Roles of chromatin assembly factor 1 in the epigenetic control of chromatin plasticity

Science China Life Sciences

Volumn 55, Issue 1, 2012, Pages 15-19

  Huang, Hai ^a,b   Jiao, Ren Jie ^a  

^a INSTITUTE OF BIOPHYSICS   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

CAF 1; chromatin plasticity; epigenetic information; histone chaperone; signal transduction

Indexed keywords

CHROMATIN ASSEMBLY FACTOR 1; HISTONE;

ANIMAL; CELL CYCLE S PHASE; CELL DIVISION; CHROMATIN; DNA REPAIR; DNA REPLICATION; GENETIC EPIGENESIS; GENETICS; METABOLISM; NUCLEOSOME; PHYSIOLOGY; REVIEW; SIGNAL TRANSDUCTION;

ANIMALS; CELL DIVISION; CHROMATIN; CHROMATIN ASSEMBLY FACTOR-1; DNA REPAIR; DNA REPLICATION; EPIGENESIS, GENETIC; HISTONES; NUCLEOSOMES; S PHASE; SIGNAL TRANSDUCTION;

EUKARYOTA;

EID: 84863011441     PISSN: 16747305     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11427-012-4269-z     Document Type: Review

References (74)

1. Richmond T J, Finch J T, Rushton B, et al. Structure of the nucleosome core particle at 7 Å resolution. Nature, 1984, 311: 532-537.
2. Kornberg R D, Thomas J O. Chromatin structure: oligomers of the histones. Science, 1974, 184: 865-868.
3. Noll M, Kornberg R D. Action of micrococcal nuclease on chromatin and the location of histone H1. J Mol Biol, 1977, 109: 393-404.
4. Luger K, Mader A W, Richmond R K, et al. Crystal structure of the nucleosome core particle at 2. 8 Å resolution. Nature, 1997, 389: 251-260.
5. Robinson P J, Fairall L, Huynh V A, et al. EM measurements define the dimensions of the "30-nm" chromatin fiber: evidence for a compact, interdigitated structure. Proc Natl Acad Sci USA, 2006, 103: 6506-6511.
6. Thoma F, Koller T, Klug A. Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin. J Cell Biol, 1979, 83: 403-427.
7. Finch J T, Klug A. Solenoidal model for superstructure in chromatin. Proc Natl Acad Sci USA, 1976, 73: 1897-1901.
8. Robinson P J, Rhodes D. Structure of the '30 nm' chromatin fibre: a key role for the linker histone. Curr Opin Struct Biol, 2006, 16: 336-343.
9. Mello J A, Sillje H H, Roche D M, et al. Human Asf1 and CAF-1 interact and synergize in a repair-coupled nucleosome assembly pathway. EMBO Rep, 2002, 3: 329-334.
10. Kirov N, Shtilbans A, Rushlow C. Isolation and characterization of a new gene encoding a member of the HIRA family of proteins from Drosophila melanogaster. Gene, 1998, 212: 323-332.
11. Monson E K, de Bruin D, Zakian V A. The yeast Cac1 protein is required for the stable inheritance of transcriptionally repressed chromatin at telomeres. Proc Natl Acad Sci USA, 1997, 94: 13081-13086.
12. Smith S, Stillman B. Purification and characterization of CAF-I, a human cell factor required for chromatin assembly during DNA replication in vitro. Cell, 1989, 58: 15-25.
13. Shibahara K, Stillman B. Replication-dependent marking of DNA by PCNA facilitates CAF-1-coupled inheritance of chromatin. Cell, 1999, 96: 575-585.
14. Krude T. Chromatin assembly during DNA replication in somatic cells. Eur J Biochem, 1999, 263: 1-5.
15. Song Y, He F, Xie G, et al. CAF-1 is essential for Drosophila development and involved in the maintenance of epigenetic memory. Dev Biol, 2007, 311: 213-222.
16. Chen Z, Tan J L, Ingouff M, et al. Chromatin assembly factor 1 regulates the cell cycle but not cell fate during male gametogenesis in Arabidopsis thaliana. Development, 2008, 135: 65-73.
17. Myung K, Pennaneach V, Kats E S, et al. Saccharomyces cerevisiae chromatin-assembly factors that act during DNA replication function in the maintenance of genome stability. Proc Natl Acad Sci USA, 2003, 100: 6640-6645.
18. Kaufman P D, Kobayashi R, Stillman B. Ultraviolet radiation sensitivity and reduction of telomeric silencing in Saccharomyces cerevisiae cells lacking chromatin assembly factor-I. Genes Dev, 1997, 11: 345-357.
19. Takami Y, Ono T, Fukagawa T, et al. Essential role of chromatin assembly factor-1-mediated rapid nucleosome assembly for DNA replication and cell division in vertebrate cells. Mol Biol Cell, 2007, 18: 129-141.
20. Worcel A, Han S, Wong M L. Assembly of newly replicated chromatin. Cell, 1978, 15: 969-977.
21. Cremisi C, Yaniv M. Sequential assembly of newly synthesized histones on replicating SV40 DNA. Biochem Biophys Res Commun, 1980, 92: 1117-1123.
22. Gruss C, Wu J, Koller T, et al. Disruption of the nucleosomes at the replication fork. EMBO J, 1993, 12: 4533-4545.
23. Gasser R, Koller T, Sogo J M. The stability of nucleosomes at the replication fork. J Mol Biol, 1996, 258: 224-239.
24. Smith S, Stillman B. Stepwise assembly of chromatin during DNA replication in vitro. EMBO J, 1991, 10: 971-980.
25. Enomoto S, Berman J. Chromatin assembly factor I contributes to the maintenance, but not the re-establishment, of silencing at the yeast silent mating loci. Genes Dev, 1998, 12: 219-232.
26. Taddei A, Roche D, Sibarita J B, et al. Duplication and maintenance of heterochromatin domains. J Cell Biol, 1999, 147: 1153-1166.
27. Verreault A, Kaufman P D, Kobayashi R, et al. Nucleosome assembly by a complex of CAF-1 and acetylated histones H3/H4. Cell, 1996, 87: 95-104.
28. Sobel R E, Cook R G, Perry C A, et al. Conservation of deposition-related acetylation sites in newly synthesized histones H3 and H4. Proc Natl Acad Sci USA, 1995, 92: 1237-1241.
29. Das C, Lucia M S, Hansen K C, et al. CBP/p300-mediated acetylation of histone H3 on lysine 56. Nature, 2009, 459: 113-117.
30. Zhang Z, Shibahara K, Stillman B. PCNA connects DNA replication to epigenetic inheritance in yeast. Nature, 2000, 408: 221-225.
31. Tyler J K, Adams C R, Chen S R, et al. The RCAF complex mediates chromatin assembly during DNA replication and repair. Nature, 1999, 402: 555-560.
32. Tyler J K, Collins K A, Prasad-Sinha J, et al. Interaction between the Drosophila CAF-1 and ASF1 chromatin assembly factors. Mol Cell Biol, 2001, 21: 6574-6584.
33. Krawitz D C, Kama T, Kaufman P D. Chromatin assembly factor I mutants defective for PCNA binding require Asf1/Hir proteins for silencing. Mol Cell Biol, 2002, 22: 614-625.
34. Xu M, Long C, Chen X, et al. Partitioning of histone H3-H4 tetramers during DNA replication-dependent chromatin assembly. Science, 2010, 328: 94-98.
35. Ahmad K, Henikoff S. The histone variant H3. 3 marks active chromatin by replication-independent nucleosome assembly. Mol Cell, 2002, 9: 1191-1200.
36. Hake S B, Garcia B A, Duncan E M, et al. Expression patterns and post-translational modifications associated with mammalian histone H3 variants. J Biol Chem, 2006, 281: 559-568.
37. Mito Y, Henikoff J G, Henikoff S. Genome-scale profiling of histone H3. 3 replacement patterns. Nat Genet, 2005, 37: 1090-1097.
38. Loyola A, Bonaldi T, Roche D, et al. PTMs on H3 variants before chromatin assembly potentiate their final epigenetic state. Mol Cell, 2006, 24: 309-316.
39. Quivy J P, Roche D, Kirschner D, et al. A CAF-1 dependent pool of HP1 during heterochromatin duplication. EMBO J, 2004, 23: 3516-3526.
40. Tagami H, Ray-Gallet D, Almouzni G, et al. Histone H3. 1 and H3. 3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis. Cell, 2004, 116: 51-61.
41. Dohke K, Miyazaki S, Tanaka K, et al. Fission yeast chromatin assembly factor 1 assists in the replication-coupled maintenance of heterochromatin. Genes Cells, 2008, 13: 1027-1043.
42. Houlard M, Berlivet S, Probst A V, et al. CAF-1 is essential for heterochromatin organization in pluripotent embryonic cells. PLoS Genet, 2006, 2: e181.
43. Huang H, Yu Z, Zhang S, et al. Drosophila CAF-1 regulates HP1-mediated epigenetic silencing and pericentric heterochromatin stability. J Cell Sci, 2010, 123: 2853-2861.
44. Clark R F, Elgin S C. Heterochromatin protein 1, a known suppressor of position-effect variegation, is highly conserved in Drosophila. Nucleic Acids Res, 1992, 20: 6067-6074.
45. Schotta G, Lachner M, Sarma K, et al. A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin. Genes Dev, 2004, 18: 1251-1262.
46. Murzina N, Verreault A, Laue E, et al. Heterochromatin dynamics in mouse cells: interaction between chromatin assembly factor 1 and HP1 proteins. Mol Cell, 1999, 4: 529-540.
47. Anderson A E, Karandikar U C, Pepple K L, et al. The enhancer of trithorax and polycomb gene Caf1/p55 is essential for cell survival and patterning in Drosophila development. Development, 2011, 138: 1957-1966.
48. Nabatiyan A, Szuts D, Krude T. Induction of CAF-1 expression in response to DNA strand breaks in quiescent human cells. Mol Cell Biol, 2006, 26: 1839-1849.
49. Polo S E, Roche D, Almouzni G. New histone incorporation marks sites of UV repair in human cells. Cell, 2006, 127: 481-493.
50. Chen C C, Carson J J, Feser J, et al. Acetylated lysine 56 on histone H3 drives chromatin assembly after repair and signals for the completion of repair. Cell, 2008, 134: 231-243.
51. Li Q, Zhou H, Wurtele H, et al. Acetylation of histone H3 lysine 56 regulates replication-coupled nucleosome assembly. Cell, 2008, 134: 244-255.
52. Zhang D, Wang D, Sun F. Drosophila melanogaster heterochromatin protein HP1b plays important roles in transcriptional activation and development. Chromosoma, 2011, 120: 97-108.
53. Li Y, Danzer J R, Alvarez P, et al. Effects of tethering HP1 to euchromatic regions of the Drosophila genome. Development, 2003, 130: 1817-1824.
54. Schwaiger M, Kohler H, Oakeley E J, et al. Heterochromatin protein 1 (HP1) modulates replication timing of the Drosophila genome. Genome Res, 2010, 20: 771-780.
55. Hwang K K, Eissenberg J C, Worman H J. Transcriptional repression of euchromatic genes by Drosophila heterochromatin protein 1 and histone modifiers. Proc Natl Acad Sci USA, 2001, 98: 11423-11427.
56. Luijsterburg M S, Dinant C, Lans H, et al. Heterochromatin protein 1 is recruited to various types of DNA damage. J Cell Biol, 2009, 185: 577-586.
57. Baldeyron C, Soria G, Roche D, et al. HP1α recruitment to DNA damage by p150CAF-1 promotes homologous recombination repair. J Cell Biol, 2011, 193: 81-95.
58. Jiao R, Bachrati C Z, Pedrazzi G, et al. Physical and functional interaction between the Bloom's syndrome gene product and the largest subunit of chromatin assembly factor 1. Mol Cell Biol, 2004, 24: 4710-4719.
59. Jiao R, Harrigan J A, Shevelev I, et al. The Werner syndrome protein is required for recruitment of chromatin assembly factor 1 following DNA damage. Oncogene, 2007, 26: 3811-3822.
60. Moggs J G, Grandi P, Quivy J P, et al. A CAF-1-PCNA-mediated chromatin assembly pathway triggered by sensing DNA damage. Mol Cell Biol, 2000, 20: 1206-1218.
61. Grewal S I, Elgin S C. Transcription and RNA interference in the formation of heterochromatin. Nature, 2007, 447: 399-406.
62. Shermoen A W, McCleland M L, O'Farrell P H. Developmental control of late replication and S phase length. Curr Biol, 2010, 20: 2067-2077.
63. Quivy J P, Gerard A, Cook A J, et al. The HP1-p150/CAF-1 interaction is required for pericentric heterochromatin replication and S-phase progression in mouse cells. Nat Struct Mol Biol, 2008, 15: 972-979.
64. Turner B M. Cellular memory and the histone code. Cell, 2002, 111: 285-291.
65. Lusser A, Kadonaga J T. Chromatin remodeling by ATP-dependent molecular machines. Bioessays, 2003, 25: 1192-1200.
66. Fischle W, Wang Y, Allis C D. Histone and chromatin cross-talk. Curr Opin Cell Biol, 2003, 15: 172-183.
67. Goodfellow H, Krejci A, Moshkin Y, et al. Gene-specific targeting of the histone chaperone asf1 to mediate silencing. Dev Cell, 2007, 13: 593-600.
68. Moshkin Y M, Kan T W, Goodfellow H, et al. Histone chaperones ASF1 and NAP1 differentially modulate removal of active histone marks by LID-RPD3 complexes during NOTCH silencing. Mol Cell, 2009, 35: 782-793.
69. Badenhorst P, Xiao H, Cherbas L, et al. The Drosophila nucleosome remodeling factor NURF is required for Ecdysteroid signaling and metamorphosis. Genes Dev, 2005, 19: 2540-2545.
70. Song H, Spichiger-Haeusermann C, Basler K. The ISWI-containing NURF complex regulates the output of the canonical Wingless pathway. EMBO Rep, 2009, 10: 1140-1146.
71. Kugler S J, Nagel A C. A novel Pzg-NURF complex regulates Notch target gene activity. Mol Biol Cell, 2010, 21: 3443-3448.
72. Kugler S J, Gehring E M, Wallkamm V, et al. The Putzig-NURF nucleosome remodeling complex is required for ecdysone receptor signaling and innate immunity in Drosophila melanogaster. Genetics, 2011, 188: 127-139.
73. Kim H J, Seol J H, Cho E J. Potential role of the histone chaperone, CAF-1, in transcription. BMB Rep, 2009, 42: 227-231.
74. Li G, Margueron R, Hu G, et al. Highly compacted chromatin formed in vitro reflects the dynamics of transcription activation in vivo. Mol Cell, 2010, 38: 41-53.