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Series GSE26855 Query DataSets for GSE26855
Status Public on Sep 18, 2012
Title Gene expression profile of H1 human embryonic stem cells, IMR90 lung fibroblasts, calcium induced keratinocytes, and primary hepatocytes
Organism Homo sapiens
Experiment type Expression profiling by array
Summary In humans, there are eleven subtypes of linker histones that exhibit cell- and tissue-specific expression. Linker histone H1 proteins bind to both the core histones and linker DNA of chromatin fibers; and not only participate in control of gene activity but also serve to stabilize higher order chromatin structure. To determine the potential roles of linker histones in differentiation, we examined the global distribution of linker histone subtype H1.5 in human IMR90 fibroblasts and H1 embryonic stem cells (hESCs). Surprisingly, H1.5 binds to and represses a large fraction of gene family clusters in fully differentiated cell types representing all three embryonic germ layers. Little or no H1.5 enrichment at gene family clusters was detected in undifferentiated hESCs or partially differentiated somatic cells. We also found that SIRT1 histone deacetylase and H3K9me2, a repressive histone modification, are also enriched at gene family cluster in IMR90 cells, likely generating a stably repressive chromatin domain. To find out the mechanism of H1.5 targeting, H1.5 or SIRT1 was depleted in IMR90 cells by siRNA, and the binding patterns of SIRT1 and H1.5 were examined. In H1.5 knockdown cells, SIRT1 binding pattern was changed dramatically, and this changed pattern highly correlates to SIRT1 distribution in hESC. However, depletion of SIRT1 could not change the global binding pattern of H1.5. Depletion of H1.5 or SIRT1 leads to up-regulation of ~50% gene family clusters. However, the sets of gene family clusters that are affected by these two factors are different, suggesting H1.5 and SIRT1 may regulate gene transcription via different pathways.
Overall design One-color array. Two replicates for each sample.
Contributor(s) Li J, Patterson M, Mikkola HK, Lowry WE, Kurdistani SK
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Submission date Jan 25, 2011
Last update date Feb 22, 2018
Contact name Jing-Yu Li
Organization name University of California, Los Angeles
Street address 615 Charles E. Young Dr. South BSRB 357
City Los Angeles
ZIP/Postal code 90095
Country USA
Platforms (1)
GPL4133 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Feature Number version)
Samples (8)
GSM661186 H1_rep1
GSM661187 H1_rep2
GSM661188 IMR90_rep1
This SubSeries is part of SuperSeries:
GSE26979 Human Linker Histone H1.5
BioProject PRJNA142003

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
GSE26855_RAW.tar 77.2 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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