E-GEOD-40886 - The genomic landscape of the somatic linker histone subtypes H1.1 to H1.5 in human cells

Status
Released on 15 June 2013, last updated on 2 June 2014
Organism
Homo sapiens
Samples (10)
Array (1)
Protocols (8)
Description
We employed the DamID technique to systematically map the genomic distribution of all canonical somatic H1 subtypes (H1.1-H1.5) in human IMR90 cells. Human cells contain up to eleven histone H1 proteins, with different spatial and temporal expression patterns. These include five canonical, replication-dependent somatic H1 subtypes (H1.1, H1.2, H1.3, H1.4 and H1.5). Despite being a key chromatin component, the genomic distribution of the somatic canonical H1 subtypes is still unknown and their role in chromatin related processes has so far remained elusive. Here we employed a DamID approach to map for the first time the genomic localization of all somatic canonical H1 subtypes in human cells. Our integrative analysis reveals novel insights into H1 subtype distribution and uncovers functional chromatin features potentially regulating the H1 genomic landscape. In general H1.2 to H1.5 are depleted from GC-rich regions and regulatory regions associated with active transcription. H1.1 shows a binding profile distinct from the other subtypes, suggesting a unique function for H1.1 in chromatin-regulated processes. Interestingly, our data indicate a novel role for somatic H1 subtypes in the three-dimensional organization of the genome by marking repressive regions within topological domains such as LADs. Our work integrates the five somatic linker histone H1 subtypes into the epigenome maps of human cells and provides a resource to refine our understanding of the significance of H1 and its heterogeneity in the control of genome function. DamID profiling of somatic linker histone variants H1.1, H1.2, H1.3, H1.4 and H1.5 in human fibroblasts. Two biological replicate samples of all H1 variants were hybridized on NimbleGen Human ChIP-chip 2.1M Economy Whole-Genome Tiling - Array GPL16055 covering small human chromosomes.
Experiment type
ChIP-chip by tiling array 
Contacts
Kinga Kamieniarz <geo@ncbi.nlm.nih.gov>, Annalisa Izzo, Kinga Kamieniarz-Gdula, Robert Schneider
Citation
The Genomic Landscape of the Somatic Linker Histone Subtypes H1.1 to H1.5 in Human Cells. Izzo A, Kamieniarz-Gdula K, Ram�rez F, Noureen N, Kind J, Manke T, van Steensel B, Schneider R. , Europe PMC 23746450
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