Linker histones chromatin

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)...

Hizume K, Yoshimura SH, Maruyama H, Kim J, Wada H, Takeyasu K (2002) Chromatin reconstitution development of a salt-dialysis method monitored by nano-technology. Arch Histol Cytol 65 405 13 Hizume K, Yoshimura SH, Takeyasu K (2004) Atomic force microscopy demonstrates a critical role of DNA superhelicity in nucleosome dynamics. Cell Biochem Biophys 40 249—262 Hizume K, Yoshimura SH, Takeyasu K (2005) Linker histone HI per se can induce three-dimensional folding of chromatin fiber. Biochemistry 44 12978-12989 Hofmann WA, de Lanerolle P (2006) Nuclear actin to polymerize or not to polymerize. J Cell Biol 172 495-496... 

Shen X, Yu L, Weir JW, Gorovsky MA (1995) Linker histones are not essential and affect chromatin condensation in vivo. Cell 82 47—56... 

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 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. 

Drabent B, Saftig P, Bode C, Doenecke D (2000) Spermatogenesis proceeds normally in mice widiout linker histone Hit. Histochem Cell Biol 113 433-442 Drabent B, Benavente R, Hoyer-Fender S (2003) Histone Hit is not replaced by Hl.l or H1.2 in pachytene spermatocytes or spermatids of Hit-deficient mice. Cytogenet Genome Res 103 307—313 Ehrenhofer-Murray AE (2004) Chromatin dynamics at DNA replication, transcription and repair. Eur J Biochem 271 2335-2349... 

Jin J, Cai Y, Li B, Conaway RC, Workman JL, Conaway JW, Kusch T (2005) In and out histone variant exchange in chromatin. Trends Biochem Sci 30 680-687 Khochbin S (2001) Histone HI diversity bridging regulatory signals to linker histone function. Gene 271 1-12... 

Woodcock CL, Skoultchi AI, Fan Y (2006) Role of linker histone in chromatin structure and function HI stoichiometry and nucleosome repeat length. Chromosome Res 14 17-25 Wu WH, Alami S, Luk E, Wu CH, Sen S, Mizuguchi G, Wei D, Wu C (2005) Swc2 is a widely conserved H2AZ-binding module essential for ATP-dependent histone exchange. Nat Struct Mol Biol 12 1064-1071... 

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... 

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... 

The nucleosome is the fundamental repeating structural unit of chromatin. It is composed of two molecules of the core histones H2A, H2B, H3, H4, approximately two superhelical turns of double-stranded DNA, and linker histone HI (H5). In addition to biochemical studies, the existence of the nucleosome was established in electron micrographs (Fig. la) [1,2], and the name nucleosome, coined to incorporate the concept of the spherical nu-bodies [3]. Micrococcal nuclease limit digestion of chromatin established the nucleosome core particle (NCP) as the portion of the nucleosome containing only the core histones surrounded by 1.75 superhelical turns of double-stranded DNA [4,5]. 

These results raise the prospect of dynamics of nucleosomes in linker histone-free chromatin, that is, of a thermal fluctuation of nucleosomes between closed negative , open , and closed positive states identified in the minicircle system. If this equilibrium exists, an extra supercoiling constraint applied to the fiber should displace it in one direction or the other depending on the sign of that constraint, and this displacement should be reversible upon its removal. 

Topology and dynamics of linker histone-containing nucleosomes in chromatin... 

Bednar, J., Horowitz, R.A., Grigoryev, S.A., Carruthers, L.M., Hansen, J.C., Koster, A.J., and Woodcock, C.L. (1998) Nucleosomes, linker DNA, and linker histone form a unique structural motif that directs the higher-order folding and compaction of chromatin. Proc. Natl. Acad. Sci. USA 95, 14173-14178. 

Carruthers, L.M. and Hansen, J.C. (2000) The core histone N termini function independently of linker histones during chromatin condensation. J. Biol. Chem. 275, 37285-37290. 

The proteins known today as linker or HI histones were initially described as the abundant lysine-rich nuclear proteins that could be separated by chromatography on ion exchange resin from other major basic nuclear proteins known today as core histones (for review see Refs. [1,2]). During gel electrophoresis of histones the HI fraction migrated as the slowest and most heterogeneous band. Upon the discovery of nucleosomal organization of chromatin in the mid 1970s it turned out that linker histones are not involved in the assembly of the nucleosomal protein core, but bind to DNA between nucleosomes (hence their name). 

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