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| Status |
Public on Dec 01, 2019 |
| Title |
The nuclear matrix protein SAFB maintains heterochromatin architecture through RNA-dependent phase separation [RIP-seq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| 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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| |
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| Overall design |
Identification and characterization of RNAs associated with SAFB in AML12 cells
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| Citation(s) |
31677973 |
| |
| Submission date |
Nov 26, 2019 |
| Last update date |
Mar 01, 2020 |
| Contact name |
Luzhang Ji |
| E-mail(s) |
jiluzhang@tongji.edu.cn
|
| Organization name |
Tongji University
|
| Street address |
1239 Siping Rd.
|
| City |
Shanghai |
| ZIP/Postal code |
200092 |
| 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 |
|
| Relations |
| BioProject |
PRJNA591959 |
| SRA |
SRP233383 |
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