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Genome-wide maps of REST and its cofactors in mouse E14 cells

ABSTRACT: We report the application of single-molecule-based sequencing technology for REST and its cofactors genome wide binding sites in E14 cells.We then combine these binding sirtes with REST regulating gene profiling, to understand REST binding and regulation in E14 cells.

ORGANISM(S): Mus musculus

PROVIDER: GSE28233 | GEO | 2011/04/01

SECONDARY ACCESSION(S): PRJNA143139

REPOSITORIES: GEO

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Genome-wide maps of REST and its cofactors in mouse E14 cells

Project description:We report the application of single-molecule-based sequencing technology for REST and its cofactors genome wide binding sites in E14 cells.We then combine these binding sirtes with REST regulating gene profiling, to understand REST binding and regulation in E14 cells. Examination of REST and 5 cofactors(RCOR1, RCOR2,RCOR3,SIN3A,SIN3B) in E14 cells, REST and SIN3A endogenous antibody were used for ChIP experiment. The stable E14 cells expressing low level exogenous RCOR1, RCOR2, RCOR3,and SIN3B with V5 tag were used for ChIP experiment with V5 antibody to obtain individual ChIP DNA.

2011-04-01 | E-GEOD-28233 | biostudies-arrayexpress

REST ChIP-chip and knockdown expression profiling

Project description:This SuperSeries is composed of the following subset Series: GSE28141: Genome-wide analysis of REST knockdown responsive gene expression in mouse ES cells GSE28233: Genome-wide maps of REST and its cofactors in mouse E14 cells Refer to individual Series

2011-03-31 | E-GEOD-28289 | biostudies-arrayexpress

E14 MGE

Project description:E14 MGE

| PRJNA670339 | ENA

ChIP-Seq of PRDM16 binding sites in E14 MGE

Project description:Identification of genome-wide PRDM16 binding sites in the medial ganglionic eminence of E14 mice

2020-10-22 | GSE159729 | GEO

Mus musculus

Project description:Genome-wide maps of REST and its cofactors in mouse E14 cells

| PRJNA143139 | ENA

Chromatin immunoprecipitation of REST/NRSF

Project description:ENCODE ChIP-chip study using 8 diverse human cell lines; 4 of neural origin (NB69, KELLY, SHSY-5Y, U373) and 4 of non-neural origin (HeLa, HepG2, HEK293 and K562) and anti-REST/NRSF antibody (Santa Cruz Biotech; sc-25398 aka H290) to asses REST-genome interactions across 1% of the human genome used in the pilot phase of the ENCODE project. Additionally the REST binding profile in K562 cells that had been transfected with REST specific siRNA oligos (72h and 96h) were determined revealing genomic in vivo binding affinity hierarchies for REST. Additionally the REST binding profile in K562 cells that had been transfected with REST specific siRNA oligos (72h and 96h) were determined

2009-03-31 | E-TABM-660 | biostudies-arrayexpress

REST–Mediated Recruitment of Polycomb Repressor Complexes in Mammalian Cells

Project description:Genome-wide analysis of REST and Polycomb binding in Rest-/- and Eed-/- mouse embryonic stem (mES) cells showed that Rest was required for PRC1 recruitment to a subset of Polycomb regulated neuronal genes. Furthermore, we found that PRC1 can be recruited to Rest binding sites independently of CpG islands and the H3K27Me3 mark., and that PRC2 was frequently increased around Rest binding sites located in CpG-rich regions in the Rest2/2 mES cells. Published here: PLoS Genet 8(3): e1002494. doi:10.1371/journal.pgen.1002494

2013-06-20 | GSE48122 | GEO

REST–Mediated Recruitment of Polycomb Repressor Complexes in Mammalian Cells

2013-06-20 | E-GEOD-48122 | biostudies-arrayexpress

Identification of genes regulated by REST in developing hearts

Project description:Selective suppression of cardiac gene expression by RE-1 silencing transcription factor (REST) in embryonic stage is essential for cardiogenesis and function; however, the underlying mechanism remains unclear. In this study, we show that REST suppression of cardiac genes during development is temporarily regulated through non-CpG methylation at REST binding sites. Gene expression analyses revealed that the expression of Hcn2 (hyperpolarization-activated cyclic nucleotide-gated ion channel 2), a REST-targeted gene, was developmentally upregulated, while DNMT3B level and REST expression was downregulated. Concurrently, bisulﬁte sequencing and chromatin immunoprecipitation (ChIP) analyses showed that non-CpG methylation of the REST site located in the Hcn2 intron 1 and its co-occupancy by REST and DNMT3B were diminished at E?. Further in vitro inhibition and in vivo myocardial deletion of Rest and Dnmt3b uncovered that non-CpG methylation of the REST site by DNMT3B promoted REST binding to suppress Hcn2 transcription in the embryonic stage. Moreover, using an integrated approach of transcriptomic analysis, ChIP assay, and bisulfate sequencing, we showed that the same mechanism regulated the expression of ~30% REST targeted genes. The expression of these genes was developmentally upregulated as Hcn2. Together, our results suggest that non-CpG methylation at a subset of transcription factor binding sites may regulate cardiac gene program critical for heart development and its dysregulation may contribute to heart disease.

2017-02-13 | GSE80378 | GEO

REST-interactome - Interactomic analysis of REST/NRSF and implications of its functional links with the transcription suppressor TRIM28 during neuronal differentiation

Project description:Namgyu Lee has participated in the experimental part of this project and she is a co-first author of the under-going manuscript. RE-1 silencing transcription factor (REST) is a transcriptional repressor with a role in regulating gene expression through binding to repressor element 1. We identified REST/NRSF-interacting proteins by proteomics-based analyses using the complementary mass spectrometry approach. Our interactome revealed 204 REST-interacting proteins. Among those proteins, nuclear proteins were mostly enriched reflecting nuclear localization of REST. The interaction networks of interactome indicated biological processes associated with mRNA processing, chromatin organization and transcription. Interactions of ALYREF, HnRNP M, HnRNP Q, NPM1, NCL, PARP1, HDAC5, TRIM28 and HMGA1 with REST were confirmed by co-immunoprecipitation. Using public microarray dataset, a highly significant overlaps were observed in differentially expressed transcripts following knockdown of REST and interacting proteins such as HDAC5, HMGA1 and TRIM28, suggesting that the REST might cross-talk with those transcription regulators to regulate transcription of shared target genes. Our interactomic study of REST implies novel cross-talks with transcription regulators by its associations with interacting proteins.

2018-10-25 | PXD003210 | Pride

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