The Genomic Landscape of the Somatic Linker Histone Subtypes H1.1 to H1.5 in Human Cells

• Published in: Cell reports (Cambridge) 2013-06, Vol.3 (6), p.2142-2154
• Main Authors: Izzo, Annalisa, Kamieniarz-Gdula, Kinga, Ramírez, Fidel, Noureen, Nighat, Kind, Jop, Manke, Thomas, van Steensel, Bas, Schneider, Robert
• Format: Article
• Language: English
• Subjects: Chromatin - chemistry; Chromatin - genetics; Chromatin - metabolism; DNA Methylation; Genomics - methods; Histones - chemistry; Histones - classification; Histones - genetics; Histones - metabolism; Humans; Protein Binding; Regulatory Sequences, Nucleic Acid
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2013.05.003

Human cells contain five canonical, replication-dependent somatic histone H1 subtypes (H1.1, H1.2, H1.3, H1.4, and H1.5). Although they are key chromatin components, the genomic distribution of the H1 subtypes is still unknown, and their role in chromatin processes has thus far remained elusive. Here, we map the genomic localization of all somatic replication-dependent H1 subtypes in human lung fibroblasts using an integrative DNA adenine methyltransferase identification (DamID) analysis. We find in general that H1.2 to H1.5 are depleted from CpG-dense regions and active regulatory regions. H1.1 shows a DamID binding profile distinct from the other subtypes, suggesting a unique function. H1 subtypes can mark specific domains and repressive regions, pointing toward a role for H1 in three-dimensional genome organization. Our work integrates H1 subtypes into the epigenome maps of human cells and provides a valuable resource to refine our understanding of the significance of H1 and its heterogeneity in the control of genome function. [Display omitted] •Mapping of the genomic distribution of all somatic H1 replication-dependent subtypes•Regulatory regions associated with active transcription are depleted of H1•H1 binding at CG-rich regions depends on their position and DNA methylation•H1 subtypes mark distinct topological domains and lamina-associated domains Schneider and colleagues employed the DNA adenine methyltransferase identification technique to systematically map the genomic distribution of all replication-dependent somatic H1 subtypes in human lung fibroblasts, thereby integrating H1 into epigenomic maps. Their analysis reveals DNA and chromatin features that potentially regulate the recruitment of H1 subtypes to chromatin, and suggests a possible role of somatic H1 subtypes in the three-dimensional organization of the genome within the cell nucleus.