DNA methyltransferase 1 and DNA methylation patterning contribute to germinal center B-cell differentiation

Blood

Volumn 118, Issue 13, 2011, Pages 3559-3569

  Shaknovich, Rita ^a   Cerchietti, Leandro ^a   Tsikitas, Lucas ^a   Kormaksson, Matthias ^a   De, Subhajyoti ^b,c   Figueroa, Maria E ^a   Ballon, Gianna ^a   Yang, Shao Ning ^a   Weinhold, Nils ^d   Reimers, Mark ^e   Clozel, Thomas ^a   Luttrop, Karin ^f   Ekstrom, Tomas J ^f   Frank, Jared ^a   Vasanthakumar, Aparna ^g   Godley, Lucy A ^g   Michor, Franziska ^b   Elemento, Olivier ^a   Melnick, Ari ^a  

^a WEILL CORNELL MEDICAL COLLEGE   (United States)

^b DANA FARBER CANCER INSTITUTE   (United States)

^c HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^d TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^e VIRGINIA COMMONWEALTH UNIVERSITY SCHOOL OF MEDICINE   (United States)

^f KAROLINSKA INSTITUTE   (Sweden)

^g UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

5 AZA 2' DEOXYCYTIDINE; ACTIVATION INDUCED CYTIDINE DEAMINASE; DNA METHYLTRANSFERASE; DNA METHYLTRANSFERASE 1; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; MITOGEN ACTIVATED PROTEIN KINASE;

ANIMAL CELL; ANIMAL EXPERIMENT; ARTICLE; B LYMPHOCYTE; B LYMPHOCYTE DIFFERENTIATION; CELL HETEROGENEITY; CONTROLLED STUDY; DNA METHYLATION; GENE EXPRESSION; GERMINAL CENTER; MOUSE; NONHUMAN; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; UPREGULATION;

EID: 80053376487     PISSN: 00064971     EISSN: 15280020     Source Type: Journal    
DOI: 10.1182/blood-2011-06-357996     Document Type: Article

References (45)

1. Ci W, Polo JM, Melnick A. B-cell lymphoma 6 and the molecular pathogenesis of diffuse large B-cell lymphoma. Curr Opin Hematol. 2008;15(4):381- 390.
2. Klein U, Dalla-Favera R. Germinal centres: role in B-cell physiology and malignancy. Nat Rev Immunol. 2008;8(1):22-33.
3. de Yebenes VG, Ramiro AR. Activation-induced deaminase: light and dark sides. Trends Mol Med. 2006;12(9):432-439.
4. Martin A, Bardwell PD, Woo CJ, Fan M, Shulman MJ, Scharff MD. Activation-induced cytidine deaminase turns on somatic hypermutation in hybridomas. Nature. 2002;415(6873):802-806. (Pubitemid 34150503)
5. Yamane A, Resch W, Kuo N, et al. Deepsequencing identification of the genomic targets of the cytidine deaminase AID and its cofactor RPA in B lymphocytes. Nat Immunol. 2011;12(1): 62-69.
6. Liu M, Schatz DG. Balancing AID and DNA repair during somatic hypermutation. Trends Immunol. 2009;30(4):173-181.
7. Pasqualucci L, Bhagat G, Jankovic M, et al. AID is required for germinal center-derived lymphomagenesis. Nat Genet. 2008;40(1):108-112.
8. Ci W, Polo JM, Cerchietti L, et al. The BCL6 transcriptional program features repression of multiple oncogenes in primary B cells and is deregulated in DLBCL. Blood. 2009;113(22):5536-5548.
9. Muto A, Tashiro S, Nakajima O, et al. The transcriptional programme of antibody class switching involves the repressor Bach2. Nature. 2004; 429(6991):566-571. (Pubitemid 38737661)
10. Shaffer AL, Yu X, He Y, Boldrick J, Chan EP, Staudt LM. BCL-6 represses genes that function in lymphocyte differentiation, inflammation, and cell cycle control. Immunity. 2000;13(2):199-212.
11. Velichutina I, Shaknovich R, Geng H, et al. EZH2- mediated epigenetic silencing in germinal center B cells contributes to proliferation and lymphomagenesis. Blood. 2010;116(24):5247-5255.
12. Khulan B, Thompson RF, Ye K, et al. Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res. 2006;16(8): 1046-1055. (Pubitemid 44162264)
13. Polo JM, Liu S, Figueroa ME, et al. Cell type of origin influences the molecular and functional properties of mouse induced pluripotent stem cells. Nat Biotechnol. 2010;28(8):848-855.
14. Herman JG, Baylin SB. Gene silencing in cancer in association with promoter hypermethylation. N Engl J Med. 2003;349(21):2042-2054. (Pubitemid 37448928)
15. Hermann A, Goyal R, Jeltsch A. The Dnmt1 DNA- (cytosine-C5)- methyltransferase methylates DNA processively with high preference for hemimethylated target sites. J Biol Chem. 2004;279(46): 48350-48359. (Pubitemid 39540991)
16. Ji H, Ehrlich LI, Seita J, et al. Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature. 2010; 467(7313):338-342.
17. Broske AM, Vockentanz L, Kharazi S, et al. DNA methylation protects hematopoietic stem cell multipotency from myeloerythroid restriction. Nat Genet. 2009;41(11):1207-1215.
18. Shaknovich R, Geng H, Johnson NA, et al. DNA methylation signatures define molecular subtypes of diffuse large B-cell lymphoma. Blood. 2010; 116(20):e81-89.
19. Martin-Subero JI, Kreuz M, Bibikova M, et al. New insights into the biology and origin of mature aggressive B-cell lymphomas by combined epigenomic, genomic, and transcriptional profiling. Blood. 2009;113(11):2488-2497.
20. Maul RW, Saribasak H, Martomo SA, et al. Uracil residues dependent on the deaminase AID in immunoglobulin gene variable and switch regions. Nat Immunol. 2011;12(1):70-76.
21. Bhutani N, Brady JJ, Damian M, Sacco A, Corbel SY, Blau HM. Reprogramming towards pluripotency requires AID-dependent DNAdemethylation. Nature. 2010;463(7284):1042-1047.
22. Fritz EL, Papavasiliou FN. Cytidine deaminases: AIDing DNA demethylation? Genes Dev. 2010; 24(19):2107-2114.
23. Popp C, Dean W, Feng S, et al. Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature. 2010;463(7284):1101-1105.
24. Shaknovich R, Figueroa ME, Melnick A. HELP (HpaII tiny fragment enrichment by ligationmediated PCR) assay for DNA methylation profiling of primary normal and malignant B lymphocytes. Methods Mol Biol. 2010;632:191-201.
25. Thompson RF, Reimers M, Khulan B, et al. An analytical pipeline for genomic representations used for cytosine methylation studies. Bioinformatics. 2008;24(9):1161-1167. (Pubitemid 351594165)
26. Karimi M, Johansson S, Stach D, et al. LUMA (LUminometric Methylation Assay) - a high throughput method to the analysis of genomic DNA methylation. Exp Cell Res. 2006;312(11): 1989-1995. (Pubitemid 43850924)
27. Song L, James SR, Kazim L, Karpf AR. Specific method for the determination of genomic DNA methylation by liquid chromatography-electrospray ionization tandem mass spectrometry. Anal Chem. 2005;77(2):504-510. (Pubitemid 40116829)
28. Eads CA, Nickel AE, Laird PW. Complete genetic suppression of polyp formation and reduction of CpG-island hypermethylation in Apc(Min/+) Dnmt1-hypomorphic Mice. Cancer Res. 2002; 62(5):1296-1299. (Pubitemid 34407781)
29. Bronner C, Achour M, Arima Y, Chataigneau T, Saya H, Schini-Kerth VB. The UHRF family: oncogenes that are drugable targets for cancer therapy in the near future? Pharmacol Ther. 2007;115(3):419-434. (Pubitemid 47362377)
30. Sharif J, Muto M, Takebayashi S, et al. The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA. Nature. 2007;450(7171):908-912. (Pubitemid 350231331)
31. Boehm JS, Zhao JJ, Yao J, et al. Integrative genomic approaches identify IKBKE as a breast cancer oncogene. Cell. 2007;129(6):1065-1079. (Pubitemid 46891036)
32. Huang H, Rambaldi I, Daniels E, Featherstone M. Expression of the Wdr9 gene and protein products during mouse development. Dev Dyn. 2003; 227(4):608-614. (Pubitemid 36951086)
33. Pardo M, Lang B, Yu L, et al. An expanded Oct4 interaction network: implications for stem cell biology, development, and disease. Cell Stem Cell. 2010;6(4):382-395.
34. Ray BN, Lee NY, How T, Blobe GC. ALK5 phosphorylation of the endoglin cytoplasmic domain regulates Smad1/5/8 signaling and endothelial cell migration. Carcinogenesis. 2010;31(3):435- 441.
35. Karimi M, Johansson S, Ekstrom TJ. Using LUMA: a Luminometric-based assay for global DNA-methylation. Epigenetics. 2006;1(1):45-48.
36. Liu M, Duke JL, Richter DJ, et al. Two levels of protection for the B cell genome during somatic hypermutation. Nature. 2008;451(7180):841-845. (Pubitemid 351253166)
37. Elemento O, Slonim N, Tavazoie S. A universal framework for regulatory element discovery across all genomes and data types. Mol Cell. 2007;28(2):337-350. (Pubitemid 47600005)
38. Michael N, Shen HM, Longerich S, Kim N, Longacre A, Storb U. The E box motif CAGGTG enhances somatic hypermutation without enhancing transcription. Immunity. 2003;19(2):235- 242.
39. Unterberger A, Andrews SD, Weaver IC, Szyf M. DNA methyltransferase 1 knockdown activates a replication stress checkpoint. Mol Cell Biol. 2006; 26(20):7575-7586. (Pubitemid 44547707)
40. Ha K, Lee GE, Palii SS, et al. Rapid and transient recruitment of DNMT1 to DNA double-strand breaks is mediated by its interaction with multiple components of the DNA damage response machinery. Hum Mol Genet. 2011;20(1):126-140.
41. Guo JU, Su Y, Zhong C, Ming GL, Song H. Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell. 2011.
42. Tanaka A, Shen HM, Ratnam S, Kodgire P, Storb U. Attracting AID to targets of somatic hypermutation. J Exp Med. 2010;207(2):405-415.
43. Papait R, Pistore C, Grazini U, et al. The PHD domain of Np95 (mUHRF1) is involved in largescale reorganization of pericentromeric heterochromatin. Mol Biol Cell. 2008;19(8):3554-3563.
44. Du Z, Song J, Wang Y, et al. DNMT1 stability is regulated by proteins coordinating deubiquitination and acetylation-driven ubiquitination. Sci Signal. 2010;3(146):ra80.
45. Sen GL, Reuter JA, Webster DE, Zhu L, Khavari PA. DNMT1 maintains progenitor function in self-renewing somatic tissue. Nature. 2010;463(7280):563-567.