- Email: [email protected]
Current progress on structural studies of nucleosomes containing histone H3 variants
Available online at www.sciencedirect.com
Current progress on structural studies of nucleosomes containing histone H3 variants Hitoshi Kurumizaka1, Naoki Horikoshi1, Hiroaki Tachiwana1,* and Wataru Kagawa2 The nucleosome is the basic repeating unit of chromatin. During the nucleosome assembly process, DNA is wrapped around two H3–H4 dimers, followed by the inclusion of two H2A–H2B dimers. The H3–H4 dimers provide the fundamental architecture of the nucleosome. Many non-allelic variants have been found for H3, but not for H4, suggesting that the functions of chromatin domains may, at least in part, be dictated by the specific H3 variant that is incorporated. A prominent example is the centromeric H3 variant, CENP-A, which specifies the function of centromeres in chromosomes. In this review, we survey the current progress in the studies of nucleosomes containing H3 variants, and discuss their implications for the architecture and dynamics of chromatin domains. Addresses 1 Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan 2 Program in Chemistry and Life Science, Department of Interdisciplinary Science and Engineering, School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino-shi, Tokyo 191-8506, Japan Corresponding author: Kurumizaka, Hitoshi ([email protected]) *
Present address: Institut Curie, Centre de Recherche, Paris F-75248, France.
Current Opinion in Structural Biology 2013, 23:109–115 This review comes from a themed issue on Protein-nucleic acid interactions Edited by Kyoshi Nagai and Song Tan
are separated by short linker DNA segments, and cover almost the entire chromosome. Thus, the nucleosome array can have a ‘beads on a string’ appearance, which folds into a higher-order structure (Figure 1). The higherorder chromatin structure not only functions to statically package the huge genomic DNA within the nucleus, but also to dynamically regulate DNA transcription, replication, recombination, and repair [1–4]. Nucleosomes containing various histone modifications and/or histone variants are considered to play important roles in the functional dynamics of chromatin [5–7]. Non-allelic isoforms exist for all histones, except for H4. The amino acid sequence differences between these isoforms and the canonical histones range from one to a few dozen, in addition to the presence of extra domains [6–9]. These non-allelic histones are defined as histone variants. The histone variants may be correctly incorporated with proper timing into specific locations of chromatin by assembly systems with their particular histone chaperones. Biochemical and cell biological studies have suggested that each histone variant plays an important role in the formation of the functional chromatin domain architecture. Perhaps the best-known example is the centromere-specific histone H3 variant, CENP-A. It is an essential component of the centromeric chromatin, and is widely conserved among eukaryotes [6,10–13]. The present review focuses on the recent developments in the structural and functional studies of histone H3 variants.
For a complete overview see the Issue and the Editorial Available online 22nd December 2012 0959-440X/$ – see front matter, # 2012 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.sbi.2012.10.009
Introduction In eukaryotes, genomic DNA bearing the genetic information is folded into chromatin. The major protein components of chromatin are histones H2A, H2B, H3, and H4, which form the nucleosome, the fundamental repeating unit of chromatin. H2A exclusively forms a heterodimer with H2B, and H3 specifically forms a heterodimer with H4. During nucleosome formation, two copies each of the H2A–H2B and H3–H4 dimers are incorporated in a stepwise manner to form a histone octamer (Figure 1). The histone octamer wraps about 150 base pairs of DNA in a left-handed orientation. In chromatin, the nucleosomes www.sciencedirect.com
Canonical nucleosome structures Histones H2A, H2B, H3, and H4 share common structural motifs, called the ‘histone fold’, in their globular domains. In addition, the N-terminal and/or C-terminal flexible tail regions are conserved among histones. The N-terminal tails are enriched with Lys, Arg, and Ser residues, which may be the target sites for post-translational modifications, such as acetylation, methylation, and phosphorylation [5]. Therefore, the N-terminal tails of histones are the major target sites for histone modifying enzymes, as well as the proteins that specifically bind to these regions containing acetyllysine, methyllysine, methylarginine, and phosphoserine. Histone tails are also considered to be important for nucleosome–nucleosome interactions within or between chromatin fibers [14,15], and modifications of histone tails may function as regulatory elements for such interactions [16,17]. Actually, the N-terminal tail of H4 directly interacts with the acidic Current Opinion in Structural Biology 2013, 23:109–115
110 Protein-nucleic acid interactions
Figure 1
H3-H4
H2A-H2B
Current Opinion in Structural Biology
Stepwise nucleosome assembly. Two H3–H4 dimers first wrap the DNA, and form a ‘tetrasome’. Two H2A–H2B dimers are then incorporated, thus establishing the mature nucleosome, called the ‘octasome’.
patch of the neighboring nucleosome in the nucleosome crystals [18,19]. In the 1.9 A˚ resolution crystal structure of the nucleosome, the histone tails are visible [19]. However, the exact path of the histone tails in this nucleosome structure may not be physiologically relevant, since the nucleosome arrangement within the crystal may not necessarily reflect a functional form of chromatin. Therefore, the detailed roles of the histone tails in the nucleosome and the higher-order chromatin structure remain as important, unanswered issues. So far, the crystal structures of nucleosomes containing the canonical histones from frog (Xenopus laevis), chicken (Gallus gallus), yeast (Saccharomyces cerevisiae), fly (Drosophila melanogaster), and human (Homo sapiens) have been reported (Table 1) [20]. Interestingly, the DNA binding path in human nucleosomes [21] is different from those of
the frog [18], chicken [22], fly [23], and yeast [24] nucleosomes, although the sequences of the DNA fragments in all of the nucleosomes were the same. By contrast, the structures of the histone octamers in these nucleosomes are quite similar. The average root mean square deviations (Ca atoms) of the visible regions of the human histone octamer structure, relative to the frog, chicken, fly, and yeast histone octamer structures, are less than 1 A˚.
Nucleosomes containing histones H3.1, H3.2, or H3.3 In human, eight non-allelic histone H3 variants, H3.1, H3.2, H3.3, H3T (H3.4), H3.5 [25], H3.X [26], H3.Y [26], and CENP-A, have been identified (Figure 2a) (Table 1). H3.1, H3.2, and H3.3 are the major histone H3 variants present in mammalian cells. H3.1 and H3.2 are produced in the S-phase of the cell cycle, and H3.1 is mainly used for
Table 1 Structures of nucleosome core particles containing canonical H3 and H3 variants Species
H3 variant
Homo sapiens
H3.1
Mus musculus Xenopus laevis
H3.2 H3.3 H3T (H3.4) H3.5 H3.X H3.Y CENP-A H3.1 H3.2
Gallus gallus Drosophila melanogaster Saccharomyces cerevisiae
H3.2 H3.2 H3.3
Structural determination a Tsunaka et al., 2005 (2CV5) [21], Tachiwana et al., 2010 (3AFA) [39] Tachiwana et al., 2011 (3AV1) [28] Tachiwana et al., 2011 (3AV2) [28] Tachiwana et al., 2010 (3A6N) [39] ND ND ND Tachiwana et al., 2011 (3AN2) [52] Chakravarthy et al., 2005 (1U35) [64] Luger et al., 1997 (1AOI) [18], Davey et al., 2002 (1KX5) [19] Harp et al., 2000 (1EQZ) [22] Clapier et al., 2008 (2PYO) [23] White et al., 2001 (1ID3) [24]
b
a
Structural determination of histone H3 variants in nucleosomes by X-ray crystallography. ‘ND’ indicates histone H3 variants, whose structures have not been reported yet. PDB IDs are indicated in parentheses. b The Mus musculus histone H3.1 structure was determined in the nucleosome containing macroH2A. Current Opinion in Structural Biology 2013, 23:109–115
www.sciencedirect.com
Structures of nucleosomes containing histone H3 variants Kurumizaka et al. 111
Figure 2
(a)
(b)
Current Opinion in Structural Biology
Amino acid sequence alignment of histone H3 variants. (a) Alignment of the human H3 variants, H3.1, H3.2, H3.3, H3T (H3.4), H3.5, H3.X, H3.Y, and CENP-A. Amino acid residues that are not conserved among these H3 variants are highlighted with a white background. (b) Human H3.1 (Homo sapiens, Hs), mouse H3.1 (Mus musculus, Mm), frog H3.2 (Xenopus laevis, Xl), chicken H3.2 (Gallus gallus, Gg), fly H3.2 (Drosophila melanogaster, Dm), and yeast H3.3 (Saccharomyces cerevisiae, Sc) are aligned. Amino acid residues that are not conserved in these H3s are highlighted with a white background.
replication-dependent chromatin assembly by the histone chaperone CAF1 [27]. Consistently, in HeLa cells, about 3fold more H3.1 is produced than H3.2 [28], suggesting that H3.1 is the major canonical histone H3 in humans. However, in frog, chicken, and fly, H3.2 is the canonical histone H3 (Figure 2b), and H3.1 is absent in these species. The crystal structures of the frog, chicken, and fly nucleosomes have been determined using H3.2 (Table 1) [18,22,23].
ATRX and DAXX [31,32], also suggesting its function in heterochromatin formation. Yeast only have the H3 variant that corresponds to H3.3, suggesting that H3.3 may be the evolutional origin of the histone H3 variants (Figure 2b). Few sequence variations exist among H3.1, H3.2, and H3.3 (Figure 2b), and the structures of their histone-fold domains are probably unaffected by these variations [28].
By contrast, H3.3 is a replacement histone variant that is constitutively expressed throughout the cell cycle, and is incorporated predominantly at transcriptionally active regions of the chromatin, suggesting its function in gene activation [29]. H3.3 incorporation is replication-independently chaperoned by the histone chaperone HIRA [30]. H3.3 also accumulates at telomeres and pericentric regions, with assistance from the specific histone chaperones
H3T (H3.4) and H3.5 are rarely expressed in tissues except for testis, suggesting their specific functions in spermatogenesis [25,33,34]. H3.X and H3.Y are the primate-specific H3 variants, and are expressed in normal and malignant human tissues [26]. H3.Y production in cells is also enhanced by stress stimuli, such as starvation and cellular density [26]. CENP-A is an essential epigenetic marker for centromeres [1,2,6,10–13].
www.sciencedirect.com
Current Opinion in Structural Biology 2013, 23:109–115
112 Protein-nucleic acid interactions
Nucleosomes containing the testis-specific histone H3T (H3.4) H3T is a human histone H3 variant that is robustly expressed in the testis [33,34]. Interestingly, the major human histone chaperones, Nap1 and sNASP, are incapable of promoting nucleosome formation with H3T [35,36]. By contrast, the histone chaperone Nap2, with about 3-fold higher expression in the testis than in other somatic tissues [37], efficiently promotes H3T nucleosome assembly [35]. These findings suggested that H3T may be incorporated into nucleosomes by a specific chaperone, such as Nap2, in the testis. H3T may also exist in somatic cells, because a proteome analysis of HeLa cell nuclear extracts identified H3T [38], although the amount of the H3 variant was extremely low [28]. Biochemical analyses revealed that the H3T nucleosome is quite unstable, as compared to the canonical H3.1 nucleosome [39]. Consistently, cell biological experiments combined with fluorescence recovery after photobleaching (FRAP) analyses indicated that H3T is incorporated into the HeLa cell chromatin, but its mobility is very fast, as compared to that of H3.1 [39]. The
crystal structure of the H3T nucleosome revealed that the overall structure is similar to that of the canonical H3.1 nucleosome, but local structural differences exist around the H3T-specific residue, Val111 (Figure 2a) [39]. A mutational analysis indicated that the Val111 residue of H3T is responsible for the instability of the H3T nucleosome [39]. Notably, Val111 is only found in human H3T, and is not conserved in the other H3 variants from various species. The unstable structure induced by the Val111 residue may play an important role in human spermatogenesis. The H3T Val111 residue is located close to the nucleosomal dyad. Mutations in this region of H3 have been reported as Sin (Swi/Snf-independent phenotype) mutations that relieve the nucleosomal barrier during transcription, probably by reducing the stability of nucleosomes [40,41]. The crystal structures of nucleosomes containing the Sin2 type-H3 mutants with amino acid substitutions for Arg116 or Thr118 revealed that these mutations either allosterically or directly reduced the histone-histone and/or histone–DNA interactions [42]. The phosphorylation of Thr118 also reportedly
Figure 3
(a)
Octasome
Hemisome
CENP-A H4 H2A H2B
(b)
CENP-A nucleosome
H3.1 nucleosome
Current Opinion in Structural Biology
Structures of human nucleosomes containing histone H3.1 and CENP-A. (a) Schematic illustration of the octasome and hemisome models with CENPA. (b) Crystal structures of the CENP-A octasome [52] (left, PDB ID = 3AN2) and the H3.1 octasome [39] (right, PDB ID = 3AFA). The CENP-A and H3.1 molecules are colored magenta and red, respectively. The H2A, H2B, and H4 molecules are colored blue, yellow, and green, respectively. In the CENP-A octasome, the DNA segments at both edges of the nucleosome are not shown, because these DNA regions are disordered in the crystal structure. Current Opinion in Structural Biology 2013, 23:109–115
www.sciencedirect.com
Structures of nucleosomes containing histone H3 variants Kurumizaka et al. 113
alters nucleosome dynamics [43]. In the H3T nucleosome, the substitution of the H3T-Val111 residue (corresponding to Ala111 of the canonical H3s) induces a local structural change, and reduces the nucleosomal stability. Interestingly, in S. cerevisiae, the Ala to Gly mutation of the H3-111 residue generated the Swi/Snf-independent phenotype [44]. Therefore, human H3T may be a natural Sin-type histone H3 that functions to enhance DNA accessibility in chromatin.
The CENP-A nucleosome structure Human CENP-A is an essential factor that dictates functional centromeres, and has been identified as a histone H3 variant that specifically localizes at centromeres [45]. CENP-A is evolutionarily distant from the other histone H3 variants, and shares only about 50% amino acid identity with the canonical H3s (Figure 2a). Recently, it has been proposed that the structure and composition of the centromeric nucleosome containing CENP-A or its ortholog dynamically changes during the cell cycle [46,47]. Interexchange between the two forms, hemisome and octasome, was suggested to occur (Figure 3a). The existence of the hemisome was first proposed from an atomic force microscopy (AFM) analysis of the nucleosome containing the fly CENP-A ortholog, CID. The hemisome was considered to contain one each of H2A, H2B, H4, and CID, and its height was estimated to be about half of that of the canonical H3 nucleosome [48,49]. A similar observation has been made for the human CENP-A nucleosomes [50]. Further in vitro and in vivo analyses of CID and yeast Cse4 demonstrated that the hemisome may wrap the DNA right-handedly [51]. However, the structural details of the hemisome still remain elusive. On the contrary, the crystal structure of the human CENP-A nucleosome revealed the details of the octasome structure [52]. The overall structure of the histone octamer containing CENP-A is similar to that of the canonical H3-containing octamers. However, the DNA structure in the CENP-A nucleosome is different from that of the H3 nucleosomes (Figure 3b). In the H3 nucleosomes, 145–147 base pairs of DNA are continuously bound to the lateral surface of the histone octamer. On the contrary, in the CENP-A nucleosome, only 121 base pairs are bound to the octamer surface, and thirteen base pairs from both DNA ends are detached from the octamer surface [52]. Biochemical studies also suggested that both ends of the DNA in the CENP-A nucleosome are more accessible than those in the H3 nucleosome [53–55]. Intriguingly, small angle X-ray scattering (SAXS) and biochemical analyses of the yeast Cse4 nucleosome also revealed that, similar to the human CENP-A nucleosome, the entry and exit regions of the DNA in the Cse4 nucleosome (octasome) are flexible [56,57]. Thus, it appears that the flexible nature of the DNA ends in the nucleosome containing CENP-A may www.sciencedirect.com
be an evolutionally conserved feature, perhaps playing an essential role in the formation of the centromeric chromatin architecture.
Concluding remarks In chromatin, the H2A–H2B dimer is relatively mobile, as compared to the H3–H4 dimer, suggesting that the H3– H4 dimer may provide the platform for the formation of functional chromatin domains. No H4 variant has been reported so far. Therefore, the H3 variants may play a central role in providing the specific physical and structural characteristics of each functional chromatin domain. The unstable nature of the H3T nucleosome and the flexible DNA edges of the CENP-A nucleosome may regulate the accessibility of the nucleosomal DNA in the chromatin domain. These physical properties of the nucleosomes containing H3 variants may also dictate the higher order folding state of chromatin [58] and the interaction with nucleosome-binding proteins [59–63]. Structural, physical, and biochemical studies of the other H3 variants, such as H3.5, H3.X, and H3.Y, will provide further important information to understand the contributions of histone H3 in gene regulation and chromatin maintenance.
Acknowledgements We apologize to the scientists whose contributions were not cited because of space limitations. This work was supported partly by Grants-in-Aid from the Japanese Society for the Promotion of Science (JSPS), and the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan. H.K. was also supported by the Waseda Research Institute for Science and Engineering.
References and recommended reading Papers of particular interest, published within the period of review, have been highlighted as: of special interest of outstanding interest 1.
Luger K, Dechassa ML, Tremethick DJ: New insights into nucleosome and chromatin structure: an ordered state or a disordered affair? Nat Rev Mol Cell Biol 2012, 13:436-447.
2.
Yuan G, Zhu B: Histone variants and epigenetic inheritance. Biochim Biophys Acta 2012, 1819:222-229.
3.
Petesch SJ, Lis JT: Overcoming the nucleosome barrier during transcript elongation. Trends Genet 2012, 28:285-294.
4.
Soria G, Polo SE, Almouzni G: Prime, repair, restore: the active role of chromatin in the DNA damage response. Mol Cell 2012, 46:722-734.
5.
Kouzarides T: Chromatin modifications and their function. Cell 2007, 128:693-705.
6.
Talbert PB, Henikoff S: Histone variants – ancient wrap artists of the epigenome. Nat Rev Mol Cell Biol 2010, 11:264-275.
7.
Szenker E, Ray-Gallet D, Almouzni G: The double face of the histone variant H3.3. Cell Res 2011, 21:421-434.
8.
Zweidler A: Core histone variants of the mouse: primary structure and differential expression. In Histone Genes: Structure, Organization and Regulation. Edited by Stein GS, Stein JL, Marzluff WF. John Wiley & Sons; 1984:339-371.
9.
Hamiche A, Shuaib M: Chaperoning the histone H3 family. Biochim Biophys Acta 2012, 1819:230-237. Current Opinion in Structural Biology 2013, 23:109–115
114 Protein-nucleic acid interactions
10. Black BE, Cleveland DW: Epigenetic centromere propagation and the nature of CENP-a nucleosomes. Cell 2011, 144:471-479. 11. Tachiwana H, Kurumizaka H: Structure of the CENP-A nucleosome and its implications for centromeric chromatin architecture. Genes Genet Syst 2011, 86:357-364. 12. Sekulic N, Black BE: Molecular underpinnings of centromere identity and maintenance. Trends Biochem Sci 2012, 37:220-229. 13. Que´net D, Dalal Y: The CENP-A nucleosome: a dynamic structure and role at the centromere. Chromosome Res 2012, 20:465-479. 14. Dorigo B, Schalch T, Bystricky K, Richmond TJ: Chromatin fiber folding: requirement for the histone H4 N-terminal tail. J Mol Biol 2003, 327:85-96. 15. Routh A, Sandin S, Rhodes D: Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure. Proc Natl Acad Sci USA 2008, 105:8872-8877. 16. Robinson PJ, An W, Routh A, Martino F, Chapman L, Roeder RG, Rhodes D: 30 nm chromatin fibre decompaction requires both H4-K16 acetylation and linker histone eviction. J Mol Biol 2008, 381:816-825. 17. Liu Y, Lu C, Yang Y, Fan Y, Yang R, Liu CF, Korolev N, Nordenskio¨ld L: Influence of histone tails and H4 tail acetylations on nucleosome–nucleosome interactions. J Mol Biol 2011, 414:749-764. 18. Luger K, Ma¨der AW, Richmond RK, Sargent DF, Richmond TJ: Crystal structure of the nucleosome core particle at 2.8 A˚ resolution. Nature 1997, 389:251-260. 19. Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ: Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 A˚ resolution. J Mol Biol 2002, 319:1097-1113. 20. Tan S, Davey CA: Nucleosome structural studies. Curr Opin Struct Biol 2011, 21:128-136. 21. Tsunaka Y, Kajimura N, Tate S, Morikawa K: Alteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle. Nucleic Acids Res 2005, 33:3424-3434.
27. Kaufman PD, Kobayashi R, Kessler N, Stillman B: The p150 and p60 subunits of chromatin assembly factor I: a molecular link between newly synthesized histones and DNA replication. Cell 1995, 81:1105-1114. 28. Tachiwana H, Osakabe A, Shiga T, Miya Y, Kimura H, Kagawa W, Kurumizaka H: Structures of human nucleosomes containing major histone H3 variants. Acta Crystallogr D Biol Crystallogr 2011, 67:578-583. The crystal structures of human nucleosomes containing H3.2 or H3.3 were reported. Histone H3 variants, H3.1, H3.2, and H3.3, were also purified from HeLa cell extracts, revealing that H3.1, H3.2, and H3.3 exist in a 7:2:1 ratio in HeLa cells. 29. Ahmad K, Henikoff S: The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol Cell 2002, 9:1191-1200. 30. Ray-Gallet D, Quivy JP, Scamps C, Martini EM, Lipinski M, Almouzni G: HIRA is critical for a nucleosome assembly pathway independent of DNA synthesis. Mol Cell 2002, 9:1091-1100. 31. Goldberg AD, Banaszynski LA, Noh KM, Lewis PW, Elsaesser SJ, Stadler S, Dewell S, Law M, Guo X, Li X et al.: Distinct factors control histone variant H3.3 localization at specific genomic regions. Cell 2010, 140:678-691. 32. Drane´ P, Ouararhni K, Depaux A, Shuaib M, Hamiche A: The death-associated protein DAXX is a novel histone chaperone involved in the replication-independent deposition of H3.3. Genes Dev 2010, 24:1253-1265. 33. Albig W, Ebentheuer J, Klobeck G, Kunz J, Doenecke D: A solitary human H3 histone gene on chromosome 1. Hum Genet 1996, 97:486-491. 34. Witt O, Albig W, Doenecke D: Testis-specific expression of a novel human H3 histone gene. Exp Cell Res 1996, 229:301-306. 35. Tachiwana H, Osakabe A, Kimura H, Kurumizaka H: Nucleosome formation with the testis-specific histone H3 variant, H3t, by human nucleosome assembly proteins in vitro. Nucleic Acids Res 2008, 36:2208-2218. 36. Osakabe A, Tachiwana H, Matsunaga T, Shiga T, Nozawa RS, Obuse C, Kurumizaka H: Nucleosome formation activity of human somatic nuclear autoantigenic sperm protein (sNASP). J Biol Chem 2010, 285:11913-11921.
22. Harp JM, Hanson BL, Timm DE, Bunick GJ: Asymmetries in the nucleosome core particle at 2.5 A˚ resolution. Acta Crystallogr D Biol Crystallogr 2000, 56:1513-1534.
37. Hu RJ, Lee MP, Johnson LA, Feinberg AP: A novel human homologue of yeast nucleosome assembly protein, 65 kb centromeric to the p57KIP2 gene, is biallelically expressed in fetal and adult tissues. Hum Mol Genet 1996, 5:1743-1748.
23. Clapier CR, Chakravarthy S, Petosa C, Ferna´ndez-Tornero C, Luger K, Mu¨ller CW: Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A– H2B histone dimer. Proteins 2008, 71:1-7.
38. Andersen JS, Lam YW, Leung AK, Ong SE, Lyon CE, Lamond AI, Mann M: Nucleolar proteome dynamics. Nature 2005, 433:77-83.
24. White CL, Suto RK, Luger K: Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions. EMBO J 2001, 20:5207-5218. 25. Schenk R, Jenke A, Zilbauer M, Wirth S, Postberg J: H3.5 is a novel hominid-specific histone H3 variant that is specifically expressed in the seminiferous tubules of human testes. Chromosoma 2011, 120:275-285. A novel human histone H3 variant, H3.5, which is highly expressed in testis, was reported, as a hominid-specific H3 variant. Analyses suggested that H3.5 prefers to localize in euchromatin, and associates with actively transcribed genes. Consistently, H3.5 is able to complement an essential function of H3.3 in cell growth. 26. Wiedemann SM, Mildner SN, Bo¨nisch C, Israel L, Maiser A, Matheisl S, Straub T, Merkl R, Leonhardt H, Kremmer E et al.: Identification and characterization of two novel primatespecific histone H3 variants, H3.X and H3.Y. J Cell Biol 2010, 190:777-791. Two novel primate-specific histone H3 variants, H3.X and H3.Y, which are expressed in normal and malignant human tissues, were identified. Endogenous H3.Y was detected in cells, and stress stimuli increased the abundance of H3.Y-expressing cells. Therefore, H3.Y may be the H3 variant that participates in cellular responses to outside stimuli. Current Opinion in Structural Biology 2013, 23:109–115
39. Tachiwana H, Kagawa W, Osakabe A, Kawaguchi K, Shiga T, Hayashi-Takanaka Y, Kimura H, Kurumizaka H: Structural basis of instability of the nucleosome containing a testis-specific histone variant, human H3T. Proc Natl Acad Sci USA 2010, 107:10454-10459. The crystal structure of the nucleosome containing human H3T was determined at 2.7 A˚ resolution, and the structural differences between the H3T and H3.1 nucleosomes were discussed. The authors also reported that the H3T nucleosome is quite unstable, as compared to the canonical H3.1 nucleosome, and the Val111 residue of the H3T nucleosome may be responsible for the instability. 40. Kruger W, Peterson CL, Sil A, Coburn C, Arents G, Moudrianakis EN, Herskowitz I: Amino acid substitutions in the structured domains of histones H3 and H4 partially relieve the requirement of the yeast SWI/SNF complex for transcription. Genes Dev 1995, 9:2770-2779. 41. Kurumizaka H, Wolffe AP: Sin mutations of histone H3: influence on nucleosome core structure and function. Mol Cell Biol 1997, 17:6953-6969. 42. Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam RS, Dyer PN, White CL, Luger K: Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions. EMBO J 2004, 23:260-271. www.sciencedirect.com
Structures of nucleosomes containing histone H3 variants Kurumizaka et al. 115
43. North JA, Javaid S, Ferdinand MB, Chatterjee N, Picking JW, Shoffner M, Nakkula RJ, Bartholomew B, Ottesen JJ, Fishel R, Poirier MG: Phosphorylation of histone H3(T118) alters nucleosome dynamics and remodeling. Nucleic Acids Res 2011, 39:6465-6474. 44. He Q, Yu C, Morse RH: Dispersed mutations in histone H3 that affect transcriptional repression and chromatin structure of the CHA1 promoter in Saccharomyces cerevisiae. Eukaryot Cell 2008, 7:1649-1660. 45. Palmer DK, O’Day K, Wener MH, Andrews BS, Margolis RL: A 17kD centromere protein (CENP-A) copurifies with nucleosome core particles and with histones. J Cell Biol 1987, 104:805-815. 46. Bui M, Dimitriadis EK, Hoischen C, An E, Que´net D, Giebe S, Nita Lazar A, Diekmann S, Dalal Y: Cell-cycle-dependent structural transitions in the human CENP-A nucleosome in vivo. Cell 2012, 150:317-326. Cell-cycle dependent dynamic structural changes were observed in the human centromeric nucleosome containing CENP-A. 47. Shivaraju M, Unruh JR, Slaughter BD, Mattingly M, Berman J, Gerton JL: Cell-cycle-coupled structural oscillation of centromeric nucleosomes in yeast. Cell 2012, 150:304-316. Cell-cycle dependent dynamic structural changes were observed in the yeast centromeric nucleosome containing Cse4. 48. Dalal Y, Wang H, Lindsay S, Henikoff S: Tetrameric structure of centromeric nucleosomes in interphase Drosophila cells. PLoS Biol 2007, 5:e218. 49. Dalal Y, Furuyama T, Vermaak D, Henikoff S: Structure, dynamics, and evolution of centromeric nucleosomes. Proc Natl Acad Sci USA 2007, 104:15974-15981. 50. Dimitriadis EK, Weber C, Gill RK, Diekmann S, Dalal Y: Tetrameric organization of vertebrate centromeric nucleosomes. Proc Natl Acad Sci USA 2010, 107:20317-20322. 51. Furuyama T, Henikoff S: Centromeric nucleosomes induce positive DNA supercoils. Cell 2009, 138:104-113. 52. Tachiwana H, Kagawa W, Shiga T, Osakabe A, Miya Y, Saito K, Hayashi-Takanaka Y, Oda T, Sato M, Park SY et al.: Crystal structure of the human centromeric nucleosome containing CENP-A. Nature 2011, 476:232-235. The crystal structure of the human CENP-A nucleosome was reported. In this structure, two CENP-A molecules were incorporated into the nucleosome with two each of histones H2A, H2B, and H4, indicating octasome formation. In the CENP-A octasome, the DNA segments at both edges of the nucleosome were flexibly detached from the histone octamer surface. 53. Conde e Silva N, Black BE, Sivolob A, Filipski J, Cleveland DW, Prunell A: CENP-A-containing nucleosomes: easier
www.sciencedirect.com
disassembly versus exclusive centromeric localization. J Mol Biol 2007, 370:555-573. 54. Sekulic N, Bassett EA, Rogers DJ, Black BE: The structure of (CENP-A-H4)(2) reveals physical features that mark centromeres. Nature 2010, 467:347-351. 55. Panchenko T, Sorensen TC, Woodcock CL, Kan ZY, Wood S, Resch MG, Luger K, Englander SW, Hansen JC, Black BE: Replacement of histone H3 with CENP-A directs global nucleosome array condensation and loosening of nucleosome superhelical termini. Proc Natl Acad Sci USA 2011, 108:16588-16593. 56. Dechassa ML, Wyns K, Li M, Hall MA, Wang MD, Luger K: Structure and Scm3-mediated assembly of budding yeast centromeric nucleosomes. Nat Commun 2011, 2:313. A structural analysis of the yeast centromeric nucleosome containing Cse4 was performed by small angle X-ray scattering. 57. Kingston IJ, Yung JS, Singleton MR: Biophysical characterization of the centromere-specific nucleosome from budding yeast. J Biol Chem 2011, 286:4021-4026. 58. Schalch T, Duda S, Sargent DF, Richmond TJ: X-ray structure of a tetranucleosome and its implications for the chromatin fibre. Nature 2005, 436:138-141. 59. Thoma¨ NH, Czyzewski BK, Alexeev AA, Mazin AV, Kowalczykowski SC, Pavletich NP: Structure of the SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54. Nat Struct Mol Biol 2005, 12:350-356. 60. Barbera AJ, Chodaparambil JV, Kelley-Clarke B, Joukov V, Walter JC, Luger K, Kaye KM: The nucleosomal surface as a docking station for Kaposi’s sarcoma herpesvirus LANA. Science 2006, 311:856-861. 61. Makde RD, England JR, Yennawar HP, Tan S: Structure of RCC1 chromatin factor bound to the nucleosome core particle. Nature 2010, 467:562-566. 62. Armache KJ, Garlick JD, Canzio D, Narlikar GJ, Kingston RE: Structural Basis of Silencing: Sir3 BAH domain in complex with a nucleosome at 3.0 A˚ resolution. Science 2011, 334:977-982. 63. Yamada K, Frouws TD, Angst B, Fitzgerald DJ, DeLuca C, Schimmele K, Sargent DF, Richmond TJ: Structure and mechanism of the chromatin remodelling factor ISW1a. Nature 2011, 472:448-453. 64. Chakravarthy S, Gundimella SK, Caron C, Perche PY, Pehrson JR, Khochbin S, Luger K: Structural characterization of the histone variant macroH2A. Mol Cell Biol 2005, 25:7616-7624.
Current Opinion in Structural Biology 2013, 23:109–115
Current progress on structural studies of nucleosomes containing histone H3 variants Hitoshi Kurumizaka1, Naoki Horikoshi1, Hiroaki Tachiwana1,* and Wataru Kagawa2 The nucleosome is the basic repeating unit of chromatin. During the nucleosome assembly process, DNA is wrapped around two H3–H4 dimers, followed by the inclusion of two H2A–H2B dimers. The H3–H4 dimers provide the fundamental architecture of the nucleosome. Many non-allelic variants have been found for H3, but not for H4, suggesting that the functions of chromatin domains may, at least in part, be dictated by the specific H3 variant that is incorporated. A prominent example is the centromeric H3 variant, CENP-A, which specifies the function of centromeres in chromosomes. In this review, we survey the current progress in the studies of nucleosomes containing H3 variants, and discuss their implications for the architecture and dynamics of chromatin domains. Addresses 1 Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan 2 Program in Chemistry and Life Science, Department of Interdisciplinary Science and Engineering, School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino-shi, Tokyo 191-8506, Japan Corresponding author: Kurumizaka, Hitoshi ([email protected]) *
Present address: Institut Curie, Centre de Recherche, Paris F-75248, France.
Current Opinion in Structural Biology 2013, 23:109–115 This review comes from a themed issue on Protein-nucleic acid interactions Edited by Kyoshi Nagai and Song Tan
are separated by short linker DNA segments, and cover almost the entire chromosome. Thus, the nucleosome array can have a ‘beads on a string’ appearance, which folds into a higher-order structure (Figure 1). The higherorder chromatin structure not only functions to statically package the huge genomic DNA within the nucleus, but also to dynamically regulate DNA transcription, replication, recombination, and repair [1–4]. Nucleosomes containing various histone modifications and/or histone variants are considered to play important roles in the functional dynamics of chromatin [5–7]. Non-allelic isoforms exist for all histones, except for H4. The amino acid sequence differences between these isoforms and the canonical histones range from one to a few dozen, in addition to the presence of extra domains [6–9]. These non-allelic histones are defined as histone variants. The histone variants may be correctly incorporated with proper timing into specific locations of chromatin by assembly systems with their particular histone chaperones. Biochemical and cell biological studies have suggested that each histone variant plays an important role in the formation of the functional chromatin domain architecture. Perhaps the best-known example is the centromere-specific histone H3 variant, CENP-A. It is an essential component of the centromeric chromatin, and is widely conserved among eukaryotes [6,10–13]. The present review focuses on the recent developments in the structural and functional studies of histone H3 variants.
For a complete overview see the Issue and the Editorial Available online 22nd December 2012 0959-440X/$ – see front matter, # 2012 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.sbi.2012.10.009
Introduction In eukaryotes, genomic DNA bearing the genetic information is folded into chromatin. The major protein components of chromatin are histones H2A, H2B, H3, and H4, which form the nucleosome, the fundamental repeating unit of chromatin. H2A exclusively forms a heterodimer with H2B, and H3 specifically forms a heterodimer with H4. During nucleosome formation, two copies each of the H2A–H2B and H3–H4 dimers are incorporated in a stepwise manner to form a histone octamer (Figure 1). The histone octamer wraps about 150 base pairs of DNA in a left-handed orientation. In chromatin, the nucleosomes www.sciencedirect.com
Canonical nucleosome structures Histones H2A, H2B, H3, and H4 share common structural motifs, called the ‘histone fold’, in their globular domains. In addition, the N-terminal and/or C-terminal flexible tail regions are conserved among histones. The N-terminal tails are enriched with Lys, Arg, and Ser residues, which may be the target sites for post-translational modifications, such as acetylation, methylation, and phosphorylation [5]. Therefore, the N-terminal tails of histones are the major target sites for histone modifying enzymes, as well as the proteins that specifically bind to these regions containing acetyllysine, methyllysine, methylarginine, and phosphoserine. Histone tails are also considered to be important for nucleosome–nucleosome interactions within or between chromatin fibers [14,15], and modifications of histone tails may function as regulatory elements for such interactions [16,17]. Actually, the N-terminal tail of H4 directly interacts with the acidic Current Opinion in Structural Biology 2013, 23:109–115
110 Protein-nucleic acid interactions
Figure 1
H3-H4
H2A-H2B
Current Opinion in Structural Biology
Stepwise nucleosome assembly. Two H3–H4 dimers first wrap the DNA, and form a ‘tetrasome’. Two H2A–H2B dimers are then incorporated, thus establishing the mature nucleosome, called the ‘octasome’.
patch of the neighboring nucleosome in the nucleosome crystals [18,19]. In the 1.9 A˚ resolution crystal structure of the nucleosome, the histone tails are visible [19]. However, the exact path of the histone tails in this nucleosome structure may not be physiologically relevant, since the nucleosome arrangement within the crystal may not necessarily reflect a functional form of chromatin. Therefore, the detailed roles of the histone tails in the nucleosome and the higher-order chromatin structure remain as important, unanswered issues. So far, the crystal structures of nucleosomes containing the canonical histones from frog (Xenopus laevis), chicken (Gallus gallus), yeast (Saccharomyces cerevisiae), fly (Drosophila melanogaster), and human (Homo sapiens) have been reported (Table 1) [20]. Interestingly, the DNA binding path in human nucleosomes [21] is different from those of
the frog [18], chicken [22], fly [23], and yeast [24] nucleosomes, although the sequences of the DNA fragments in all of the nucleosomes were the same. By contrast, the structures of the histone octamers in these nucleosomes are quite similar. The average root mean square deviations (Ca atoms) of the visible regions of the human histone octamer structure, relative to the frog, chicken, fly, and yeast histone octamer structures, are less than 1 A˚.
Nucleosomes containing histones H3.1, H3.2, or H3.3 In human, eight non-allelic histone H3 variants, H3.1, H3.2, H3.3, H3T (H3.4), H3.5 [25], H3.X [26], H3.Y [26], and CENP-A, have been identified (Figure 2a) (Table 1). H3.1, H3.2, and H3.3 are the major histone H3 variants present in mammalian cells. H3.1 and H3.2 are produced in the S-phase of the cell cycle, and H3.1 is mainly used for
Table 1 Structures of nucleosome core particles containing canonical H3 and H3 variants Species
H3 variant
Homo sapiens
H3.1
Mus musculus Xenopus laevis
H3.2 H3.3 H3T (H3.4) H3.5 H3.X H3.Y CENP-A H3.1 H3.2
Gallus gallus Drosophila melanogaster Saccharomyces cerevisiae
H3.2 H3.2 H3.3
Structural determination a Tsunaka et al., 2005 (2CV5) [21], Tachiwana et al., 2010 (3AFA) [39] Tachiwana et al., 2011 (3AV1) [28] Tachiwana et al., 2011 (3AV2) [28] Tachiwana et al., 2010 (3A6N) [39] ND ND ND Tachiwana et al., 2011 (3AN2) [52] Chakravarthy et al., 2005 (1U35) [64] Luger et al., 1997 (1AOI) [18], Davey et al., 2002 (1KX5) [19] Harp et al., 2000 (1EQZ) [22] Clapier et al., 2008 (2PYO) [23] White et al., 2001 (1ID3) [24]
b
a
Structural determination of histone H3 variants in nucleosomes by X-ray crystallography. ‘ND’ indicates histone H3 variants, whose structures have not been reported yet. PDB IDs are indicated in parentheses. b The Mus musculus histone H3.1 structure was determined in the nucleosome containing macroH2A. Current Opinion in Structural Biology 2013, 23:109–115
www.sciencedirect.com
Structures of nucleosomes containing histone H3 variants Kurumizaka et al. 111
Figure 2
(a)
(b)
Current Opinion in Structural Biology
Amino acid sequence alignment of histone H3 variants. (a) Alignment of the human H3 variants, H3.1, H3.2, H3.3, H3T (H3.4), H3.5, H3.X, H3.Y, and CENP-A. Amino acid residues that are not conserved among these H3 variants are highlighted with a white background. (b) Human H3.1 (Homo sapiens, Hs), mouse H3.1 (Mus musculus, Mm), frog H3.2 (Xenopus laevis, Xl), chicken H3.2 (Gallus gallus, Gg), fly H3.2 (Drosophila melanogaster, Dm), and yeast H3.3 (Saccharomyces cerevisiae, Sc) are aligned. Amino acid residues that are not conserved in these H3s are highlighted with a white background.
replication-dependent chromatin assembly by the histone chaperone CAF1 [27]. Consistently, in HeLa cells, about 3fold more H3.1 is produced than H3.2 [28], suggesting that H3.1 is the major canonical histone H3 in humans. However, in frog, chicken, and fly, H3.2 is the canonical histone H3 (Figure 2b), and H3.1 is absent in these species. The crystal structures of the frog, chicken, and fly nucleosomes have been determined using H3.2 (Table 1) [18,22,23].
ATRX and DAXX [31,32], also suggesting its function in heterochromatin formation. Yeast only have the H3 variant that corresponds to H3.3, suggesting that H3.3 may be the evolutional origin of the histone H3 variants (Figure 2b). Few sequence variations exist among H3.1, H3.2, and H3.3 (Figure 2b), and the structures of their histone-fold domains are probably unaffected by these variations [28].
By contrast, H3.3 is a replacement histone variant that is constitutively expressed throughout the cell cycle, and is incorporated predominantly at transcriptionally active regions of the chromatin, suggesting its function in gene activation [29]. H3.3 incorporation is replication-independently chaperoned by the histone chaperone HIRA [30]. H3.3 also accumulates at telomeres and pericentric regions, with assistance from the specific histone chaperones
H3T (H3.4) and H3.5 are rarely expressed in tissues except for testis, suggesting their specific functions in spermatogenesis [25,33,34]. H3.X and H3.Y are the primate-specific H3 variants, and are expressed in normal and malignant human tissues [26]. H3.Y production in cells is also enhanced by stress stimuli, such as starvation and cellular density [26]. CENP-A is an essential epigenetic marker for centromeres [1,2,6,10–13].
www.sciencedirect.com
Current Opinion in Structural Biology 2013, 23:109–115
112 Protein-nucleic acid interactions
Nucleosomes containing the testis-specific histone H3T (H3.4) H3T is a human histone H3 variant that is robustly expressed in the testis [33,34]. Interestingly, the major human histone chaperones, Nap1 and sNASP, are incapable of promoting nucleosome formation with H3T [35,36]. By contrast, the histone chaperone Nap2, with about 3-fold higher expression in the testis than in other somatic tissues [37], efficiently promotes H3T nucleosome assembly [35]. These findings suggested that H3T may be incorporated into nucleosomes by a specific chaperone, such as Nap2, in the testis. H3T may also exist in somatic cells, because a proteome analysis of HeLa cell nuclear extracts identified H3T [38], although the amount of the H3 variant was extremely low [28]. Biochemical analyses revealed that the H3T nucleosome is quite unstable, as compared to the canonical H3.1 nucleosome [39]. Consistently, cell biological experiments combined with fluorescence recovery after photobleaching (FRAP) analyses indicated that H3T is incorporated into the HeLa cell chromatin, but its mobility is very fast, as compared to that of H3.1 [39]. The
crystal structure of the H3T nucleosome revealed that the overall structure is similar to that of the canonical H3.1 nucleosome, but local structural differences exist around the H3T-specific residue, Val111 (Figure 2a) [39]. A mutational analysis indicated that the Val111 residue of H3T is responsible for the instability of the H3T nucleosome [39]. Notably, Val111 is only found in human H3T, and is not conserved in the other H3 variants from various species. The unstable structure induced by the Val111 residue may play an important role in human spermatogenesis. The H3T Val111 residue is located close to the nucleosomal dyad. Mutations in this region of H3 have been reported as Sin (Swi/Snf-independent phenotype) mutations that relieve the nucleosomal barrier during transcription, probably by reducing the stability of nucleosomes [40,41]. The crystal structures of nucleosomes containing the Sin2 type-H3 mutants with amino acid substitutions for Arg116 or Thr118 revealed that these mutations either allosterically or directly reduced the histone-histone and/or histone–DNA interactions [42]. The phosphorylation of Thr118 also reportedly
Figure 3
(a)
Octasome
Hemisome
CENP-A H4 H2A H2B
(b)
CENP-A nucleosome
H3.1 nucleosome
Current Opinion in Structural Biology
Structures of human nucleosomes containing histone H3.1 and CENP-A. (a) Schematic illustration of the octasome and hemisome models with CENPA. (b) Crystal structures of the CENP-A octasome [52] (left, PDB ID = 3AN2) and the H3.1 octasome [39] (right, PDB ID = 3AFA). The CENP-A and H3.1 molecules are colored magenta and red, respectively. The H2A, H2B, and H4 molecules are colored blue, yellow, and green, respectively. In the CENP-A octasome, the DNA segments at both edges of the nucleosome are not shown, because these DNA regions are disordered in the crystal structure. Current Opinion in Structural Biology 2013, 23:109–115
www.sciencedirect.com
Structures of nucleosomes containing histone H3 variants Kurumizaka et al. 113
alters nucleosome dynamics [43]. In the H3T nucleosome, the substitution of the H3T-Val111 residue (corresponding to Ala111 of the canonical H3s) induces a local structural change, and reduces the nucleosomal stability. Interestingly, in S. cerevisiae, the Ala to Gly mutation of the H3-111 residue generated the Swi/Snf-independent phenotype [44]. Therefore, human H3T may be a natural Sin-type histone H3 that functions to enhance DNA accessibility in chromatin.
The CENP-A nucleosome structure Human CENP-A is an essential factor that dictates functional centromeres, and has been identified as a histone H3 variant that specifically localizes at centromeres [45]. CENP-A is evolutionarily distant from the other histone H3 variants, and shares only about 50% amino acid identity with the canonical H3s (Figure 2a). Recently, it has been proposed that the structure and composition of the centromeric nucleosome containing CENP-A or its ortholog dynamically changes during the cell cycle [46,47]. Interexchange between the two forms, hemisome and octasome, was suggested to occur (Figure 3a). The existence of the hemisome was first proposed from an atomic force microscopy (AFM) analysis of the nucleosome containing the fly CENP-A ortholog, CID. The hemisome was considered to contain one each of H2A, H2B, H4, and CID, and its height was estimated to be about half of that of the canonical H3 nucleosome [48,49]. A similar observation has been made for the human CENP-A nucleosomes [50]. Further in vitro and in vivo analyses of CID and yeast Cse4 demonstrated that the hemisome may wrap the DNA right-handedly [51]. However, the structural details of the hemisome still remain elusive. On the contrary, the crystal structure of the human CENP-A nucleosome revealed the details of the octasome structure [52]. The overall structure of the histone octamer containing CENP-A is similar to that of the canonical H3-containing octamers. However, the DNA structure in the CENP-A nucleosome is different from that of the H3 nucleosomes (Figure 3b). In the H3 nucleosomes, 145–147 base pairs of DNA are continuously bound to the lateral surface of the histone octamer. On the contrary, in the CENP-A nucleosome, only 121 base pairs are bound to the octamer surface, and thirteen base pairs from both DNA ends are detached from the octamer surface [52]. Biochemical studies also suggested that both ends of the DNA in the CENP-A nucleosome are more accessible than those in the H3 nucleosome [53–55]. Intriguingly, small angle X-ray scattering (SAXS) and biochemical analyses of the yeast Cse4 nucleosome also revealed that, similar to the human CENP-A nucleosome, the entry and exit regions of the DNA in the Cse4 nucleosome (octasome) are flexible [56,57]. Thus, it appears that the flexible nature of the DNA ends in the nucleosome containing CENP-A may www.sciencedirect.com
be an evolutionally conserved feature, perhaps playing an essential role in the formation of the centromeric chromatin architecture.
Concluding remarks In chromatin, the H2A–H2B dimer is relatively mobile, as compared to the H3–H4 dimer, suggesting that the H3– H4 dimer may provide the platform for the formation of functional chromatin domains. No H4 variant has been reported so far. Therefore, the H3 variants may play a central role in providing the specific physical and structural characteristics of each functional chromatin domain. The unstable nature of the H3T nucleosome and the flexible DNA edges of the CENP-A nucleosome may regulate the accessibility of the nucleosomal DNA in the chromatin domain. These physical properties of the nucleosomes containing H3 variants may also dictate the higher order folding state of chromatin [58] and the interaction with nucleosome-binding proteins [59–63]. Structural, physical, and biochemical studies of the other H3 variants, such as H3.5, H3.X, and H3.Y, will provide further important information to understand the contributions of histone H3 in gene regulation and chromatin maintenance.
Acknowledgements We apologize to the scientists whose contributions were not cited because of space limitations. This work was supported partly by Grants-in-Aid from the Japanese Society for the Promotion of Science (JSPS), and the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan. H.K. was also supported by the Waseda Research Institute for Science and Engineering.
References and recommended reading Papers of particular interest, published within the period of review, have been highlighted as: of special interest of outstanding interest 1.
Luger K, Dechassa ML, Tremethick DJ: New insights into nucleosome and chromatin structure: an ordered state or a disordered affair? Nat Rev Mol Cell Biol 2012, 13:436-447.
2.
Yuan G, Zhu B: Histone variants and epigenetic inheritance. Biochim Biophys Acta 2012, 1819:222-229.
3.
Petesch SJ, Lis JT: Overcoming the nucleosome barrier during transcript elongation. Trends Genet 2012, 28:285-294.
4.
Soria G, Polo SE, Almouzni G: Prime, repair, restore: the active role of chromatin in the DNA damage response. Mol Cell 2012, 46:722-734.
5.
Kouzarides T: Chromatin modifications and their function. Cell 2007, 128:693-705.
6.
Talbert PB, Henikoff S: Histone variants – ancient wrap artists of the epigenome. Nat Rev Mol Cell Biol 2010, 11:264-275.
7.
Szenker E, Ray-Gallet D, Almouzni G: The double face of the histone variant H3.3. Cell Res 2011, 21:421-434.
8.
Zweidler A: Core histone variants of the mouse: primary structure and differential expression. In Histone Genes: Structure, Organization and Regulation. Edited by Stein GS, Stein JL, Marzluff WF. John Wiley & Sons; 1984:339-371.
9.
Hamiche A, Shuaib M: Chaperoning the histone H3 family. Biochim Biophys Acta 2012, 1819:230-237. Current Opinion in Structural Biology 2013, 23:109–115
114 Protein-nucleic acid interactions
10. Black BE, Cleveland DW: Epigenetic centromere propagation and the nature of CENP-a nucleosomes. Cell 2011, 144:471-479. 11. Tachiwana H, Kurumizaka H: Structure of the CENP-A nucleosome and its implications for centromeric chromatin architecture. Genes Genet Syst 2011, 86:357-364. 12. Sekulic N, Black BE: Molecular underpinnings of centromere identity and maintenance. Trends Biochem Sci 2012, 37:220-229. 13. Que´net D, Dalal Y: The CENP-A nucleosome: a dynamic structure and role at the centromere. Chromosome Res 2012, 20:465-479. 14. Dorigo B, Schalch T, Bystricky K, Richmond TJ: Chromatin fiber folding: requirement for the histone H4 N-terminal tail. J Mol Biol 2003, 327:85-96. 15. Routh A, Sandin S, Rhodes D: Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure. Proc Natl Acad Sci USA 2008, 105:8872-8877. 16. Robinson PJ, An W, Routh A, Martino F, Chapman L, Roeder RG, Rhodes D: 30 nm chromatin fibre decompaction requires both H4-K16 acetylation and linker histone eviction. J Mol Biol 2008, 381:816-825. 17. Liu Y, Lu C, Yang Y, Fan Y, Yang R, Liu CF, Korolev N, Nordenskio¨ld L: Influence of histone tails and H4 tail acetylations on nucleosome–nucleosome interactions. J Mol Biol 2011, 414:749-764. 18. Luger K, Ma¨der AW, Richmond RK, Sargent DF, Richmond TJ: Crystal structure of the nucleosome core particle at 2.8 A˚ resolution. Nature 1997, 389:251-260. 19. Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ: Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 A˚ resolution. J Mol Biol 2002, 319:1097-1113. 20. Tan S, Davey CA: Nucleosome structural studies. Curr Opin Struct Biol 2011, 21:128-136. 21. Tsunaka Y, Kajimura N, Tate S, Morikawa K: Alteration of the nucleosomal DNA path in the crystal structure of a human nucleosome core particle. Nucleic Acids Res 2005, 33:3424-3434.
27. Kaufman PD, Kobayashi R, Kessler N, Stillman B: The p150 and p60 subunits of chromatin assembly factor I: a molecular link between newly synthesized histones and DNA replication. Cell 1995, 81:1105-1114. 28. Tachiwana H, Osakabe A, Shiga T, Miya Y, Kimura H, Kagawa W, Kurumizaka H: Structures of human nucleosomes containing major histone H3 variants. Acta Crystallogr D Biol Crystallogr 2011, 67:578-583. The crystal structures of human nucleosomes containing H3.2 or H3.3 were reported. Histone H3 variants, H3.1, H3.2, and H3.3, were also purified from HeLa cell extracts, revealing that H3.1, H3.2, and H3.3 exist in a 7:2:1 ratio in HeLa cells. 29. Ahmad K, Henikoff S: The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol Cell 2002, 9:1191-1200. 30. Ray-Gallet D, Quivy JP, Scamps C, Martini EM, Lipinski M, Almouzni G: HIRA is critical for a nucleosome assembly pathway independent of DNA synthesis. Mol Cell 2002, 9:1091-1100. 31. Goldberg AD, Banaszynski LA, Noh KM, Lewis PW, Elsaesser SJ, Stadler S, Dewell S, Law M, Guo X, Li X et al.: Distinct factors control histone variant H3.3 localization at specific genomic regions. Cell 2010, 140:678-691. 32. Drane´ P, Ouararhni K, Depaux A, Shuaib M, Hamiche A: The death-associated protein DAXX is a novel histone chaperone involved in the replication-independent deposition of H3.3. Genes Dev 2010, 24:1253-1265. 33. Albig W, Ebentheuer J, Klobeck G, Kunz J, Doenecke D: A solitary human H3 histone gene on chromosome 1. Hum Genet 1996, 97:486-491. 34. Witt O, Albig W, Doenecke D: Testis-specific expression of a novel human H3 histone gene. Exp Cell Res 1996, 229:301-306. 35. Tachiwana H, Osakabe A, Kimura H, Kurumizaka H: Nucleosome formation with the testis-specific histone H3 variant, H3t, by human nucleosome assembly proteins in vitro. Nucleic Acids Res 2008, 36:2208-2218. 36. Osakabe A, Tachiwana H, Matsunaga T, Shiga T, Nozawa RS, Obuse C, Kurumizaka H: Nucleosome formation activity of human somatic nuclear autoantigenic sperm protein (sNASP). J Biol Chem 2010, 285:11913-11921.
22. Harp JM, Hanson BL, Timm DE, Bunick GJ: Asymmetries in the nucleosome core particle at 2.5 A˚ resolution. Acta Crystallogr D Biol Crystallogr 2000, 56:1513-1534.
37. Hu RJ, Lee MP, Johnson LA, Feinberg AP: A novel human homologue of yeast nucleosome assembly protein, 65 kb centromeric to the p57KIP2 gene, is biallelically expressed in fetal and adult tissues. Hum Mol Genet 1996, 5:1743-1748.
23. Clapier CR, Chakravarthy S, Petosa C, Ferna´ndez-Tornero C, Luger K, Mu¨ller CW: Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A– H2B histone dimer. Proteins 2008, 71:1-7.
38. Andersen JS, Lam YW, Leung AK, Ong SE, Lyon CE, Lamond AI, Mann M: Nucleolar proteome dynamics. Nature 2005, 433:77-83.
24. White CL, Suto RK, Luger K: Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions. EMBO J 2001, 20:5207-5218. 25. Schenk R, Jenke A, Zilbauer M, Wirth S, Postberg J: H3.5 is a novel hominid-specific histone H3 variant that is specifically expressed in the seminiferous tubules of human testes. Chromosoma 2011, 120:275-285. A novel human histone H3 variant, H3.5, which is highly expressed in testis, was reported, as a hominid-specific H3 variant. Analyses suggested that H3.5 prefers to localize in euchromatin, and associates with actively transcribed genes. Consistently, H3.5 is able to complement an essential function of H3.3 in cell growth. 26. Wiedemann SM, Mildner SN, Bo¨nisch C, Israel L, Maiser A, Matheisl S, Straub T, Merkl R, Leonhardt H, Kremmer E et al.: Identification and characterization of two novel primatespecific histone H3 variants, H3.X and H3.Y. J Cell Biol 2010, 190:777-791. Two novel primate-specific histone H3 variants, H3.X and H3.Y, which are expressed in normal and malignant human tissues, were identified. Endogenous H3.Y was detected in cells, and stress stimuli increased the abundance of H3.Y-expressing cells. Therefore, H3.Y may be the H3 variant that participates in cellular responses to outside stimuli. Current Opinion in Structural Biology 2013, 23:109–115
39. Tachiwana H, Kagawa W, Osakabe A, Kawaguchi K, Shiga T, Hayashi-Takanaka Y, Kimura H, Kurumizaka H: Structural basis of instability of the nucleosome containing a testis-specific histone variant, human H3T. Proc Natl Acad Sci USA 2010, 107:10454-10459. The crystal structure of the nucleosome containing human H3T was determined at 2.7 A˚ resolution, and the structural differences between the H3T and H3.1 nucleosomes were discussed. The authors also reported that the H3T nucleosome is quite unstable, as compared to the canonical H3.1 nucleosome, and the Val111 residue of the H3T nucleosome may be responsible for the instability. 40. Kruger W, Peterson CL, Sil A, Coburn C, Arents G, Moudrianakis EN, Herskowitz I: Amino acid substitutions in the structured domains of histones H3 and H4 partially relieve the requirement of the yeast SWI/SNF complex for transcription. Genes Dev 1995, 9:2770-2779. 41. Kurumizaka H, Wolffe AP: Sin mutations of histone H3: influence on nucleosome core structure and function. Mol Cell Biol 1997, 17:6953-6969. 42. Muthurajan UM, Bao Y, Forsberg LJ, Edayathumangalam RS, Dyer PN, White CL, Luger K: Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions. EMBO J 2004, 23:260-271. www.sciencedirect.com
Structures of nucleosomes containing histone H3 variants Kurumizaka et al. 115
43. North JA, Javaid S, Ferdinand MB, Chatterjee N, Picking JW, Shoffner M, Nakkula RJ, Bartholomew B, Ottesen JJ, Fishel R, Poirier MG: Phosphorylation of histone H3(T118) alters nucleosome dynamics and remodeling. Nucleic Acids Res 2011, 39:6465-6474. 44. He Q, Yu C, Morse RH: Dispersed mutations in histone H3 that affect transcriptional repression and chromatin structure of the CHA1 promoter in Saccharomyces cerevisiae. Eukaryot Cell 2008, 7:1649-1660. 45. Palmer DK, O’Day K, Wener MH, Andrews BS, Margolis RL: A 17kD centromere protein (CENP-A) copurifies with nucleosome core particles and with histones. J Cell Biol 1987, 104:805-815. 46. Bui M, Dimitriadis EK, Hoischen C, An E, Que´net D, Giebe S, Nita Lazar A, Diekmann S, Dalal Y: Cell-cycle-dependent structural transitions in the human CENP-A nucleosome in vivo. Cell 2012, 150:317-326. Cell-cycle dependent dynamic structural changes were observed in the human centromeric nucleosome containing CENP-A. 47. Shivaraju M, Unruh JR, Slaughter BD, Mattingly M, Berman J, Gerton JL: Cell-cycle-coupled structural oscillation of centromeric nucleosomes in yeast. Cell 2012, 150:304-316. Cell-cycle dependent dynamic structural changes were observed in the yeast centromeric nucleosome containing Cse4. 48. Dalal Y, Wang H, Lindsay S, Henikoff S: Tetrameric structure of centromeric nucleosomes in interphase Drosophila cells. PLoS Biol 2007, 5:e218. 49. Dalal Y, Furuyama T, Vermaak D, Henikoff S: Structure, dynamics, and evolution of centromeric nucleosomes. Proc Natl Acad Sci USA 2007, 104:15974-15981. 50. Dimitriadis EK, Weber C, Gill RK, Diekmann S, Dalal Y: Tetrameric organization of vertebrate centromeric nucleosomes. Proc Natl Acad Sci USA 2010, 107:20317-20322. 51. Furuyama T, Henikoff S: Centromeric nucleosomes induce positive DNA supercoils. Cell 2009, 138:104-113. 52. Tachiwana H, Kagawa W, Shiga T, Osakabe A, Miya Y, Saito K, Hayashi-Takanaka Y, Oda T, Sato M, Park SY et al.: Crystal structure of the human centromeric nucleosome containing CENP-A. Nature 2011, 476:232-235. The crystal structure of the human CENP-A nucleosome was reported. In this structure, two CENP-A molecules were incorporated into the nucleosome with two each of histones H2A, H2B, and H4, indicating octasome formation. In the CENP-A octasome, the DNA segments at both edges of the nucleosome were flexibly detached from the histone octamer surface. 53. Conde e Silva N, Black BE, Sivolob A, Filipski J, Cleveland DW, Prunell A: CENP-A-containing nucleosomes: easier
www.sciencedirect.com
disassembly versus exclusive centromeric localization. J Mol Biol 2007, 370:555-573. 54. Sekulic N, Bassett EA, Rogers DJ, Black BE: The structure of (CENP-A-H4)(2) reveals physical features that mark centromeres. Nature 2010, 467:347-351. 55. Panchenko T, Sorensen TC, Woodcock CL, Kan ZY, Wood S, Resch MG, Luger K, Englander SW, Hansen JC, Black BE: Replacement of histone H3 with CENP-A directs global nucleosome array condensation and loosening of nucleosome superhelical termini. Proc Natl Acad Sci USA 2011, 108:16588-16593. 56. Dechassa ML, Wyns K, Li M, Hall MA, Wang MD, Luger K: Structure and Scm3-mediated assembly of budding yeast centromeric nucleosomes. Nat Commun 2011, 2:313. A structural analysis of the yeast centromeric nucleosome containing Cse4 was performed by small angle X-ray scattering. 57. Kingston IJ, Yung JS, Singleton MR: Biophysical characterization of the centromere-specific nucleosome from budding yeast. J Biol Chem 2011, 286:4021-4026. 58. Schalch T, Duda S, Sargent DF, Richmond TJ: X-ray structure of a tetranucleosome and its implications for the chromatin fibre. Nature 2005, 436:138-141. 59. Thoma¨ NH, Czyzewski BK, Alexeev AA, Mazin AV, Kowalczykowski SC, Pavletich NP: Structure of the SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54. Nat Struct Mol Biol 2005, 12:350-356. 60. Barbera AJ, Chodaparambil JV, Kelley-Clarke B, Joukov V, Walter JC, Luger K, Kaye KM: The nucleosomal surface as a docking station for Kaposi’s sarcoma herpesvirus LANA. Science 2006, 311:856-861. 61. Makde RD, England JR, Yennawar HP, Tan S: Structure of RCC1 chromatin factor bound to the nucleosome core particle. Nature 2010, 467:562-566. 62. Armache KJ, Garlick JD, Canzio D, Narlikar GJ, Kingston RE: Structural Basis of Silencing: Sir3 BAH domain in complex with a nucleosome at 3.0 A˚ resolution. Science 2011, 334:977-982. 63. Yamada K, Frouws TD, Angst B, Fitzgerald DJ, DeLuca C, Schimmele K, Sargent DF, Richmond TJ: Structure and mechanism of the chromatin remodelling factor ISW1a. Nature 2011, 472:448-453. 64. Chakravarthy S, Gundimella SK, Caron C, Perche PY, Pehrson JR, Khochbin S, Luger K: Structural characterization of the histone variant macroH2A. Mol Cell Biol 2005, 25:7616-7624.
Current Opinion in Structural Biology 2013, 23:109–115