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Series GSE213413 Query DataSets for GSE213413
Status Public on Oct 09, 2023
Title Functional dissection of PRC1 subunits RYBP and YAF2 during neural differentiation of embryonic stem cells
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Polycomb repressive complex 1 (PRC1) comprises two different complexes: CBX-containing canonical PRC1 (cPRC1) and RYBP/YAF2-containing variant PRC1 (vPRC1). RYBP and its paralog YAF2 recruit vPRC1 to catalyze H2AK119ub through a positive-feedback model. Here, we show that expression of RYBP and YAF2 decreases and increases, respectively, during neural differentiation of embryonic stem cells (ESCs). Rybp knockout impairs neural differentiation by activating Wnt signaling and derepressing nonneuroectoderm-associated genes. However, Yaf2 knockout promotes neural differentiation and leads to redistribution of RYBP binding, increases enrichment of RYBP and H2AK119ub on the RYBP-YAF2 co-targeted genes, and prevents ectopic derepression of nonneuroectoderm-associated genes in neural-differentiated cells. Furthermore, the phase separations mediated by RYBP alone or together with RING1B are easier and more stable than those by YAF2, which might facilitate the deposition of H2AK119ub more abundantly by RYBP-PRC1 than YAF2-PRC1. Together, this study reveals that RYBP might maintain repressed chromatin more strongly and function differentially in regulating mESC neural differentiation compared with YAF2.
 
Overall design Comparative gene expression profiling analysis of RNA-seq data in wild-type, Rybp-/- and Yaf2-/- mESCs and their neural differentiated cells.
 
Contributor(s) Hu G, Liu Y, Yao H
Citation(s) 37935677
Submission date Sep 15, 2022
Last update date Jan 08, 2024
Contact name gongcheng Hu
Organization name Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences
Street address 190 Kai Yuan Avenue, Science Park, Guangzhou, China
City guangzhou
State/province guangdong
ZIP/Postal code 510530
Country China
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (18)
GSM6585870 RNAseq_D0_wild_type_rep1
GSM6585871 RNAseq_D0_wild_type_rep2
GSM6585872 RNAseq_D0_Rybp_knockout_rep1
This SubSeries is part of SuperSeries:
GSE213416 Functional Dissection of Variant Polycomb Repressive Complex 1 Subunits RYBP and YAF2 during Neural Differentiation of Embryonic Stem Cells
Relations
BioProject PRJNA880999

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

Supplementary file Size Download File type/resource
GSE213413_nor_counts.tsv.gz 1.7 Mb (ftp)(http) TSV
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Raw data are available in SRA
Processed data are available on Series record

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