Comment[ArrayExpressAccession] E-GEOD-40886 MAGE-TAB Version 1.1 Public Release Date 2013-06-15 Investigation Title The genomic landscape of the somatic linker histone subtypes H1.1 to H1.5 in human cells Comment[Submitted Name] The genomic landscape of the somatic linker histone subtypes H1.1 to H1.5 in human cells Experiment 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. Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Kamieniarz Schneider Izzo Kamieniarz-Gdula Person First Name Kinga Robert Annalisa Kinga Person Email geo@ncbi.nlm.nih.gov Person Affiliation Max-Planck Institute of Immunobiology and Epigenetics Person Address Max-Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, Freiburg, Germany Person Roles submitter Protocol Name P-GSE40886-2 P-GSE40886-1 P-GSE40886-6 P-GSE40886-7 P-GSE40886-3 P-GSE40886-4 P-GSE40886-5 P-GSE40886-8 Protocol Description Raw data from each array (2 channels) were loess normalized and median centered. All arrays where then quantile normalized together and the arrays (not dye-swaps) were averaged. Software: R/Bioconductor. ID_REF = VALUE = Normalized log2 ratio (experimental/reference) averaged from 2 biological replicates Raw data from each array (2 channels) were loess normalized and median centered. All arrays where then quantile normalized together and the dye-swap arrays were averaged. Software: R/Bioconductor. ID_REF = VALUE = Normalized log2 ratio (experimental/reference) averaged from 2 biological replicates 1 µg purified methyl-PCR DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy dye-coupled nonamers (Trilink Biotech) according to NimbleGen Sample Labeling protocol in NimbleGen Array User's Guide, v4.1 (http://www.nimblegen.com/products/lit/lit.html). 13 µg labeled DNA per, 2.4 µl alignment oligo and 24 µl NimbleGen hybridiziation component A and 1x hybridization buffer in a total volume of 120 µl were heated to 98°C for 5 min and hybridized in a TECAN hybridization station for 16 hrs. at 42°C. Slides were washed sequentially with NimbleGen wash buffers I, II and III with 0.1 mM DTT at 42°C, 25°C, and 23°C, respectively. IMR90 cells were transducted with the lentiviruses and harvested after 2 days. IMR90 cells (Coriell) were cultured in DMEM medium (Invitrogen) supplemeted with 15% of FCS (Sigma), non-essential amino-acids (Sigma) and antibiotics. Genomic DNA was extracted following the manufacture instructions (Dneasy Blood & Tissue, Qiagen) Microarrays were scanned in a DNA Microarray Scanner (Model G2505B, Serial number US22502518) from Agilent Technologies, which uses Scan Control software (Version A.6.11). Slides were first placed in a slide holder before putting it in the Scanner Carousel, which was installed in the scanner. Slides were scanned at multiple PMT (100/70/30/10%) for each channel at 5 um resolution using a suitable scan area. Protocol Type normalization data transformation protocol normalization data transformation protocol labelling protocol hybridization protocol sample treatment protocol growth protocol nucleic acid extraction protocol array scanning protocol Experimental Factor Name SAMPLE TYPE Experimental Factor Type sample type Publication Title The Genomic Landscape of the Somatic Linker Histone Subtypes H1.1 to H1.5 in Human Cells. Publication Author List Izzo A, Kamieniarz-Gdula K, Ram�rez F, Noureen N, Kind J, Manke T, van Steensel B, Schneider R PubMed ID 23746450 Publication DOI 10.1016/j.celrep.2013.05.003 Comment[SecondaryAccession] GSE40886 Comment[GEOReleaseDate] 2013-06-15 Comment[ArrayExpressSubmissionDate] 2012-09-14 Comment[GEOLastUpdateDate] 2013-06-15 Comment[AEExperimentType] ChIP-chip by tiling array SDRF File E-GEOD-40886.sdrf.txt