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Title: Large organized chromatin K9-modifications (LOCKs) distinguish differentiated from embryonic stem cells      
availability:
available
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instance of dataset
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not applicable
refinement:
curated
dateReleased:
05-01-2014
ID:
E-GEOD-13445
description:
Higher eukaryotes must adapt a totipotent genome to specialized cell types with a stable but limited repertoire of functions. One potential mechanism for lineage restriction is changes in chromatin, and differentiation-related chromatin changes have been observed for individual genes. We have taken a genome-wide view of histone H3 lysine-9 dimethylation (H3K9Me2). We find that differentiated tissues exhibit surprisingly large K9-modified regions (up to 4.9 Mb), that are highly conserved between human and mouse, and differentiation-specific, covering only ~4% of the genome in undifferentiated mouse embryonic stem (ES) cells, compared to 31% in differentiated ES cells, ~46% in liver and ~10% in brain. They require histone methyltransferase G9a, and are inversely related to expression of genes within them, and we term them Large Organized Chromatin K9-modifications (LOCKs). LOCKs are are substantially lost in cancer cell lines, and they may provide a cell type-heritable mechanism for phenotypic plasticity in development and disease. Chromatin was isolated without sonication or formalin cross linking, by digested with micrococcal nuclease, and then chromatin immunoprecipitation was performed with an antibody specific to H3K9Me2. ChIP and input DNA were amplified, labeled by Cy5 and Cy3 respectively, and hybridized to NimbleGen tilling arrays.
keywords:
ChIP-chip by tiling array
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storedIn:
Array Express
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true
accessURL: https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-13445
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JSON
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OmicsDI
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accessType:
download
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accessURL: www.omicsdi.org/ws/dataset/arrayexpress-repository/E-GEOD-13445.json
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XML
storedIn:
OmicsDI
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not compressed
accessType:
download
authorization:
none
authentication:
none
primary:
false
accessURL: http://www.omicsdi.org/ws/dataset/arrayexpress-repository/E-GEOD-13445.xml
ID:
SCR:014747
name:
Omics Discovery Index
abbreviation:
OmicsDI
homePage: http://www.omicsdi.org/