Cell cycle regulation of human DNA repair and chromatin remodeling genes

DNA Repair

Volumn 30, Issue , 2015, Pages 53-67

  Mjelle, Robin ^a   Hegre, Siv Anita ^a   Aas, Per Arne ^a   Slupphaug, Geir ^a   Drabløs, Finn ^a   Sætrom, Pål ^a   Krokan, Hans E ^a  

^a NORWEGIAN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Norway)

Author keywords

Cell cycle; Chromatin remodeling genes; DNA repair genes

Indexed keywords

CHROMATIN ASSEMBLY FACTOR 1; DOUBLE STRANDED DNA; TRANSCRIPTION FACTOR E2F;

ARTICLE; CELL CYCLE REGULATION; CELL CYCLE S PHASE; CHROMATIN ASSEMBLY AND DISASSEMBLY; DNA END JOINING REPAIR; DNA REPAIR; EXCISION REPAIR; FANCONI ANEMIA; G1 PHASE CELL CYCLE CHECKPOINT; HOMOLOGOUS RECOMBINATION; MISMATCH REPAIR; PRIORITY JOURNAL; RECOMBINATION REPAIR; REGULATORY MECHANISM; CELL CYCLE; GENE EXPRESSION; GENETICS; HUMAN; PHYSIOLOGY;

CELL CYCLE; CHROMATIN ASSEMBLY AND DISASSEMBLY; DNA REPAIR; GENE EXPRESSION; HUMANS;

EID: 84927125607     PISSN: 15687864     EISSN: 15687856     Source Type: Journal    
DOI: 10.1016/j.dnarep.2015.03.007     Document Type: Article

References (138)

1. Daniel J.A., Nussenzweig A. The AID-induced DNA damage response in chromatin. Mol. Cell 2013, 50:309-321.
2. Fong Y.W., Cattoglio C., Tjian R. The intertwined roles of transcription and repair proteins. Mol. Cell 2013, 52:291-302.
3. Sancar A., Lindsey-Boltz L.A., Unsal-Kacmaz K., Linn S. Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints. Annu. Rev. Biochem 2004, 73:39-85.
4. Houtgraaf J.H., Versmissen J., van der Giessen W.J. A concise review of DNA damage checkpoints and repair in mammalian cells. Cardiovasc. Revasc. Med. 2006, 7:165-172.
5. Cimprich K.A., Cortez D. ATR: an essential regulator of genome integrity. Nat. Rev. Mol. Cell Biol. 2008, 9:616-627.
6. Krokan H.E., Bjoras M. Base excision repair. Cold Spring Harb. Perspect. Biol. 2013, 5:a012583.
7. Baldeyron C., Soria G., Roche D., Cook A.J., Almouzni G. HP1alpha recruitment to DNA damage by p150CAF-1 promotes homologous recombination repair. J. Cell Biol. 2011, 193:81-95.
8. Hagen L., Kavli B., Sousa M.M., Torseth K., Liabakk N.B., Sundheim O., Pena-Diaz J., Otterlei M., Horning O., Jensen O.N., Krokan H.E., Slupphaug G. Cell cycle-specific UNG2 phosphorylations regulate protein turnover, activity and association with RPA. EMBO J. 2008, 27:51-61.
9. Hardeland U., Kunz C., Focke F., Szadkowski M., Schar P. Cell cycle regulation as a mechanism for functional separation of the apparently redundant uracil DNA glycosylases TDG and UNG2. Nucleic Acids Res. 2007, 35:3859-3867.
10. Otterlei M., Warbrick E., Nagelhus T.A., Haug T., Slupphaug G., Akbari M., Aas P.A., Steinsbekk K., Bakke O., Krokan H.E. Post-replicative base excision repair in replication foci. EMBO J. 1999, 18:3834-3844.
11. Fischer J.A., Caradonna S. Analysis of nuclear uracil-DNA glycosylase (nUDG) turnover during the cell cycle. Methods Mol. Biol. 2011, 761:137-149.
12. Marra G., Chang C.L., Laghi L.A., Chauhan D.P., Young D., Boland C.R. Expression of human MutS homolog 2 (hMSH2) protein in resting and proliferating cells. Oncogene 1996, 13:2189-2196.
13. Seifert M., Reichrath J. The role of the human DNA mismatch repair gene hMSH2 in DNA repair, cell cycle control and apoptosis: implications for pathogenesis, progression and therapy of cancer. J. Mol. Histol. 2006, 37:301-307.
14. Jiricny J. Postreplicative mismatch repair. Cold Spring Harb. Perspect. Biol. 2013, 5:a012633.
15. Scharer O.D. Nucleotide excision repair in eukaryotes. Cold Spring Harb. Perspect. Biol. 2013, 5:a012609.
16. Chiruvella K.K., Liang Z., Wilson T.E. Repair of double-strand breaks by end joining. Cold Spring Harb. Perspect. Biol. 2013, 5:a012757.
17. Jasin M., Rothstein R. Repair of strand breaks by homologous recombination. Cold Spring Harb. Perspect. Biol. 2013, 5:a012740.
18. Deans A.J., West S.C. DNA interstrand crosslink repair and cancer. Nat. Rev. Cancer 2011, 11:467-480.
19. Jandt U., Platas Barradas O., Portner R., Zeng A.P. Mammalian cell culture synchronization under physiological conditions and population dynamic simulation. Appl. Microbiol. Biotechnol. 2014.
20. Bar-Joseph Z., Siegfried Z., Brandeis M., Brors B., Lu Y., Eils R., Dynlacht B.D., Simon I. Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:955-960.
21. Cho R.J., Huang M., Campbell M.J., Dong H., Steinmetz L., Sapinoso L., Hampton G., Elledge S.J., Davis R.W., Lockhart D.J. Transcriptional regulation and function during the human cell cycle. Nat. Genet. 2001, 27:48-54.
22. Pena-Diaz J., Hegre S.A., Anderssen E., Aas P.A., Mjelle R., Gilfillan G.D., Lyle R., Drablos F., Krokan H.E., Saetrom P. Transcription profiling during the cell cycle shows that a subset of Polycomb-targeted genes is upregulated during DNA replication. Nucleic Acids Res. 2013, 41:2846-2856.
23. Peng X., Karuturi R.K., Miller L.D., Lin K., Jia Y., Kondu P., Wang L., Wong L.S., Liu E.T., Balasubramanian M.K., Liu J. Identification of cell cycle-regulated genes in fission yeast. Mol. Biol. Cell 2005, 16:1026-1042.
24. Spellman P.T., Sherlock G., Zhang M.Q., Iyer V.R., Anders K., Eisen M.B., Brown P.O., Botstein D., Futcher B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 1998, 9:3273-3297.
25. Whitfield M.L., Sherlock G., Saldanha A.J., Murray J.I., Ball C.A., Alexander K.E., Matese J.C., Perou C.M., Hurt M.M., Brown P.O., Botstein D. Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol. Biol. Cell 2002, 13:1977-2000.
26. Jensen L.J., Jensen T.S., de Lichtenberg U., Brunak S., Bork P. Co-evolution of transcriptional and post-translational cell-cycle regulation. Nature 2006, 443:594-597.
27. van der Meijden C.M., Lapointe D.S., Luong M.X., Peric-Hupkes D., Cho B., Stein J.L., van Wijnen A.J., Stein G.S. Gene profiling of cell cycle progression through S-phase reveals sequential expression of genes required for DNA replication and nucleosome assembly. Cancer Res. 2002, 62:3233-3243.
28. Chen F., Nastasi A., Shen Z., Brenneman M., Crissman H., Chen D.J. Cell cycle-dependent protein expression of mammalian homologs of yeast DNA double-strand break repair genes Rad51 and Rad52. Mutat. Res. 1997, 384:205-211.
29. Krude T., Keller C. Chromatin assembly during S phase: contributions from histone deposition, DNA replication and the cell division cycle. Cell. Mol. Life Sci. 2001, 58:665-672.
30. Vignali M., Hassan A.H., Neely K.E., Workman J.L. ATP-dependent chromatin-remodeling complexes. Mol. Cell. Biol. 2000, 20:1899-1910.
31. Wood R.D., Mitchell M., Lindahl T. Human DNA repair genes, 2005. Mutat. Res. 2005, 577:275-283.
32. Wood R.D., Mitchell M., Sgouros J., Lindahl T. Human DNA repair genes. Science 2001, 291:1284-1289.
33. Stumpf C.R., Moreno M.V., Olshen A.B., Taylor B.S., Ruggero D. The translational landscape of the mammalian cell cycle. Mol. Cell 2013, 52:574-582.
34. Trapnell C., Pachter L., Salzberg S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25:1105-1111.
35. Trapnell C., Hendrickson D.G., Sauvageau M., Goff L., Rinn J.L., Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat. Biotechnol. 2013, 31:46-53.
36. Leng N., Dawson J.A., Thomson J.A., Ruotti V., Rissman A.I., Smits B.M., Haag J.D., Gould M.N., Stewart R.M., Kendziorski C. EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics 2013, 29:1035-1043.
37. Bravo R. Synthesis of the nuclear protein cyclin (PCNA) and its relationship with DNA replication. Exp. Cell Res. 1986, 163:287-293.
38. Simbulan-Rosenthal C.M., Rosenthal D.S., Boulares A.H., Hickey R.J., Malkas L.H., Coll J.M., Smulson M.E. Regulation of the expression or recruitment of components of the DNA synthesome by poly(ADP-ribose) polymerase. Biochemistry 1998, 37:9363-9370.
39. Wang J., Chen J., Gong Z. TopBP1 controls BLM protein level to maintain genome stability. Mol. Cell 2013, 52:667-678.
40. Dimitrov S.D., Lu D., Naetar N., Hu Y., Pathania S., Kanellopoulou C., Livingston D.M. Physiological modulation of endogenous BRCA1 p220 abundance suppresses DNA damage during the cell cycle. Genes Dev. 2013, 27:2274-2291.
41. Guo Z., Kanjanapangka J., Liu N., Liu S., Liu C., Wu Z., Wang Y., Loh T., Kowolik C., Jamsen J., Zhou M., Truong K., Chen Y., Zheng L., Shen B. Sequential posttranslational modifications program FEN1 degradation during cell-cycle progression. Mol. Cell 2012, 47:444-456.
42. Geiman T.M., Muegge K. Lsh, an SNF2/helicase family member, is required for proliferation of mature T lymphocytes. Proc. Natl. Acad. Sci. U. S. A. 2000, 97:4772-4777.
43. Polo S.E., Theocharis S.E., Klijanienko J., Savignoni A., Asselain B., Vielh P., Almouzni G. Chromatin assembly factor-1, a marker of clinical value to distinguish quiescent from proliferating cells. Cancer Res. 2004, 64:2371-2381.
44. Heck M.M., Hittelman W.N., Earnshaw W.C. Differential expression of DNA topoisomerases I and II during the eukaryotic cell cycle. Proc. Natl. Acad. Sci. U. S. A. 1988, 85:1086-1090.
45. Yamanaka S., Campbell N.R., An F., Kuo S.C., Potter J.J., Mezey E., Maitra A., Selaru F.M. Coordinated effects of microRNA-494 induce G(2)/M arrest in human cholangiocarcinoma. Cell Cycle 2012, 11:2729-2738.
46. Kaidi A., Jackson S.P. KAT5 tyrosine phosphorylation couples chromatin sensing to ATM signalling. Nature 2013, 498:70-74.
47. Strom L., Lindroos H.B., Shirahige K., Sjogren C. Postreplicative recruitment of cohesin to double-strand breaks is required for DNA repair. Mol. Cell 2004, 16:1003-1015.
48. Gregg S.Q., Robinson A.R., Niedernhofer L.J. Physiological consequences of defects in ERCC1-XPF DNA repair endonuclease. DNA Repair (Amst) 2011, 10:781-791.
49. Hazra T.K., Izumi T., Boldogh I., Imhoff B., Kow Y.W., Jaruga P., Dizdaroglu M., Mitra S. Identification and characterization of a human DNA glycosylase for repair of modified bases in oxidatively damaged DNA. Proc. Natl. Acad. Sci. U. S. A. 2002, 99:3523-3528.
50. Nagelhus T.A., Slupphaug G., Lindmo T., Krokan H.E. Cell cycle regulation and subcellular localization of the major human uracil-DNA glycosylase. Exp. Cell Res. 1995, 220:292-297.
51. Muller S.J., Caradonna S. Cell cycle regulation of a human cyclin-like gene encoding uracil-DNA glycosylase. J. Biol. Chem. 1993, 268:1310-1319.
52. Nilsen H., Rosewell I., Robins P., Skjelbred C.F., Andersen S., Slupphaug G., Daly G., Krokan H.E., Lindahl T., Barnes D.E. Uracil-DNA glycosylase (UNG)-deficient mice reveal a primary role of the enzyme during DNA replication. Mol. Cell 2000, 5:1059-1065.
53. Kavli B., Sundheim O., Akbari M., Otterlei M., Nilsen H., Skorpen F., Aas P.A., Hagen L., Krokan H.E., Slupphaug G. hUNG2 is the major repair enzyme for removal of uracil from U:A matches, U:G mismatches, and U in single-stranded DNA, with hSMUG1 as a broad specificity backup. J. Biol. Chem. 2002, 277:39926-39936.
54. Hegde M.L., Hegde P.M., Bellot L.J., Mandal S.M., Hazra T.K., Li G.M., Boldogh I., Tomkinson A.E., Mitra S. Prereplicative repair of oxidized bases in the human genome is mediated by NEIL1 DNA glycosylase together with replication proteins. Proc. Natl. Acad. Sci. U. S. A. 2013, 110:E3090-E3099.
55. Neurauter G., Scholl-Burgi S., Haara A., Geisler S., Mayersbach P., Schennach H., Fuchs D. Simultaneous measurement of phenylalanine and tyrosine by high performance liquid chromatography (HPLC) with fluorescence detection. Clin. Biochem. 2013, 46:1848-1851.
56. Strom C.E., Johansson F., Uhlen M., Szigyarto C.A., Erixon K., Helleday T. Poly (ADP-ribose) polymerase (PARP) is not involved in base excision repair but PARP inhibition traps a single-strand intermediate. Nucleic Acids Res. 2011, 39:3166-3175.
57. Akbari M., Pena-Diaz J., Andersen S., Liabakk N.B., Otterlei M., Krokan H.E. Extracts of proliferating and non-proliferating human cells display different base excision pathways and repair fidelity. DNA Repair (Amst) 2009, 8:834-843.
58. Levy N., Oehlmann M., Delalande F., Nasheuer H.P., Van Dorsselaer A., Schreiber V., de Murcia G., Menissier-de Murcia J., Maiorano D., Bresson A. XRCC1 interacts with the p58 subunit of DNA Pol alpha-primase and may coordinate DNA repair and replication during S phase. Nucleic Acids Res. 2009, 37:3177-3188.
59. Ogi T., Limsirichaikul S., Overmeer R.M., Volker M., Takenaka K., Cloney R., Nakazawa Y., Niimi A., Miki Y., Jaspers N.G., Mullenders L.H., Yamashita S., Fousteri M.I., Lehmann A.R. Three DNA polymerases, recruited by different mechanisms, carry out NER repair synthesis in human cells. Mol. Cell 2010, 37:714-727.
60. Li Z., Musich P.R., Serrano M.A., Dong Z., Zou Y. XPA-mediated regulation of global nucleotide excision repair by ATR Is p53-dependent and occurs primarily in S-phase. PLoS ONE 2011, 6:e28326.
61. Yu S.L., Kang M.S., Kim H.Y., Gorospe C.M., Kim T.S., Lee S.K. The PCNA binding domain of Rad2p plays a role in mutagenesis by modulating the cell cycle in response to DNA damage. DNA Repair (Amst) 2014, 16:1-10.
62. Klingler H., Hemmerle C., Bannwart F., Haider R., Cattaruzza M.S., Marra G. Expression of the hMSH6 mismatch-repair protein in colon cancer and HeLa cells. Swiss Med. Wkly. 2002, 132:57-63.
63. Meyers M., Theodosiou M., Acharya S., Odegaard E., Wilson T., Lewis J.E., Davis T.W., Wilson-Van Patten C., Fishel R., Boothman D.A. Cell cycle regulation of the human DNA mismatch repair genes hMSH2, hMLH1, and hPMS2. Cancer Res. 1997, 57:206-208.
64. Snowden T., Acharya S., Butz C., Berardini M., Fishel R. hMSH4-hMSH5 recognizes Holliday Junctions and forms a meiosis-specific sliding clamp that embraces homologous chromosomes. Mol. Cell 2004, 15:437-451.
65. Kee Y., D'Andrea A.D. Molecular pathogenesis and clinical management of Fanconi anemia. J. Clin. Invest. 2012, 122:3799-3806.
66. Smogorzewska A., Desetty R., Saito T.T., Schlabach M., Lach F.P., Sowa M.E., Clark A.B., Kunkel T.A., Harper J.W., Colaiacovo M.P., Elledge S.J. A genetic screen identifies FAN1, a Fanconi anemia-associated nuclease necessary for DNA interstrand crosslink repair. Mol. Cell 2010, 39:36-47.
67. Beck C., Robert I., Reina-San-Martin B., Schreiber V., Dantzer F. Poly(ADP-ribose) polymerases in double-strand break repair: focus on PARP1, PARP2 and PARP3. Exp. Cell Res. 2014.
68. De Lorenzo S.B., Patel A.G., Hurley R.M., Kaufmann S.H. The elephant and the blind men: making sense of PARP inhibitors in homologous recombination deficient tumor cells. Front. Oncol. 2013, 3:228.
69. Li M., Yu X. Function of BRCA1 in the DNA damage response is mediated by ADP-ribosylation. Cancer Cell 2013, 23:693-704.
70. Pezza R.J., Voloshin O.N., Volodin A.A., Boateng K.A., Bellani M.A., Mazin A.V., Camerini-Otero R.D. The dual role of HOP2 in mammalian meiotic homologous recombination. Nucleic Acids Res. 2014, 42:2346-2357.
71. Yuan J., Chen J. FIGNL1-containing protein complex is required for efficient homologous recombination repair. Proc. Natl. Acad. Sci. U. S. A. 2013, 110:10640-10645.
72. Manthei K.A., Keck J.L. The BLM dissolvasome in DNA replication and repair. Cell. Mol. Life Sci. 2013, 70:4067-4084.
73. Kim D.S., Franklyn J.A., Smith V.E., Stratford A.L., Pemberton H.N., Warfield A., Watkinson J.C., Ishmail T., Wakelam M.J., McCabe C.J. Securin induces genetic instability in colorectal cancer by inhibiting double-stranded DNA repair activity. Carcinogenesis 2007, 28:749-759.
74. Romero F., Multon M.C., Ramos-Morales F., Dominguez A., Bernal J.A., Pintor-Toro J.A., Tortolero M. Human securin, hPTTG, is associated with Ku heterodimer, the regulatory subunit of the DNA-dependent protein kinase. Nucleic Acids Res. 2001, 29:1300-1307.
75. Uhlmann F. Chromosome cohesion and separation: from men and molecules. Curr. Biol. 2003, 13:R104-R114.
76. Waizenegger I., Gimenez-Abian J.F., Wernic D., Peters J.M. Regulation of human separase by securin binding and autocleavage. Curr. Biol. 2002, 12:1368-1378.
77. Karra H., Pitkanen R., Nykanen M., Talvinen K., Kuopio T., Soderstrom M., Kronqvist P. Securin predicts aneuploidy and survival in breast cancer. Histopathology 2012, 60:586-596.
78. Dominguez A., Ramos-Morales F., Romero F., Rios R.M., Dreyfus F., Tortolero M., Pintor-Toro J.A. hpttg, a human homologue of rat pttg, is overexpressed in hematopoietic neoplasms. Evidence for a transcriptional activation function of hPTTG. Oncogene 1998, 17:2187-2193.
79. Heaney A.P., Singson R., McCabe C.J., Nelson V., Nakashima M., Melmed S. Expression of pituitary-tumour transforming gene in colorectal tumours. Lancet 2000, 355:716-719.
80. Solbach C., Roller M., Fellbaum C., Nicoletti M., Kaufmann M. PTTG mRNA expression in primary breast cancer: a prognostic marker for lymph node invasion and tumor recurrence. Breast 2004, 13:80-81.
81. Tong Y., Eigler T. Transcriptional targets for pituitary tumor-transforming gene-1. J. Mol. Endocrinol. 2009, 43:179-185.
82. Kim D., Pemberton H., Stratford A.L., Buelaert K., Watkinson J.C., Lopes V., Franklyn J.A., McCabe C.J. Pituitary tumour transforming gene (PTTG) induces genetic instability in thyroid cells. Oncogene 2005, 24:4861-4866.
83. Yu R., Lu W., Chen J., McCabe C.J., Melmed S. Overexpressed pituitary tumor-transforming gene causes aneuploidy in live human cells. Endocrinology 2003, 144:4991-4998.
84. Mermoud J.E., Rowbotham S.P., Varga-Weisz P.D. Keeping chromatin quiet: how nucleosome remodeling restores heterochromatin after replication. Cell Cycle 2011, 10:4017-4025.
85. Peterson C.L., Almouzni G. Nucleosome dynamics as modular systems that integrate DNA damage and repair. Cold Spring Harb. Perspect. Biol. 2013, 5.
86. Kadyrova L.Y., Blanko E.R., Kadyrov F.A. CAF-I-dependent control of degradation of the discontinuous strands during mismatch repair. Proc. Natl. Acad. Sci. U. S. A. 2011, 108:2753-2758.
87. Schopf B., Bregenhorn S., Quivy J.P., Kadyrov F.A., Almouzni G., Jiricny J. Interplay between mismatch repair and chromatin assembly. Proc. Natl. Acad. Sci. U. S. A. 2012, 109:1895-1900.
88. Zhu Q., Wani G., Arab H.H., El-Mahdy M.A., Ray A., Wani A.A. Chromatin restoration following nucleotide excision repair involves the incorporation of ubiquitinated H2A at damaged genomic sites. DNA Repair (Amst) 2009, 8:262-273.
89. Burrage J., Termanis A., Geissner A., Myant K., Gordon K., Stancheva I. The SNF2 family ATPase LSH promotes phosphorylation of H2AX and efficient repair of DNA double-strand breaks in mammalian cells. J. Cell Sci. 2012, 125:5524-5534.
90. Obayashi T., Okamura Y., Ito S., Tadaka S., Motoike I.N., Kinoshita K. COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals. Nucleic Acids Res. 2013, 41:D1014-D1020.
91. von Eyss B., Maaskola J., Memczak S., Mollmann K., Schuetz A., Loddenkemper C., Tanh M.D., Otto A., Muegge K., Heinemann U., Rajewsky N., Ziebold U. The SNF2-like helicase HELLS mediates E2F3-dependent transcription and cellular transformation. EMBO J. 2012, 31:972-985.
92. Ciro M., Prosperini E., Quarto M., Grazini U., Walfridsson J., McBlane F., Nucifero P., Pacchiana G., Capra M., Christensen J., Helin K. ATAD2 is a novel cofactor for MYC, overexpressed and amplified in aggressive tumors. Cancer Res. 2009, 69:8491-8498.
93. Hsia E.Y., Goodson M.L., Zou J.X., Privalsky M.L., Chen H.W. Nuclear receptor coregulators as a new paradigm for therapeutic targeting. Adv. Drug Deliv. Rev. 2010, 62:1227-1237.
94. Revenko A.S., Kalashnikova E.V., Gemo A.T., Zou J.X., Chen H.W. Chromatin loading of E2F-MLL complex by cancer-associated coregulator ANCCA via reading a specific histone mark. Mol. Cell. Biol. 2010, 30:5260-5272.
95. Caron C., Lestrat C., Marsal S., Escoffier E., Curtet S., Virolle V., Barbry P., Debernardi A., Brambilla C., Brambilla E., Rousseaux S., Khochbin S. Functional characterization of ATAD2 as a new cancer/testis factor and a predictor of poor prognosis in breast and lung cancers. Oncogene 2010, 29:5171-5181.
96. Duan M.R., Smerdon M.J. Histone H3 Lysine 14 (H3K14) acetylation facilitates DNA repair in a positioned nucleosome by stabilizing the binding of the chromatin remodeler RSC (remodels structure of chromatin). J. Biol. Chem. 2014, 289:8353-8363.
97. Boussouar F., Jamshidikia M., Morozumi Y., Rousseaux S., Khochbin S. Malignant genome reprogramming by ATAD2. Biochim. Biophys. Acta 2013, 1829:1010-1014.
98. Fouret R., Laffaire J., Hofman P., Beau-Faller M., Mazieres J., Validire P., Girard P., Camilleri-Broet S., Vaylet F., Leroy-Ladurie F., Soria J.C., Fouret P. A comparative and integrative approach identifies ATPase family, AAA domain containing 2 as a likely driver of cell proliferation in lung adenocarcinoma. Clin. Cancer Res. 2012, 18:5606-5616.
99. Kalashnikova E.V., Revenko A.S., Gemo A.T., Andrews N.P., Tepper C.G., Zou J.X., Cardiff R.D., Borowsky A.D., Chen H.W. ANCCA/ATAD2 overexpression identifies breast cancer patients with poor prognosis, acting to drive proliferation and survival of triple-negative cells through control of B-Myb and EZH2. Cancer Res. 2010, 70:9402-9412.
100. Raeder M.B., Birkeland E., Trovik J., Krakstad C., Shehata S., Schumacher S., Zack T.I., Krohn A., Werner H.M., Moody S.E., Wik E., Stefansson I.M., Holst F., Oyan A.M., Tamayo P., Mesirov J.P., Kalland K.H., Akslen L.A., Simon R., Beroukhim R., Salvesen H.B. Integrated genomic analysis of the 8q24 amplification in endometrial cancers identifies ATAD2 as essential to MYC-dependent cancers. PLOS ONE 2013, 8:e54873.
101. Zou J.X., Revenko A.S., Li L.B., Gemo A.T., Chen H.W. ANCCA, an estrogen-regulated AAA+ ATPase coactivator for ERalpha, is required for coregulator occupancy and chromatin modification. Proc. Natl. Acad. Sci. U. S. A. 2007, 104:18067-18072.
102. Jarvis C.D., Geiman T., Vila-Storm M.P., Osipovich O., Akella U., Candeias S., Nathan I., Durum S.K., Muegge K. A novel putative helicase produced in early murine lymphocytes. Gene 1996, 169:203-207.
103. Liu Y., Gong Z., Sun L., Li X. FOXM1 and androgen receptor co-regulate CDC6 gene transcription and DNA replication in prostate cancer cells. Biochim. Biophys. Acta 2014, 1839:297-305.
104. Waseem A., Ali M., Odell E.W., Fortune F., Teh M.T. Downstream targets of FOXM1: CEP55 and HELLS are cancer progression markers of head and neck squamous cell carcinoma. Oral Oncol. 2010, 46:536-542.
105. Laoukili J., Kooistra M.R., Bras A., Kauw J., Kerkhoven R.M., Morrison A., Clevers H., Medema R.H. FoxM1 is required for execution of the mitotic programme and chromosome stability. Nat. Cell Biol. 2005, 7:126-136.
106. Teh M.T., Gemenetzidis E., Patel D., Tariq R., Nadir A., Bahta A.W., Waseem A., Hutchison I.L. FOXM1 induces a global methylation signature that mimics the cancer epigenome in head and neck squamous cell carcinoma. PLoS ONE 2012, 7:e34329.
107. Zhu H., Geiman T.M., Xi S., Jiang Q., Schmidtmann A., Chen T., Li E., Muegge K. Lsh is involved in de novo methylation of DNA. EMBO J. 2006, 25:335-345.
108. Fan T., Schmidtmann A., Xi S., Briones V., Zhu H., Suh H.C., Gooya J., Keller J.R., Xu H., Roayaei J., Anver M., Ruscetti S., Muegge K. DNA hypomethylation caused by Lsh deletion promotes erythroleukemia development. Epigenetics 2008, 3:134-142.
109. Myant K., Stancheva I. LSH cooperates with DNA methyltransferases to repress transcription. Mol. Cell. Biol. 2008, 28:215-226.
110. Yan Q., Huang J., Fan T., Zhu H., Muegge K. Lsh, a modulator of CpG methylation, is crucial for normal histone methylation. EMBO J. 2003, 22:5154-5162.
111. Zhou R., Han L., Li G., Tong T. Senescence delay and repression of p16INK4a by Lsh via recruitment of histone deacetylases in human diploid fibroblasts. Nucleic Acids Res. 2009, 37:5183-5196.
112. Lee D.W., Zhang K., Ning Z.Q., Raabe E.H., Tintner S., Wieland R., Wilkins B.J., Kim J.M., Blough R.I., Arceci R.J. Proliferation-associated SNF2-like gene (PASG): a SNF2 family member altered in leukemia. Cancer Res. 2000, 60:3612-3622.
113. Ceballos S.J., Heyer W.D. Functions of the Snf2/Swi2 family Rad54 motor protein in homologous recombination. Biochim. Biophys. Acta 2011, 1809:509-523.
114. Zhang Z., Fan H.Y., Goldman J.A., Kingston R.E. Homology-driven chromatin remodeling by human RAD54. Nat. Struct. Mol. Biol. 2007, 14:397-405.
115. Oh S., Wang Y., Zimbric J., Hendrickson E.A. Human LIGIV is synthetically lethal with the loss of Rad54B-dependent recombination and is required for certain chromosome fusion events induced by telomere dysfunction. Nucleic Acids Res. 2013, 41:1734-1749.
116. Dykhuizen E.C., Hargreaves D.C., Miller E.L., Cui K., Korshunov A., Kool M., Pfister S., Cho Y.J., Zhao K., Crabtree G.R. BAF complexes facilitate decatenation of DNA by topoisomerase IIalpha. Nature 2013, 497:624-627.
117. Grant G.D., Brooks L., Zhang X., Mahoney J.M., Martyanov V., Wood T.A., Sherlock G., Cheng C., Whitfield M.L. Identification of cell cycle-regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors. Mol. Biol. Cell 2013, 24:3634-3650.
118. Masuda K., Ouchida R., Takeuchi A., Saito T., Koseki H., Kawamura K., Tagawa M., Tokuhisa T., Azuma T., Wang O.J. DNA polymerase theta contributes to the generation of C/G mutations during somatic hypermutation of Ig genes. Proc. Natl. Acad. Sci. U. S. A. 2005, 102:13986-13991.
119. Zmudzka B.Z., Fornace A., Collins J., Wilson S.H. Characterization of DNA polymerase beta mRNA: cell-cycle and growth response in cultured human cells. Nucleic Acids Res. 1988, 16:9587-9596.
120. Kidane D., Jonason A.S., Gorton T.S., Mihaylov I., Pan J., Keeney S., de Rooij D.G., Ashley T., Keh A., Liu Y., Banerjee U., Zelterman D., Sweasy J.B. DNA polymerase beta is critical for mouse meiotic synapsis. EMBO J. 2010, 29:410-423.
121. Dianov G.L., Hubscher U. Mammalian base excision repair: the forgotten archangel. Nucleic Acids Res. 2013, 41:3483-3490.
122. Zhao Y., Brickner J.R., Majid M.C., Mosammaparast N. Crosstalk between ubiquitin and other post-translational modifications on chromatin during double-strand break repair. Trends Cell Biol. 2014.
123. Branzei D., Foiani M. Regulation of DNA repair throughout the cell cycle. Nat. Rev. Mol. Cell Biol. 2008, 9:297-308.
124. Wang L.C., Gautier J. The Fanconi anemia pathway and ICL repair: implications for cancer therapy. Crit. Rev. Biochem. Mol. Biol. 2010, 45:424-439.
125. Williams S.A., Wilson J.B., Clark A.P., Mitson-Salazar A., Tomashevski A., Ananth S., Glazer P.M., Semmes O.J., Bale A.E., Jones N.J., Kupfer G.M. Functional and physical interaction between the mismatch repair and FA-BRCA pathways. Hum. Mol. Genet. 2011, 20:4395-4410.
126. McMahon L.W., Sangerman J., Goodman S.R., Kumaresan K., Lambert M.W. Human alpha spectrin II and the FANCA, FANCC, and FANCG proteins bind to DNA containing psoralen interstrand cross-links. Biochemistry 2001, 40:7025-7034.
127. Zhang P., Herbig U., Coffman F., Lambert M.W. Non-erythroid alpha spectrin prevents telomere dysfunction after DNA interstrand cross-link damage. Nucleic Acids Res. 2013, 41:5321-5340.
128. Williams H.L., Gottesman M.E., Gautier J. The differences between ICL repair during and outside of S phase. Trends Biochem. Sci. 2013, 38:386-393.
129. Thorslund T., West S.C. BRCA2: a universal recombinase regulator. Oncogene 2007, 26:7720-7730.
130. Marmorstein L.Y., Kinev A.V., Chan G.K., Bochar D.A., Beniya H., Epstein J.A., Yen T.J., Shiekhattar R. A human BRCA2 complex containing a structural DNA binding component influences cell cycle progression. Cell 2001, 104:247-257.
131. Shrivastav M., De Haro L.P., Nickoloff J.A. Regulation of DNA double-strand break repair pathway choice. Cell Res. 2008, 18:134-147.
132. Furuta T., Takemura H., Liao Z.Y., Aune G.J., Redon C., Sedelnikova O.A., Pilch D.R., Rogakou E.P., Celeste A., Chen H.T., Nussenzweig A., Aladjem M.I., Bonner W.M., Pommier Y. Phosphorylation of histone H2AX and activation of Mre11, Rad50, and Nbs1 in response to replication-dependent DNA double-strand breaks induced by mammalian DNA topoisomerase I cleavage complexes. J. Biol. Chem. 2003, 278:20303-20312.
133. Lee J.H., Paull T.T. Direct activation of the ATM protein kinase by the Mre11/Rad50/Nbs1 complex. Science 2004, 304:93-96.
134. Symington L.S., Gautier J. Double-strand break end resection and repair pathway choice. Annu. Rev. Genet. 2011, 45:247-271.
135. Papamichos-Chronakis M., Peterson C.L. Chromatin and the genome integrity network. Nat. Rev. Genet. 2013, 14:62-75.
136. Bennett G., Papamichos-Chronakis M., Peterson C.L. DNA repair choice defines a common pathway for recruitment of chromatin regulators. Nat. Commun. 2013, 4:2084.
137. Menoni H., Gasparutto D., Hamiche A., Cadet J., Dimitrov S., Bouvet P., Angelov D. ATP-dependent chromatin remodeling is required for base excision repair in conventional but not in variant H2A.Bbd nucleosomes. Mol. Cell. Biol. 2007, 27:5949-5956.
138. Nakanishi S., Prasad R., Wilson S.H., Smerdon M. Different structural states in oligonucleosomes are required for early versus late steps of base excision repair. Nucleic Acids Res. 2007, 35:4313-4321.