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Series GSE141113 Query DataSets for GSE141113
Status Public on Dec 01, 2019
Title The nuclear matrix protein SAFB maintains heterochromatin architecture through RNA-dependent phase separation [HiChIP]
Organism Mus musculus
Experiment type Other
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 H3K9me3 HiChIP data in Ctrl and Safb KD AML12 cells.
 
Citation(s) 31677973
Submission date Nov 27, 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 (8)
GSM4195082 Control-K9me3-HiChip-Rep1
GSM4195083 Control-K9me3-HiChip-Rep1-plus
GSM4195084 Control-K9me3-HiChip-Rep2
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 PRJNA592152
SRA SRP233493

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
GSE141113_Control-K9me3-HiChip-Rep1_merge_allValidPairs.hic 273.4 Mb (ftp)(http) HIC
GSE141113_Control-K9me3-HiChip-Rep2_merge_allValidPairs.hic 294.0 Mb (ftp)(http) HIC
GSE141113_SAFB-K9me3-HiChip-Rep1_merge_allValidPairs.hic 231.4 Mb (ftp)(http) HIC
GSE141113_SAFB-K9me3-HiChip-Rep2_merge_allValidPairs.hic 362.0 Mb (ftp)(http) HIC
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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