Regulation of Cellular Dynamics and Chromosomal Binding Site Preference of Linker Histones H1.0 and H1.X

Abstract

Linker histones play important roles in the genomic organization of mammalian cells. Of the linker histone variants, H1.X shows the most dynamic behavior in the nucleus. Recent research has suggested that the linker histone variants H1.X and H1.0 have different chromosomal binding site preferences. However, it remains unclear how the dynamics and binding site preferences of linker histones are determined. Here, we biochemically demonstrated that the DNA/nucleosome and histone chaperone binding activities of H1.X are significantly lower than those of other linker histones. This explains why H1.X moves more rapidly than other linker histones in vivo. Domain swapping between H1.0 and H1.X suggests that the globular domain (GD) and C-terminal domain (CTD) of H1.X independently contribute to the dynamic behavior of H1.X. Our results also suggest that the N-terminal domain (NTD), GD, and CTD cooperatively determine the preferential binding sites, and the contribution of each domain for this determination is different depending on the target genes. We also found that linker histones accumulate in the nucleoli when the nucleosome binding activities of the GDs are weak. Our results contribute to understanding the molecular mechanisms of dynamic behaviors, binding site selection, and localization of linker histones. Histones, including linker histones, are highly basic proteins that randomly bind to DNA. To maintain genomic integrity, DNA binding of histones should be strictly controlled. It has been established that random DNA binding of histones abrogates the sequential nucleosome assembly process (1). Histone chaperones directly bind to histones and transfer them to DNA to assemble the chromatin structure. In addition, histone chaperones have been suggested to play an important role in inhibiting the unfavorable DNA binding of histones (1). Our previous studies identified template activating factor I (TAF-I), nucleosome assembly protein 1 (NAP1), and nucleophosmin/B23 as factors involved in regulating the transcription and replication of adenovirus chromatin (2, 3). Recently, all three proteins, TAF-I, NAP1, and B23, were found to function as linker histone chaperones (4-7). A nucleolar protein, nucleolin (NCL), and prothymosin ␣ (ProT␣) were shown to regulate linker histone-chromatin binding (8-10).Linker histones are comprised of three regions: the N-terminal domain (NTD), central globular domain (GD), and C-terminal domain (CTD). The GDs of about 80 amino acids are able to reside on the DNA entry and exit sites of a nucleosome (11). Recent structural analysis of the GD of chicken linker histone H5 demonstrated that the GD makes contact with two extended DNA strands from the nucleosome and the nucleosome dyad (12). The CTD of linker histones are generally basic and rich in lysines, alanines, and prolines. The CTD plays a critical role in the condensation of DNA through its random DNA binding activity (13,14). The GD and CTD show distinct DNA binding activity (15), but neither is sufficient to stably associate with nu...

Temporally and Spatially Regulated Expression of the Linker Histone H1fx During Mouse Development

“…The H1fx protein is localized at the coding regions, the RNA polymerase II-enriched regions and the hypomethylated CpG islands in the genome, 28,29 and it shows significantly lower binding affinity to DNA/nucleosome and histone chaperones compared with H1f0. 31 These characteristics suggest that H1fx is involved in the regulation of transcriptional processes of significant transcription factors governing embryogenesis. Although we indeed observed the nuclear localization of H1fx ( Fig.…”

“…28,29 Furthermore, H1fx possesses significantly lower binding affinity to DNA/nucleosome and histone chaperone, which causes its rapid translocation to regulate differential gene expression and chromatin remodeling. 30,31 Although previous in vitro studies suggested that H1fx played important roles in the transcriptional regulation, in vivo examinations will be needed to clarify its physiological function. In the present study, therefore, we sought to determine the expression patterns of H1fx to properly characterize this protein.…”

Assembly and remodeling of viral DNA and RNA replicons regulated by cellular molecular chaperones

“…Biochemical analysis has also revealed that TAF-I maintains proper chromatosome formation through the deposition of histone H1 onto nucleosome core particles (NCPs) and by excluding an excess amount of histone H1 from NCPs (Fig. 2b) (Kato et al 2011;Okuwaki et al 2016). Fluorescence recovery after photobleaching (FRAP) analyses of linker histone H1.1 suggested that TAF-I is involved in the dynamic exchange of histone H1.1 on chromatin in vivo (Kato et al 2011).…”

Histone H1 chaperone activity of TAF‐I is regulated by its subtype‐dependent intramolecular interaction

“…TAF-I remodels the Ad core structure via interaction with viral core protein VII, and we have also previously shown that TAF-I has a core histone chaperone activity (Kawase et al 1996;Haruki et al 2003). TAF-I has a dual nature and can either promote chromatosome formation by deposition of histone H1 on nucleosome core particle (NCP) or cause chromatosome disassembly by eviction of histone H1 from NCP in vitro (Okuwaki et al 2016). TAF-I has a dual nature and can either promote chromatosome formation by deposition of histone H1 on nucleosome core particle (NCP) or cause chromatosome disassembly by eviction of histone H1 from NCP in vitro (Okuwaki et al 2016).…”

“…Additionally, we have reported that TAF-I functions as a histone chaperone by regulating the chromatin-binding activity of linker histone H1 in vitro and in vivo (Kato et al 2011). TAF-I has a dual nature and can either promote chromatosome formation by deposition of histone H1 on nucleosome core particle (NCP) or cause chromatosome disassembly by eviction of histone H1 from NCP in vitro (Okuwaki et al 2016). Additionally, TAF-I can dissociate histone H1 from nonspecific H1-DNA aggregates (Kato et al 2011).…”