 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 07, 2022 |
| Title |
MCM complexes are barriers that restrict loops and TADs |
| Organism |
Homo sapiens |
| Experiment type |
Other
|
| Summary |
Eukaryotic genomes are compacted into loops and topologically associating domains (TADs), which contribute to transcription, recombination and genomic stability. Cohesin extrudes DNA into loops that are thought to lengthen until it encounters CTCF boundaries. Little is known whether loop extrusion is impeded by macromolecular machines. We demonstrate that the replicative helicase MCM is a barrier that restricts loops and TADs in G1 phase. Single-nucleus Hi-C of one-cell embryos revealed that MCM loading reduces CTCF-anchored loops and increases TAD boundary insulation, suggesting loop extrusion is impeded before reaching CTCF. Single-molecule imaging provides evidence that MCM are physical barriers that constrain cohesin translocation in vitro. Simulations are consistent with MCM as abundant, random barriers with low permeability. We conclude that distinct loop extrusion barriers contribute to shaping 3D genomes.
|
| |
|
| Overall design |
in situ Hi-C and micro-C from HCT116 MCM2-AID cells, treated with DMSO or Auxin, and with or without triptolide treatment
|
| |
|
| Contributor(s) |
Dequeker B, Gassler J, Powell S, Gaspar I, Flyamer I, Tachibana K |
| Citation(s) |
35585235 |
| |
| Submission date |
Aug 10, 2020 |
| Last update date |
Jun 06, 2022 |
| Contact name |
Ilya M. Flyamer |
| E-mail(s) |
[email protected]
|
| Organization name |
Friedrich Miescher Institute for Biomedical Research
|
| Lab |
Giorgetti
|
| Street address |
Maulbeerstrasse 66
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platforms (2) |
| GPL21697 |
NextSeq 550 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (22)
|
|
| Relations |
| BioProject |
PRJNA656247 |
| SRA |
SRP276886 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE155971_AUX_TRP.hg38.mapq_30.100.mcool |
4.8 Gb |
(ftp)(http) |
MCOOL |
| GSE155971_DMSO_TRP.hg38.mapq_30.100.mcool |
5.2 Gb |
(ftp)(http) |
MCOOL |
| GSE155971_G1_AUX_merged.hg38.mapq_30.100.mcool |
8.7 Gb |
(ftp)(http) |
MCOOL |
| GSE155971_G1_AUX_rep1.hg38.mapq_30.100.mcool |
5.6 Gb |
(ftp)(http) |
MCOOL |
| GSE155971_G1_AUX_rep2.hg38.mapq_30.100.mcool |
4.4 Gb |
(ftp)(http) |
MCOOL |
| GSE155971_G1_DMSO_merged.hg38.mapq_30.100.mcool |
9.5 Gb |
(ftp)(http) |
MCOOL |
| GSE155971_G1_DMSO_rep1.hg38.mapq_30.100.mcool |
6.0 Gb |
(ftp)(http) |
MCOOL |
| GSE155971_G1_DMSO_rep2.hg38.mapq_30.100.mcool |
4.9 Gb |
(ftp)(http) |
MCOOL |
| GSE155971_RAW.tar |
113.6 Gb |
(http)(custom) |
TAR (of MCOOL, PAIRS) |
| GSE155971_stats_table.txt.gz |
584 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...