REST ChIP-seq in human and mouse hippocampus
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ABSTRACT:
PROVIDER: PRJNA603079 | ENA |
REPOSITORIES: ENA
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Project description:The transcriptional repressor REST (RE1 Silencing Transcription Factor) is a master regulator of thousands of neuronal genes that together impart the terminally differentiated neuronal phenotype. Because of this unique feature, REST has been, and continues to be, a widely used model for understanding neurogenesis and neuronal cell function. These studies have focused primarily on murine embryonic development, but recent studies have pointed to distinct postnatal roles for REST in stroke, epilepsy, aging and cognitive decline. The function of REST in healthy human brain tissue, however, still remains poorly characterized. Here, we present deep sequencing chromatin immunoprecipitation evidence for divergent REST function in normal mouse and human postmortem adult hippocampus. In mouse, REST occupies only 221 peaks that are divided between prototypical REST target genes shared with non-neuronal cells, as well as peaks unique to the hippocampus. Surprisingly, the mouse hippocampal-unique sites are not conserved in human, which contains 1886 REST peaks unique to the hippocampus. Further, the REST peaks unique to the hippocampus represent a potentially new category of target genes encoding proteins important in the immune response. Our results suggest the possibility that REST protects against aberrant immunological responses during normal human aging and that mouse may not model this aging function.
2020-07-24 | GSE144226 | GEO
Project description:Multiple protein complexes and histone marks have been implicated and/or associated with gene repression in ES cells. To gain insights into repressive complexes present at repressed genes and their associated chromatin state, we profiled REST, MCAF1, Ring1b and H4K20me3 in mouse ES cells. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. ChIP was performed using an antibody against REST, MCAF1, Ring1b and H4K20me3.
2011-01-19 | E-GEOD-26680 | biostudies-arrayexpress
Project description:In this experiment, we exposed mice to ethanol injections on postnatal days 4 and 7. We then extracted whole-hippocampus on postnatal day 70. We performed MeDIP-chip using an antibody against 5mC. We also perfomed MEDME anaylsis using a chip with fully methylated DNA to act as a control. We found alterations in both modifications at many sites, including oxidative stress genes and imprinted loci. We also found many affect lipid metabolism pathways. Comparision of neonatal ethanol-injected with saline injected C57BL/6J mouse hippocampus in adulthood (day 70)
2015-07-25 | E-GEOD-71313 | biostudies-arrayexpress
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
Project description:To gain a deeper insight into roles of Arid1a in mice hippocampus development, we performed ChIP-seq and RNA-seq to analyze the genome-wide changes of histone marks and transcriptome changes before and after Arid1a deletion in hippocampus of the E16.5 and P21 mouse using Cre-lox system.
2021-12-31 | GSE169562 | GEO
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
Project description:Multiple protein complexes and histone marks have been implicated and/or associated with gene repression in ES cells. To gain insights into repressive complexes present at repressed genes and their associated chromatin state, we profiled REST, MCAF1, Ring1b and H4K20me3 in mouse ES cells.
2011-01-19 | GSE26680 | GEO
Project description:Kif5C associated RNAs from mouse hippocampus
| PRJNA625255 | ENA
Project description:We performed ChIP-seq to identify genome-wide REST (NRSF) binding in the human CD4+ T cells. The data were compared to REST occupancy in additional 15 human cell types analyzed by the ENCODE project (GSE32465) in order to study the dynamics and context-dependent functions of REST-chromatin interaction.
2014-08-06 | GSE49570 | GEO
Project description:We performed ChIP-seq to identify genome-wide REST (NRSF) binding in the human CD4+ T cells. The data were compared to REST occupancy in additional 15 human cell types analyzed by the ENCODE project (GSE32465) in order to study the dynamics and context-dependent functions of REST-chromatin interaction. Identification of REST binding by ChIP-seq in human CD4+ T cells.
2014-08-06 | E-GEOD-49570 | biostudies-arrayexpress