1000.mcool 467.7 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t8hr-ICRF-6hr-readded-R1R2R3.sampled.hg38.mapq_30.1000.mcool 638.9 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t9hr-DMSO-5hr-G1Sort-ICRFTiming_R1R2.sampled.hg38.mapq_30.1000.mcool 451.8 Mb (ftp)(http) MCOOL
GSE198610_TI-HiC-Dpn-HeLa-MitoticRelease-t9hr-ICRF-5hr-G1Sort-ICRFTiming_R1R2.sampled.hg38.mapq_30.1000.mcool 451.2 Mb (ftp)(http) MCOOL
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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