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Series GSE46134 Query DataSets for GSE46134
Status Public on Apr 29, 2013
Title High Resolution Mapping of H1 Linker Histone Variants in Embryonic Stem Cells
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary H1 linker histones facilitate higher order chromatin folding and are essential for mammalian development. To achieve high resolution mapping of H1 variants H1d and H1c in embryonic stem cells (ESCs), we have established a knock-in system and shown that the N-terminally tagged H1 proteins are functionally interchangeable to their endogenous counterparts in vivo. H1d and H1c are depleted from GC- and gene-rich regions and active promoters, inversely correlated with H3K4me3, but positively correlated with H3K9me3 and associated with characteristic sequence features. Surprisingly, both H1d and H1c are significantly enriched at major satellites, which display increased nucleosome spacing compared with bulk chromatin. While also depleted at active promoters and enriched at major satellites, overexpressed H10 displays differential binding patterns in specific repetitive sequences compared with H1d and H1c. Depletion of H1c, H1d and H1e causes pericentric chromocenter clustering and de-repression of major satellites. These results integrate the localization of an understudied type of chromatin proteins, namely the H1 variants, into the epigenome map of mouse ESCs, and we identify significant changes at pericentric heterochromatin upon depletion of this epigenetic mark.
Overall design Mapping linker histone H1 variants H1d, H1c and H10 as well as 3 core histone modifications in mouse ESC genome.
Contributor(s) Cao K, Lailler N, Dong X, Bouhassira EE, Fan Y
Citation(s) 23633960
Submission date Apr 17, 2013
Last update date May 15, 2019
Contact name Yuhong Fan
Organization name Georgia Institute of Technology
Department School of Biology and the Petit Institute for Bioengineering and Bioscience
Street address IBB 2313, 315 Ferst Drive
City Atlanta
State/province Georgia
ZIP/Postal code 30332
Country USA
Platforms (2)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (18)
GSM1124777 Input-a
GSM1124778 H3K4me3-1
GSM1124779 H3K4me3-2
BioProject PRJNA197331
SRA SRP021132

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Supplementary file Size Download File type/resource
GSE46134_RAW.tar 3.1 Gb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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