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| Status |
Public on Apr 18, 2024 |
| Title |
Condensin I folds the C. elegans genome [Hi-C] |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Other
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| Summary |
Structural Maintenance of chromosomes (SMC) complexes, cohesin and condensins, have been named after their roles during meiosis and mitosis. Recent data in mammalian cells and Drosophila have described the additional role of cohesin for genome folding into loops and domains during interphase. However, determinants of genome folding in holocentric species remain unclear. Using high resolution chromosome conformation capture, we show that overlapping large-scale nuclear localization and small-scale epigenomic states compartmentalize the C. elegans genome. By systematically and acutely inactivating each SMC complex, we observe that in contrast to other studied systems, cohesin creates small loops, while condensin I has a major role in genome folding: its inactivation causes genome-wide decompaction, chromosome mixing, loss of loops and TAD structures and reinforcement of fine-scale epigenomic compartments. Counter-intuitively, removal of condensin I and its X-specific variant condensin IDC from the X chromosomes led to the formation of a loop compartment coinciding with a subset of previously characterized loading sites for condensin IDC and bound by the X-targeting complex SDC. While transcriptional changes were limited for all autosomes upon cohesin and condensin II inactivation, removal of condensin I/IDC from the X chromosome led to transcriptional up-regulation of X-linked genes demonstrating that a sustained role for condensin IDC in gene regulation. Finally, while condensin I inactivation leads to reduced lifespan, we show that this reduction is due to X-specific gene upregulation rather than global genome decompaction.
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| Overall design |
To optimise the protocol, wild type strains were tested first. Once the protocol was established, Hi-C was performed on 6 different strains including the control. All the strains used in this study have two biological replicates.
HiC on entire animals, following cleavage of cohesin's kleisins COH-1 and SCC-1. Two biological repeats, sequenced on a iSeq and Novaseq
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| Contributor(s) |
Das M, Semple J, Haemmerli A, Scotton J, Gitchev T, Mozziconacci J, Campos J, Meister P |
| Citation(s) |
39039278 |
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| Submission date |
Mar 29, 2022 |
| Last update date |
Jul 23, 2024 |
| Contact name |
Peter Meister |
| E-mail(s) |
peter.meister@unibe.ch
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| Phone |
+41316844609
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| Organization name |
University of Bern
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| Department |
Institute of Cell Biology
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| Lab |
Cell Fate and Nuclear Organization
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| Street address |
Baltzerstrasse 4
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| City |
Bern |
| State/province |
Schweiz |
| ZIP/Postal code |
3012 |
| Country |
Switzerland |
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| Platforms (2) |
| GPL22765 |
Illumina HiSeq 4000 (Caenorhabditis elegans) |
| GPL26672 |
Illumina NovaSeq 6000 (Caenorhabditis elegans) |
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| Samples (16)
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| This SubSeries is part of SuperSeries: |
| GSE199723 |
Condensin I folds the C. elegans genome |
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| Relations |
| BioProject |
PRJNA821239 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE199721_RAW.tar |
1.5 Gb |
(http)(custom) |
TAR (of COOL) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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