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Status |
Public on Dec 01, 2019 |
Title |
The nuclear matrix protein SAFB maintains heterochromatin architecture through RNA-dependent phase separation [Hi-C] |
Organism |
Mus musculus |
Experiment type |
Other
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Summary |
Eukaryotic chromosomes fold into topologically associating domains (TADs), which further gather in active (A) or inactive (B) genomic compartments. Here we show that Scaffold Attachment Factor B (SAFB), a nuclear matrix-associated protein with RNA binding functions, modulates global chromatin condensation in a dosage-dependent manner. Upon the depletion of SAFB, the genome coverage of Lamina-associated-domains (LADs) decreases from 53.33% to 45.93%, and both inter- and intra-TAD chromatin-chromatin interactions in compartment B decrease significantly. In the nucleus, SAFB favorably co-localizes with H3K9me3, a marker of heterochromatin, and the disruption of SAFB leads to a collapse of H3K9me3 foci. Furthermore, we show that SAFB proteins can form liquid-liquid phase separation in the cell and in vitro. Intriguingly, SAFB interacts with RNAs from repetitive elements enriched in heterochromatin (e.g., Major Satellites and LINE1), which can promote SAFB-mediated phase separation, depending on the density of SAFB recognizing motifs in the RNAs.
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Overall design |
Hi-C data in Ctrl and Safb KD AML12 cells.
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Citation(s) |
31677973 |
BioProject |
PRJNA591953 |
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Submission date |
Nov 26, 2019 |
Last update date |
Mar 01, 2020 |
Contact name |
Bo Wen |
E-mail(s) |
bowen75@fudan.edu.cn
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Organization name |
Fudan University
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Street address |
130 Dongan Rd.
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City |
ShangHai |
ZIP/Postal code |
200032 |
Country |
China |
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Platforms (1) |
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Samples (4)
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This SubSeries is part of SuperSeries: |
GSE125037 |
The Nuclear Matrix Protein SAFB Cooperates with Major Satellite RNAs to Stabilize Heterochromatin Architecture Partially through Phase Separation |
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Relations |
SRA |
SRP233380 |
Supplementary file |
Size |
Download |
File type/resource |
GSE141080_RAW.tar |
6.8 Gb |
(http)(custom) |
TAR (of HIC) |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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