Reduction of Hox gene expression by histone H1 depletion

• Published in: PloS one 2012-06, Vol.7 (6), p.e38829-e38829
• Main Authors: Zhang, Yunzhe, Liu, Zheng, Medrzycki, Magdalena, Cao, Kaixiang, Fan, Yuhong
• Format: Article
• Language: English
• Subjects: Analysis; Animals; Bioengineering; Biology; Biomarkers - metabolism; Body Patterning - genetics; Body Patterning - physiology; Chromatin; Chromatin Assembly and Disassembly - genetics; Chromatin Assembly and Disassembly - physiology; Chromatin Immunoprecipitation; Chromatography, High Pressure Liquid; Clonal deletion; Deoxyribonucleic acid; Depletion; DNA; DNA methylation; Embryo cells; Embryogenesis; Embryoid Bodies - metabolism; Embryonic development; Embryonic growth stage; Embryonic stem cells; Embryonic Stem Cells - metabolism; Embryos; Folding; Gene expression; Gene Expression Regulation, Developmental - physiology; Gene loci; Gene regulation; Genes; Genes, Homeobox - physiology; Genomes; Histone H1; Histones; Histones - deficiency; HOX gene; Immunoglobulins; Karyotyping; Lethality; Mammals; Mice; Mice, Knockout; Pattern formation; Polymerase chain reaction; Real-Time Polymerase Chain Reaction; Reduction; Reverse Transcriptase Polymerase Chain Reaction; Stem cell transplantation; Stem cells; Trends
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0038829

The evolutionarily conserved homeotic (Hox) genes are organized in clusters and expressed collinearly to specify body patterning during embryonic development. Chromatin reorganization and decompaction are intimately connected with Hox gene activation. Linker histone H1 plays a key role in facilitating folding of higher order chromatin structure. Previous studies have shown that deletion of three somatic H1 subtypes together leads to embryonic lethality and that H1c/H1d/H1e triple knockout (TKO) embryonic stem cells (ESCs) display bulk chromatin decompaction. To investigate the potential role of H1 and higher order chromatin folding in the regulation of Hox gene expression, we systematically analyzed the expression of all 39 Hox genes in triple H1 null mouse embryos and ESCs by quantitative RT-PCR. Surprisingly, we find that H1 depletion causes significant reduction in the expression of a broad range of Hox genes in embryos and ESCs. To examine if any of the three H1 subtypes (H1c, H1d and H1e) is responsible for decreased expression of Hox gene in triple-H1 null ESCs, we derived and characterized H1c(-/-), H1d(-/-), and H1e(-/-) single-H1 null ESCs. We show that deletion of individual H1 subtypes results in down-regulation of specific Hox genes in ESCs. Finally we demonstrate that, in triple-H1- and single-H1-null ESCs, the levels of H3K4 trimethylation (H3K4me3) and H3K27 trimethylation (H3K27me3) were affected at specific Hox genes with decreased expression. Our data demonstrate that marked reduction in total H1 levels causes significant reduction in both expression and the level of active histone mark H3K4me3 at many Hox genes and that individual H1 subtypes may also contribute to the regulation of specific Hox gene expression. We suggest possible mechanisms for such an unexpected role of histone H1 in Hox gene regulation.