Histone linker

Chromatin is composed of nucleosomes, where each comprise 147 base pairs of DNA wrapped around an octamer oftwo copies of each histone H2A, H2B, H3, and H4. Nucleosomes are folded into higher-order structures that are stabilized by linker histones. Chromatin structure can be altered by enzymes that posttranslationally modify histones (e.g., through phosphorylation, acetylation, methylation, or ubiquitination) or by ATP-driven chromatin-remodeling complexes that alter nucleosome position and/or composition. 

Histones are small, basic proteins required to condense DNA into chromatin. They have been first described and named in 1884 by Albrecht Kossel. There are five main histones HI, H2A, H2B, H3 andH4. An octamer of core histones H2A, H2B, H3 andH4 is located inside a nucleosome, the central building block of chromatin, with about 150 base pairs of DNA wrapped around. The basic nature of histones, mediated by the high content of lysine and arginine residues, allows a direct interaction with the acidic phosphate back bone of DNA. The fifth histone HI is located outside at the junction between nucleosomes and is referred to as the linker histone. Besides the main histones, so-called histone variants are known, which replace core histones in certain locations like centromers. 

Figure 1. Hierarchical model of chromosome structure, (a) In interphase cells, DNA is packed in a nucleus as forming nucleosome and chromatin, (b) DNA forms nucleosome structure together with core histone octamer, which is then folded up into 30nm fiber with a help of linker histone HI. This 30 nm fiber is further folded into 80 nm fiber and 300 nm loop structures in a nucleus. In mitosis, chromosome is highly condensed. Proteins which are involved in each folding step are indicated above and non-protein factors are indicated below, (c) The amino acid sequences of histone tails (H2A, H2B, H3 and H4) are shown to indicate acetylation, methylation and phosphorylation sites. (See Colour Plate 1.)...

Linker histones (HI, H5 and others) are also major components of metaphase chromosome, and occupy 5.8% of the total protein amount (Uchiyama et al, 2005). They play an important role in the formation of the 30 nm fiber (see also section 2.3). These linker histones carry more lysine residues ( 30% of the total amino acids) than the core histones and have a core domain in the middle part that binds to a nucleosome. The linker histones could be easily extracted from the chromatin with 0.5 M NaCl, whereas the core histone octamers need more than 0.8 M NaCl to dissociate from nucleosomes. 

Biochemical reconstitution of the 30 nm fiber has recently been succeeded by using a salt-dialysis procedure with a long DNA template (>100 kb) (Hizume et al, 2005). AFM imaging of the reconstituted chromatin has shown that the beads-on-a-string structure of the nucleosomes ( 400 nucleosomes on 100 kb DNA) are converted to a thicker fiber in the presence of histone HI. The thickness of the fiber changes reversibly between 20 nm and 30 nm, depending on the salt environment (in 50 mM and 100 mM NaCl, respectively) (Fig. 4) namely, the linker histone directly promotes a thicker fiber formation in a salt-dependent manner. 

Figure 4. In vitro reconstituted 30 nm chromatin fiber. Dynamic structural changes in the chromatin fiber in the absence (top) or presence (bottom) of linker histone HI with different NaCl concentration were observed by AFM. Nucleosomes were reconstituted on the 106 kb plasmid and then fixed in the buffer containing 50 mM (top left) or 100 mM NaCl (top right). Nucleosomes were well-spread in 50 mM NaCl but attached each other and partially aggregated in 100 mM NaCl. After the addition of histone HI, the thicker fibers were formed. The width of the fibers is 20nm in 50mM NaCl (bottom left) or 30 nm in lOOmM NaCl (bottom right)...

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Gagne et al, 2003). Some non-sequence-specific DNA-binding proteins, such as the linker histone HI, may even have a greater affinity for PAR than DNA (Malanga et al., 1998). Thus, an understanding of PAR is an important aspect of understanding the biology of PARP-1 and other PARPs. 

The genetic information of eukaryotic cells is propagated in the form of chromosomal DNA. Besides the nucleic acid component, chromosomes contain architectural proteins as stoichiometric components, which are involved in the protective compaction of the fragile DNA double strands. Together, the DNA and proteins form a nucleoprotein structure called chromatin. The fundamental repeating unit of chromatin is the nucleosome core particle. It consists of about 147 base pairs of DNA wrapped around a histone octamer of a (H3/H4)2 tetramer and two (H2A-H2B) heterodimers. One molecule of the linker histone HI (or H5) binds the linker DNA region between two nucleosome core particles (Bates and Thomas 1981). 

In the mid-pachytene stage of meiosis. Hit becomes preferentially enriched in testicular cells and contributes to up to 50% of the total chromosomal linker histones (Cole et al. 1986). The deletion of Hit has no effect on viability and fertility of mice (Drabent et al. 2000). It is not quite clear whether other HI variants are upregulated in pachytene spermatocytes of Hit-deficient animals and compensate for the loss of Hit (Drabent et al. 2003 Nayernia et al. 2005). Thus, very little is known about... 

Figure 3. Representative linker histone variants from human (Homo sapiens H.s.), and yeast (Saccha-romyces cerevisiae S.c.). The globular domain indicates the winged helix DNA binding domain that is common for all linker histones. Hlc is a typical somatic linker histone common for most cells. H° is expressed in all somatic cells, but is more abundant in terminally differentiated tissues. Hlfoo is an oocyte-specific linker histone. The structure of S. cerevisiae Hholp with two globular domains is a notable deviation...

In general, the differences in expression and structure of HI variants strongly suggests that variants of linker histones have important roles in chromatin architecture, and might be essential players in the epigenetic control of developmental gene expression. Future studies will be necessary to identify factors that target, modify, and mobilize different linker histones. 

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Kepert J.F Mazurkiewicz J, Heuvelman GL, Toth KF, Rippe K (2005) NAPl modulates binding of linker histone HI to chromatin and induces an extended chromatin fiber conformation. J. Biol. Chem 280 34063-34072... 

Richardson RT, Alekseev OM, Grossman G, Widgren EE, Thresher R, Wagner EJ, Sullivan KD, Marzluff WF, O rand MG (2006). NASP, a linker histone chaperone that is required for cell proliferation. J. Biol. Chem 281 21526-21534... 

Figure 1. Linker Histone HI CDK phosphorylation site in mammahan cells. (See Colour plate 17.)...

Herrera RE, Chen E, Weinberg RA (1996) Increased histone HI phosphorylation and relaxed chromatin structure in Rb-deficient fibroblasts. Proc Natl Acad Sci USA 93(21) 11510-11515 Hirota T, Lipp JJ, Toh BH, Peters JM (2005) Histone H3 serine 10 phosphorylation by Aurora B causes HPl dissociation from heterochromatin. Nature 438(7071) 1176—1180 Horn PJ, Carruthers LM, Logie C, Hill DA, Solomon MJ, Wade PA, Imbalzano AN, Hansen JC, Peterson CL (2002) Phosphorylation of linker histones regulates ATP-dependent chromatin remodeling enzymes. Nat Struct Biol 9(4) 263—267... 

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