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| Status |
Public on Apr 18, 2024 |
| Title |
Condensin I folds the C. elegans genome [RNA-seq] |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Expression profiling by high throughput sequencing
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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 |
In this study, a total of 40 samples were analysed that comprise of 9 different strains in which different SMC complexes were inactivated and their controls. Each strain/condition has 3-4 biological replicates.
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| Contributor(s) |
Das M, Semple J, Scotton J, Annan A, 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 (1) |
| GPL26672 |
Illumina NovaSeq 6000 (Caenorhabditis elegans) |
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| Samples (40)
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| GSM5982652 |
RNA-seq: TEV control replicate 1, BATCH 1 |
| GSM5982653 |
RNA-seq: TEV control replicate 2, BATCH 1 |
| GSM5982654 |
RNA-seq: TEV control replicate 3, BATCH 1 |
| GSM5982655 |
RNA-seq: TEV control replicate 4, BATCH 1 |
| GSM5982656 |
RNA-seq: TEV control replicate 1, BATCH 2 |
| GSM5982657 |
RNA-seq: TEV control replicate 2, BATCH 2 |
| GSM5982658 |
RNA-seq: TEV control replicate 3, BATCH 2 |
| GSM5982659 |
RNA-seq: dpy-26cs TEV replicate 1, BATCH 1 |
| GSM5982660 |
RNA-seq: dpy-26cs TEV replicate 2, BATCH 1 |
| GSM5982661 |
RNA-seq: dpy-26cs TEV replicate 3, BATCH 1 |
| GSM5982662 |
RNA-seq: dpy-26cs TEV replicate 4, BATCH 1 |
| GSM5982663 |
RNA-seq: kle-2cs TEV replicate 1, BATCH 1 |
| GSM5982664 |
RNA-seq: kle-2cs TEV replicate 2, BATCH 1 |
| GSM5982665 |
RNA-seq: kle-2cs TEV replicate 3, BATCH 1 |
| GSM5982666 |
RNA-seq: kle-2cs TEV replicate 4, BATCH 1 |
| GSM5982667 |
RNA-seq: scc-1cs TEV replicate 1, BATCH 1 |
| GSM5982668 |
RNA-seq: scc-1cs TEV replicate 2, BATCH 1 |
| GSM5982669 |
RNA-seq: scc-1cs TEV replicate 3, BATCH 1 |
| GSM5982670 |
RNA-seq: scc-1cs TEV replicate 4, BATCH 1 |
| GSM5982671 |
RNA-seq: coh-1cs TEV replicate 1, BATCH 2 |
| GSM5982672 |
RNA-seq: coh-1cs TEV replicate 2, BATCH 2 |
| GSM5982673 |
RNA-seq: coh-1cs TEV replicate 3, BATCH 2 |
| GSM5982674 |
RNA-seq: scc-1cs coh-1cs TEV replicate 1, BATCH 2 |
| GSM5982675 |
RNA-seq: scc-1cs coh-1cs TEV replicate 2, BATCH 2 |
| GSM5982676 |
RNA-seq: scc-1cs coh-1cs TEV replicate 3, BATCH 2 |
| GSM5982677 |
RNA-seq: sdc-3AID auxin replicate 1, BATCH 4 |
| GSM5982678 |
RNA-seq: sdc-3AID auxin replicate 2, BATCH 4 |
| GSM5982679 |
RNA-seq: sdc-3AID auxin replicate 3, BATCH 4 |
| GSM5982680 |
RNA-seq: sdc-3AID control replicate 1, BATCH 4 |
| GSM5982681 |
RNA-seq: sdc-3AID control replicate 2, BATCH 4 |
| GSM5982682 |
RNA-seq: sdc-3AID control replicate 3, BATCH 4 |
| GSM5982683 |
RNA-seq: dpy-26cs sdc-3AID auxin replicate 1, BATCH 3 |
| GSM5982684 |
RNA-seq: dpy-26cs sdc-3AID auxin replicate 2, BATCH 3 |
| GSM5982685 |
RNA-seq: dpy-26cs sdc-3AID auxin replicate 3, BATCH 3 |
| GSM5982686 |
RNA-seq: TEV TIR1 auxin control replicate 1, BATCH 3 |
| GSM5982687 |
RNA-seq: TEV TIR1 auxin control replicate 2, BATCH 3 |
| GSM5982688 |
RNA-seq: TEV TIR1 auxin control replicate 3, BATCH 3 |
| GSM5982689 |
RNA-seq: TEV auxin control replicate 1, BATCH 3 |
| GSM5982690 |
RNA-seq: TEV auxin control replicate 2, BATCH 3 |
| GSM5982691 |
RNA-seq: TEV auxin control replicate 3, BATCH 3 |
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| This SubSeries is part of SuperSeries: |
| GSE199723 |
Condensin I folds the C. elegans genome |
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| Relations |
| BioProject |
PRJNA821226 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE199717_RAW.tar |
46.9 Mb |
(http)(custom) |
TAR (of SF) |
| GSE199717_sumFR_366_B_UniqueMultiple.bw |
129.6 Mb |
(ftp)(http) |
BW |
| GSE199717_sumFR_366_C_UniqueMultiple.bw |
139.7 Mb |
(ftp)(http) |
BW |
| GSE199717_sumFR_366_D_UniqueMultiple.bw |
132.6 Mb |
(ftp)(http) |
BW |
| GSE199717_sumFR_382_B_UniqueMultiple.bw |
127.3 Mb |
(ftp)(http) |
BW |
| GSE199717_sumFR_775_B_UniqueMultiple.bw |
126.1 Mb |
(ftp)(http) |
BW |
| GSE199717_sumFR_784_B_UniqueMultiple.bw |
130.7 Mb |
(ftp)(http) |
BW |
| GSE199717_sumFR_821_D_UniqueMultiple.bw |
142.3 Mb |
(ftp)(http) |
BW |
| GSE199717_sumFR_822_A_UniqueMultiple.bw |
132.8 Mb |
(ftp)(http) |
BW |
| GSE199717_sumFR_822_C_UniqueMultiple.bw |
128.7 Mb |
(ftp)(http) |
BW |
| GSE199717_sumFR_823_D_UniqueMultiple.bw |
145.8 Mb |
(ftp)(http) |
BW |
| GSE199717_sumFR_828_C_UniqueMultiple.bw |
141.0 Mb |
(ftp)(http) |
BW |
| GSE199717_sumFR_844_C_UniqueMultiple.bw |
145.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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