Possible role of H1 histone in replication timing

Development Growth and Differentiation

Volumn 57, Issue 1, 2015, Pages 1-9

  Flickinger, Reed A ^a  

^a UNIVERSITY AT BUFFALO   (United States)

Author keywords

AT rich; DNA; H1 histone

Indexed keywords

DNA; HIGH MOBILITY GROUP PROTEIN; HISTONE H1; NUCLEAR RNA; THYMIDINE TRIPHOSPHATE; CHROMATIN; HISTONE;

AT RICH SEQUENCE; CELL CYCLE G1 PHASE; CELL CYCLE S PHASE; CELL DENSITY; CELL DIFFERENTIATION; CELL ELONGATION; CELL NUCLEUS MATRIX; CHROMATIN; CPG ISLAND; DNA BASE COMPOSITION; DNA REPLICATION TIMING; EMBRYONIC STEM CELL; HISTONE ACETYLATION; HISTONE PHOSPHORYLATION; HUMAN; MATRIX ATTACHMENT REGION; NONHUMAN; REPLICON; REVIEW; ACETYLATION; ANIMAL; DNA REPLICATION; GENETICS; METABOLISM; PHOSPHORYLATION; PHYSIOLOGY; PROTEIN PROCESSING;

ACETYLATION; ANIMALS; CHROMATIN; DNA REPLICATION; HISTONES; HUMANS; PHOSPHORYLATION; PROTEIN PROCESSING, POST-TRANSLATIONAL;

EID: 84921601128     PISSN: 00121592     EISSN: 1440169X     Source Type: Journal    
DOI: 10.1111/dgd.12190     Document Type: Review

References (88)

1. Alexandrow, M. G. & Hamlin, J. L. 2005. Chromatin decondensation in S phase involves recruitment of Cdk2 by Cdc45 and histone H1 phosphorylation. J. Cell Biol. 168, 875-886.
2. Anachova, B., Djeliova, V. & Russev, G. 2005. Nuclear matrix support of DNA replication. J. Cell. Biochem. 96, 951-961.
3. Anglana, M., Apiou, F., Bensiman, A. & Debatisse, M. 2003. Dynamics of DNA replication in mammalian somatic cells: nucleotide pool modulates origin choice and interorigin spacing. Cell 114, 385-394.
4. Aparicio, J. G., Viggiani, C. J., Gibson, D. G. & Aparicio, O. M. 2004. The Rpd3-Sin3 histone deacetylase regulates replication timing and enables intra-S origin control in Saccharomyces cerivisiae. Mol. Cell. Biol. 24, 4769-4780.
5. Bailey, J. A., Carrel, L., Chakrararti, A. & Eichler, E. E. 2000. Molecular evidence for a relationship between LINE-1 elements and X-chromosome inactivation. Proc. Natl Acad. Sci. USA 97, 6634-6639.
6. Berezney, R., Dubey, D. D. & Huberman, J. A. 2000. Heterogeneity of eukaryotic replicons, replicon clusters and replication foci. Chromosoma 108, 471-484.
7. Bleher, R. & Martin, R. 1999. Nucleo-cytoplasmic translocation of histone H1 during the HeLa cell cycle. Chromosoma 108, 308-316.
8. Bordignon, V., Clarke, H. J. & Smith, L. C. 2001. Factors controlling the loss of immunoreactive somatic histone H1 from blastomere nuclei in oocyte cytoplasm: a potential marker of nuclear reprogramming. Dev. Biol. 233, 192-203.
9. Buongiorno-Nardelli, M., Micheli, G., Carri, M. T. & Marilley, M. 1982. A relationship between replicon size and supercoiled loop domains in the eukaryotic genome. Nature 298, 100-102.
10. Catez, F., Yang, H., Tracey, K. J., Reeves, R., Mistelli, T. J. & Bustin, M. 2004. Network of dynamic interactions between histone H1 and high-mobility group proteins in chromatin. Mol. Cell. Biol. 24, 4321-4328.
11. Cayrou, C., Coulombe, P., Vigneron, A., Stanojcic, S., Ganier, O., Peiffer, I., Rivals, E., Puy, A., Laurent-Chablier, S., Desprat, R. & Mechali, M. 2011. Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features. Genome Res. 21, 1438-1449.
12. Comings, D. E. 1972. Replicative heterogeneity of mammalian DNA. Exp. Cell Res. 71, 106-112.
13. Courbet, S., Gay, S., Arnoult, N., Wronka, G., Anglana, M., Brison, O., Debatisse, M. 2008. Replication fork movement sets chromatin loop size and origin choice in mammalian cells. Nature 455, 557-566.
14. Cui, F. & Zhurkin, V. B. 2009. Distinctive sequence patterns in methylated and yeast nucleosomes: implications for linker histone binding to AT-rich and methylated DNA. Nucleic Acids Res. 37, 2818-2829.
15. Dai, J., Chuang, R.-Y. & Kelly, T. J. 2005. DNA replication origins in the Schizosaccharomyces pombe genome. Proc. Natl Acad. Sci. USA 102, 337-342.
16. Daniel, J. C. & Flickinger, R. A. 1971. Nuclear DNA-like RNA in developing frog embryos. Exp. Cell Res. 64, 285-290.
17. Delgado, S., Gomez, M., Bird, A. & Antequera, E. 1998. Initiation of DNA replication at CpG islands in mammalian chromosomes. EMBO J. 17, 2426-2435.
18. DePamphilis, M. L. 2005. Cell cycle dependent regulation of the origin recognition complex. Cell Cycle 4, 70-79.
19. Dimitrova, D. S. & Gilbert, D. M. 1999. The spatial position and replication timing of chromosomal domains are both established in early G1 phase. Mol. Cell 4, 983-993.
20. Djeliova, V., Russev, G. & Anachova, B. 2001a. Dynamics of association of origins of DNA replication with the nuclear matrix during the cell cycle. Nucleic Acids Res. 29, 3181-3187.
21. Djeliova, V., Russev, G. & Anachova, B. 2001b. Distribution of DNA replication origins between matrix-attached and loop DNA in mammalian cells. J. Cell. Biochem. 80, 353-359.
22. Dou, Y., Mizzon, C. A., Abrams, M., Allis, C. D. & Gorovsky, M. A. 1999. Phosphorylation of linker histone H1 regulates gene expression in vivo by mimicking H1 removal. Mol. Cell 4, 641-647.
23. Efroni, S., Duttagupta, R., Cheng, J., Dehghani, H., Hoeppner, D. J., Dash, C., Bazett-Jones, D. P., Le Grice, S., McKay, R. D., Buetow, K. H., Gingeras, T. R., Misteli, T. & Meshorer, E. 2008. Global transcription in pluripotent embryonic stem cells. Cell Stem Cell 2, 437-447.
24. Flickinger, R. A. 2001. Replication timing and cell differentiation. Differentiation 69, 18-26.
25. Flickinger, R. A. & Richman, R. 1983. Incorporation of deoxycytidine triphosphate and thymidine triphosphate into nuclear DNA in vitro during early and late S phase in frog embryos. Cell Differ. 12, 233-237.
26. Flickinger, R. A., Givens, R., Pine, S. & Sepanik, P. 1986. Factors controlling the size of DNA loops in frog embryos and Friend erythroleukemia cells. Cell Differ. 19, 59-71.
27. Gasser, S. M. & Laemmli, U. K. 1986. The organization of chromatic loops: characterization of a scaffold attachment site. EMBO J. 5, 511-518.
28. Gay, S., Luchages, A.M., Millot, G.A., Courbet, S., Letessier, A., Debatisse, M. & Brison, O. 2010. Nucleotide supply, not local histone acetylation, sets replication origin usage in transcribed regions. EMBO Rep. 11, 698-704.
29. Girard-Reydet, C., Gregoire, A., Vassetzky, Y. & Méchali, M. 2004. DNA replication initiates at domains overlapping with nuclear matrix attachment regions in the Xenopus and mouse c-myc promoter. Gene 332, 129-138.
30. Goldar, A., Marsolier-Kergoat, M.-C. & Hyrien, O. 2009. Universal temporal profile of replication origin activation in eukaryotes. PLoS ONE 4, e5899.
31. Goren, A., Tabib, A., Hecht, M. & Cedar, H. 2008. DNA replication timing of the human β-globin domain is controlled by histone modification at the origin. Genes Dev. 22, 1319-1324.
32. Grabar, F. & Flickinger, R. A. 1981. Sizes and rates of elongation of replicons in the frog embryo. Rouxs Arch. Dev. Biol. 190, 55-57.
33. Green, A., Lönn, A., Peterson, K. H., Öllinger, K. & Rundquist, I. 2010. Translocation of histone H1 subtypes between chromatin and cytoplasm during mitosis in normal human fibroblasts. Cytometry A 77A, 478-484.
34. Guilbaud, G., Rappailles, A., Baker, A., Chen, C. L., Arneodo, A., Goldar, A., d'Aubenton-Carafa, Y., Thermes, C., Audit, B. & Hyrien, O. 2011. Evidence for sequential and increasing activation of replication origins along replication timing gradients in the human genome. PLoS Comput. Biol. 7, e1002322.
35. Happel, N., Warneboldt, J., Hänecke, K., Haller, F. & Doencke, D. 2009. H1 subtype expression during cell proliferation and growth arrest. Cell Cycle 8, 2226-2232.
36. Hiratani, Y., Ryba, T., Itoh, M., Yokochi, T., Schwaiger, M., Chang, C. W., Lyou, Y., Townes, T. M., Schübeler, D. & Gilbert, D. M. 2008. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol. 6, e245.
37. Housman, D. & Huberman, J. A. 1975. Changes in the rate of DNA replication fork movement during S phase in mammalian cells. J. Mol. Biol. 94, 173-181.
38. Iyer, V. & Struhl, K. 1995. Poly (dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic structure. EMBO J. 14, 2570-2579.
39. Ji, K.-H., Xiong, J., Hu, K.-M., Fan, L.-X. & Liu, H.-Q. 2008. Simultaneous expression of Oct4 and genes of three germ layers in single cell-derived multipotent adult progenitor cells. Ann. Hematol. 87, 431-438.
40. Jordan, I. K., Rogozin, I. B., Glazko, G. V. & Koonin, E. V. 2003. Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends Genet. 19, 68-72.
41. Kaplan, N., Moore, I.K., Fondufe-Mittendorf, Y., Gossett, A. J., Tillo, D., Field, Y., LeProust, E. M., Hughes, T. R., Lieb, J. D., Widom, J. & Segal, E. 2009. The DNA-encoded nucleosome organization of a eukaryote genome. Nature 458, 362-366.
42. Katsuno, Y., Suzuki, A., Sugimura, K., Okumura, K., Zineldeen, D. H., Shimada, M., Niida, H., Mizuno, T., Hanaoka, F. & Nakanishi, M. 2009. Cyclin A-Cdk1 regulates the origin firing program in mammalian cells. Proc. Natl Acad. Sci. USA 106, 3184-3189.
43. Labit, H., Perewosko, I., Germe, T., Hyrien, O. & Marheineke, K. 2008. DNA replication timing is deterministic of the level of chromosomal domains but stochastic at the level of replicons in Xenopus egg extracts. Nucleic Acids Res. 36, 5623-5634.
44. Lagarkova, M. A., Svetlova, E., Giacca, M., Falashi, A. & Razin, S. V. 1998. DNA loop anchorage region colocalizes with the replication origin located downstream of the human gene encoding lamin B2. J. Cell. Biochem. 69, 13-18.
45. Lemaitre, J.-M., Danis, E., Pasero, P., Vassetzky, Y. & Méchali, M. 2005. Mitotic remodeling of the replicon and chromosomal structure. Cell 123, 787-801.
46. Leonard, A. C. & Méchali, M. 2013. DNA replication origins. Cold Spring Harb. Perspect. Biol. 5, a010116.
47. Lever, M. A., Th'ng, J. P., Sun, X. & Hendzel, M. J. 2000. Rapid exchange of histone H1 on chromatin in living human cells. Nature 408, 873-875.
48. Li, F., Chen, J., Solessio, E. & Gilbert, D. M. 2003. Spatial distribution and specification of mammalian replication origins during G1 phase. J. Cell Biol. 161, 257-266.
49. Liapunova, N. A. 1994. Organization of replication units and DNA replication in mammalian cells as studied by DNA fiber autoradiography. Int. Rev. Cytol. 154, 261-308.
50. Loberg, H. & Rundquist, I. 2006. Affinity of linker histone for chromatin in situ analyzed using DAPI as a cytochemical probe. Cytometry 46, 1-9.
51. Lu, Z. H., Sittman, D. B., Romanowski, P. & Leno, G. H. 1998. Histone H1 reduces the frequency of initiation in Xenopus egg extract by limiting the assembly of prereplication complexes on sperm chromatin. Mol. Biol. Cell 9, 1163-1176.
52. Lu, Z. H., Xu, H. & Leno, G. H. 1999. DNA replication in quiescent cell nuclei; regulation by the nuclear envelope and chromatin structure. Mol. Biol. Cell 10, 4091-4106.
53. Lu, J., Li, F., Murphy, S., Davidson, M. W. & Gilbert, D. M. 2010. G2 phase chromatin lacks determinants of replication timing. J. Cell Biol. 189, 967-980.
54. Lubelsky, Y., Sasaki, T., Kuipers, M. A. et al. 2011. Prereplication complex proteins assemble at regions of low nucleosome occupancy within the Chinese hamster dihydrofolate reductase initiation zone. Nucleic Acids Res. 39, 3141-3155.
55. Ma, H., Samarabandu, J., Devdhar, R.S., Acharya, R., Cheng, P. C., Meng, C. & Berezney, R. 1998. Spatial and temporal dynamics of DNA replication sites in mammalian cells. J. Cell Biol. 143, 1415-1425.
56. Malinsky, J., Koberna, K., Staněk, D., Mašata, M., Votruba, I. & Raška, I. 2000. The supply of exogenous deoxyribonucleotides accelerates the speed of the replication fork in early S phase. J. Cell Sci. 114, 747-750.
57. Mantiero, D., Mackenzie, A., Donaldson, A. & Zegerman, P. 2011. Limiting replication initiation factors execute the temporal programme of origin firing in budding yeast. EMBO J. 30, 4805-4814.
58. Mistelli, T., Gunjan, A., Hock, R., Bustin, M. & Brown, D. T. 2000. Dynamic binding of histone H1 to chromatin in living cells. Nature 408, 877-881.
59. Nelson, H. C. M. 1987. The structure of an oligo (dA) oligo (dT) tract and its biological implications. Nature 330, 221-226.
60. Painter, R. B. & Schaefer, A. W. 1971. Variation in the rate of DNA chain growth through the S phase in HeLa cells. J. Mol. Biol. 58, 289-295.
61. Perry, C. A. & Annunziato, A. T. 1991. Histone acetylation reduces H1-mediated nucleosome interactions during chromatin assembly. Exp. Cell Res. 196, 337-345.
62. +) nuclear RNA of frog embryos and Friend erythroleukemia cells. Dev. Growth Differ. 30, 9-14.
63. Popova, E.Y., Grigoryev, S.A., Fan, Y., Skoultchi, A. I., Zhang, S. S. & Barnstable, C. J. 2013. Developmentally regulated linker histone H1c promotes heterochromatin condensation and mediates structural integrity of rod photoreceptors in mouse retina. J. Biol. Chem. 288, 17895-17907.
64. Radichev, I., Parashkevova, A. & Anachova, B. 2005. Initiation of DNA replication at a nuclear matrix-attached chromatin fraction. J. Cell. Physiol. 203, 71-77.
65. Razin, S. V., Vassetzky, Y. S. & Hancock, R. 1991. Nuclear matrix attachment regions and topoisomerase II binding and reaction sites in the vicinity of a chicken DNA replication origin. Biochem. Biophys. Res. Commu. 177, 265-270.
66. Remington, J. A. & Flickinger, R. A. 1971. The time of DNA replication in the cell cycle in relation to RNA synthesis in frog embryos. J. Cell. Physiol. 77, 411-422.
67. Remington, J. A. & Flickinger, R. A. 1978. Timing of incorporation of tritiated nucleosides into DNA and RNA of embryonic cells of Rana pipiens. Dev. Growth Differ. 20, 11-15.
68. Rhind, N. & Gilbert, D. M. 2013. DNA replication timing. Cold Spring Harb. Perspect. Biol. 5, a010132.
69. Roque, A., Orrego, M., Ponte, I. & Suau, P. 2004. The preferential binding of histone H1 to DNA scaffold-associated regions is determined by its C-terminal domain. Nucleic Acids Res. 32, 6111-6119.
70. Russinoff, S., Miran, S., Gowda, A. L. & Lucas, P. A. 2011. Osteosarcoma cells differentiate into phenotypes from all three dermal layers. Clin. Orthop. Relat. Res. 469, 2895-2904.
71. Ryba, T., Hiratani, I., Lu, J., Itoh, M., Kulik, M., Zhang, J., Schulz, T. C., Robins, A. J., Dalton, S. & Gilbert, D. M. 2010. Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Genome Res. 20, 761-770.
72. Sadoni, M., Cardoso, N. C., Stelzer, E. H. K., Leonhardt, H. & Zink, D. 2004. Stable chromosomal units determine the spatial and temporal organization of DNA replication. J. Cell Sci. 117, 5353-5365.
73. Stanojcic, S., Lemaitre, J.-M., Brodolin, K., Danis, E. & Méchali, M. 2008. In Xenopus egg extracts, DNA replication initiates preferentially at or near asymmetric AT sequences. Mol. Cell. Biol. 28, 5265-5274.
74. Suter, B., Schnappauf, G. & Thoma, F. 2000. Poly (dA·dT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo. Nucleic Acids Res. 28, 4083-4089.
75. Takebayashi, S-I., Sugimura, K., Saito, T., Sato, C., Fukushima, Y., Taguchi, H. & Okumura, K. 2005. Regulation of replication at the R/G chromosomal band boundary and pericentromeric heterochromatin of mammalian cells. Exp. Cell Res. 304, 162-174.
76. Talasz, H., Helliger, W., Pushendorf, B. & Lindner, H. 1996. In vivo phosphorylation of histone H1 variants during the cell cycle. Biochemistry 35, 1761-1767.
77. Tanaka, S., Nakato, R., Katou, Y., Shirahige, K. & Araki, H. 2011. Origin association of Sid3, Sid7, and Cdc45 proteins is a key step for determination of origin-firing timing. Curr. Biol. 21, 2055-2063.
78. Thiriet, C. & Hayes, J. J. 2009. Linker histone phosphorylation regulates global timing of replication origin firing. J. Biol. Chem. 284, 2823-2829.
79. Thomae, A.W., Pich, D., Brocher, J., Spindler, M. P., Berens, C., Hock, R., Hammerschmidt, W. & Schepers, A. 2008. Interaction between HMGA1a and the origin recognition complex creates site-specific replication origins. Proc. Natl Acad. Sci. USA 105, 1692-1697.
80. Thomson, A. M., Gillespie, P. J. & Blow, J. 2010. Replication factory activation can be decoupled from the replication timing program by modulating Cdk levels. J. Cell Biol. 188, 209-227.
81. Vogelauer, M., Rubbi, L., Lucas, I., Brewer, B. J. & Grunstein, M. 2002. Histone acetylation regulates the time of replication origin firing. Mol. Cell 10, 1223-1233.
82. Woodcock, C. L., Skoultchi, A. & Fan, Y. 2006. Role of linker histone in chromatin structure and function: H1 stoichiometry and nucleosome repeat length. Chromosome Res. 14, 17-25.
83. Woodfine, K., Feigler, H., Beare, D. M. et al. 2004. Replication timing of the human genome. Hum. Mol. Genet. 13, 191-202.
84. Wu, P.-Y. & Nurse, P. 2009. Establishing the program of origin firing during S phase in fission yeast. Cell 136, 852-864.
85. Wu, L. H., Kuehl, L. & Rechsteiner, M. 1986. Dynamic behavior of histone H1 microinjected into HeLa cells. J. Cell Biol. 103, 465-474.
86. Yang, S. G. H., Rhind, N. & Bechoefer, J. 2010. Modeling genome-wide replication kinetics reveals a mechanism for regulation of replication timing. Mol. Syst. Biol. 6, 404.
87. Zhao, K., Käs, E., Gonzalez, E. & Laemmli, U. K. 1993. SAR-dependent mobilization of histone H1 by HMG-I/Y in vitro: HMG-I/Y is enriched in H1-depleted chromatin. EMBO J. 12, 3237-3247.
88. Zhong, Y., Nellimoottil, T., Pease, J.M., Knott, S. R., Villwock, S. K., Yee, J. M., Jancuska, J. M., Rege, S., Tecklenburg, M., Sclafani, R. A., Tavaré, S. & Aparicio, O. M. 2013. The level of origin firing inversely affects the rate of replication fork progression. J. Cell Biol. 201, 373-383.