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| Status |
Public on Mar 09, 2021 |
| Title |
Nuclear organization and replication timing are coupled through RIF1-PP1 interaction |
| Organism |
Mus musculus |
| Experiment type |
Other
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| Summary |
Three-dimensional genome organisation and replication timing are known to be correlated, however, it remains unknown whether nuclear architecture overall plays an instructive role in the replication-timing program and, if so, how. Here we demonstrate that RIF1 is a molecular hub that co-regulates both processes. Both nuclear organisation and replication timing depend upon the interaction between RIF1 and PP1. However, whereas nuclear architecture requires the full complement of RIF1 and its interaction with PP1, replication timing is not sensitive to RIF1 dosage. RIF1’s role in replication timing also extends beyond its interaction with PP1. Availing of this separation-of-function approach, we have therefore identified in RIF1 dual function the molecular bases of the co-dependency of the replication-timing program and nuclear architecture.
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| Overall design |
Hi-C experiments were performed on RIf1 WT, targeted WT (tgWT), heterozygous (het), non-PP1-interacting (DP) and knock-out (KO) mouse ES cells. For all conditions three replicates were analyzed (except het, with one replicate).
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| Contributor(s) |
Gnan S, Flyamer IM, Klein KN, Castelli E, Rapp A, Maiser A, Chen N, Weber P, Enervald E, Cardoso MC, Bickmore WA, Gilbert DM, Buonomo SC |
| Citation(s) |
34006872 |
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| Submission date |
Apr 07, 2020 |
| Last update date |
Jun 03, 2021 |
| Contact name |
Ilya M. Flyamer |
| E-mail(s) |
flyamer@gmail.com
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| Organization name |
Friedrich Miescher Institute for Biomedical Research
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| Lab |
Giorgetti
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| Street address |
Maulbeerstrasse 66
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| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
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| Platforms (2) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL21626 |
NextSeq 550 (Mus musculus) |
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| Samples (13)
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| Relations |
| BioProject |
PRJNA623577 |
| SRA |
SRP255620 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE148244_RAW.tar |
7.5 Gb |
(http)(custom) |
TAR (of MCOOL) |
| GSE148244_Rif1-DP.mm10.mapq_30.1000.mcool |
1.6 Gb |
(ftp)(http) |
MCOOL |
| GSE148244_Rif1-KO.mm10.mapq_30.1000.mcool |
1.0 Gb |
(ftp)(http) |
MCOOL |
| GSE148244_Rif1-WT.mm10.mapq_30.1000.mcool |
1.2 Gb |
(ftp)(http) |
MCOOL |
| GSE148244_Rif1-tgWT.mm10.mapq_30.1000.mcool |
1.5 Gb |
(ftp)(http) |
MCOOL |
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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