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Series GSE141084 Query DataSets for GSE141084
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.
 
Overall design Identification and characterization of RNAs associated with SAFB in AML12 cells
 
Citation(s) 31677973
Submission date Nov 26, 2019
Last update date Mar 01, 2020
Contact name Bo Wen
E-mail(s) bowen75@fudan.edu.cn
Organization name Fudan University
Street address 130 Dongan Rd.
City ShangHai
ZIP/Postal code 200032
Country China
 
Platforms (1)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (4)
GSM4194771 IgG_RIPseq_rep1
GSM4194772 IgG_RIPseq_rep2
GSM4194773 SAFB_RIPseq_rep1
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

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE141084_SAFB_RIP_tpm_table.txt.gz 753.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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