GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE150254 Query DataSets for GSE150254
Status Public on Apr 14, 2021
Title Mechanism of REST/NRSF Regulation of Clustered Protocadherin Alpha Genes
Organisms Homo sapiens; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Repressor element-1 silencing transcription factor (REST) or neuron-restrictive silencer factor (NRSF) is a zinc-finger (ZF) containing transcriptional repressor that recognizes thousands of neuron-restrictive silencer elements (NRSEs) in mammalian genomes. How REST/NRSF regulates gene expression remains incompletely understood. Here, we investigate the binding pattern and regulation mechanism of REST/NRSF in the clustered protocadherin (PCDH) genes. We find that REST/NRSF directionally forms base-specific interactions with NRSEs via tandem ZFs in an anti-parallel manner but with striking conformational changes. In addition, REST/NRSF recruitment to the HS5-1 enhancer leads to the decrease of long-range enhancer-promoter interactions and downregulation of the clustered PCDH alpha genes. Thus, REST/NRSF represses PCDH alpha gene expression through directional binding to a repertoire of NRSEs within the distal enhancer and variable target genes.
Overall design We performed ChIP-nexus experiments in HEC-1-B and SK-N-SH cells to pinpoint the NRSEs, and uncover the DNA-recognition code of NRSF. We performed ChIP-Seq experiments for REST, H3K4me3, H3K27ac after REST knockdown by shRNA or HS5-1 NRSE deletion in HEC-1-B cells and HEK293T cells by CRISPR/Cas9, and for REST, H3K4me3, CTCF after HS5-1 NRSE deletion in mice by CRISPR/Cas9. RNA-seq results revealed the influence on the expression of clustered Pcdh alpha by knockdown of NRSF or deletion of HS 5-1 NRSE in HEC-1-B and HEK293T cells, or in mouse cortex, and kidney, taking wild-type (WT) as control. QHR-4C experiments were used to supervise the DNA interactions between PCDH apha promoters and HS5-1 in the HEC-1-B cells after REST knockdown or HS5-1 NRSE deletion, and in the kidney of HS5-1 NRSE-deleted mice.
Contributor(s) Tang Y, Wu Q
Citation(s) 33849071
Submission date May 11, 2020
Last update date Sep 09, 2022
Contact name Yuanxiao Tang
Organization name Shanghai Jiao Tong University
Street address Dongchuan Road 800
City Shanghai
ZIP/Postal code 200240
Country China
Platforms (4)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL20795 HiSeq X Ten (Homo sapiens)
Samples (95)
GSM4544336 NRSF_H_ChIP-nexus_rep1
GSM4544337 NRSF_H_ChIP-nexus_rep2
GSM4544338 NRSF_S_ChIP-nexus_rep1
BioProject PRJNA631681
SRA SRP261089

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
GSE150254_NRSF_hec1b.bedgraph.gz 205.8 Mb (ftp)(http) BEDGRAPH
GSE150254_NRSF_sknsh.bedgraph.gz 388.0 Mb (ftp)(http) BEDGRAPH
GSE150254_RAW.tar 9.4 Gb (http)(custom) TAR (of BEDGRAPH, TXT, XLS)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap