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A comparison of the rest complex binding patterns in embryonic stem cells and epiblast stem cells
- Source :
- PLoS ONE, Vol 9, Iss 4, p e95374 (2014), PLoS ONE
- Publication Year :
- 2014
- Publisher :
- Public Library of Science (PLoS), 2014.
-
Abstract
- We detected and characterized the binding sites of the representative Rest complex components Rest, Sin3A, and Lsd1. We compared their binding patterns in mouse embryonic stem (ES) cells and epiblast stem (EpiS) cells. We found few Rest sites unique to the EpiS cells. The ES-unique site features were distinct from those of the common sites, namely, the signal intensities were weaker, and the characteristic gene function categories differed. Our analyses showed that the Rest binding sites do not always overlap with the Sin3A and Lsd1 binding sites. The Sin3A binding pattern differed remarkably between the ES and EpiS cells and was accompanied by significant changes in acetylated-histone patterns in the surrounding regions. A series of transcriptome analyses in the same cell types unexpectedly showed that the putative target gene transcript levels were not dramatically different despite dynamic changes in the Rest complex binding patterns and chromatin statuses, which suggests that Rest is not the sole determinant of repression at its targets. Nevertheless, we identified putative Rest targets with explicitly enhanced transcription upon Rest knock-down in 143 and 60 common and ES-unique Rest target genes, respectively. Among such sites, several genes are involved in ES cell proliferation. In addition, we also found that long, intergenic non-coding RNAs were apparent Rest targets and shared similar features with the protein-coding target genes. Interestingly, such non-coding target genes showed less conservation through evolution than protein-coding targets. As a result of differences in the components and targets of the Rest complex, its functional roles may differ in ES and EpiS cells.
- Subjects :
- Epigenomics
Cell type
Chromatin Immunoprecipitation
Transcription, Genetic
lcsh:Medicine
Biology
Transcriptome
Mice
Animal Cells
Molecular Cell Biology
Genetics
Animals
Binding site
lcsh:Science
Gene
Embryonic Stem Cells
Histone Demethylases
Multidisciplinary
Binding Sites
Stem Cells
lcsh:R
Biology and Life Sciences
Computational Biology
Oxidoreductases, N-Demethylating
Cell Biology
Genomics
Genome Analysis
Embryonic stem cell
Chromatin
Repressor Proteins
Sin3 Histone Deacetylase and Corepressor Complex
Gene Knockdown Techniques
Epigenetics
RNA, Long Noncoding
lcsh:Q
Stem cell
Cellular Types
Chromatin immunoprecipitation
Transcriptome Analysis
Germ Layers
Research Article
Developmental Biology
Protein Binding
Subjects
Details
- Language :
- English
- ISSN :
- 19326203
- Volume :
- 9
- Issue :
- 4
- Database :
- OpenAIRE
- Journal :
- PLoS ONE
- Accession number :
- edsair.doi.dedup.....765963c70833e305be4683bfb9dc2092