The PHD domain of the sea urchin RAG2 homolog, SpRAG2L, recognizes dimethylated lysine 4 in histone H3 tails

Developmental and Comparative Immunology

Volumn 32, Issue 10, 2008, Pages 1221-1230

  Wilson, David R ^a   Norton, Darrell D ^a   Fugmann, Sebastian D ^a  

^a NATIONAL INSTITUTE ON AGING   (United States)

Author keywords

Chromatin; H3K4 methylation; PHD domain; RAG2; SpRAG1L; SpRAG2L; Strongylocentrotus purpuratus; V(D)J recombination

Indexed keywords

DNA; HISTONE H3; HOMEODOMAIN PROTEIN; LYSINE DERIVATIVE; RAG1 PROTEIN; RAG2 PROTEIN;

ARTICLE; CHROMATIN; ENZYME ACTIVITY; GENETIC RECOMBINATION; HUMAN; HUMAN CELL; INVERTEBRATE; MOLECULAR RECOGNITION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN LOCALIZATION; PROTEIN METHYLATION; SEA URCHIN; STRONGYLOCENTROTUS; STRUCTURAL HOMOLOGY;

ECHINOIDEA; INVERTEBRATA; STRONGYLOCENTROTUS PURPURATUS;

EID: 45049086632     PISSN: 0145305X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.dci.2008.03.012     Document Type: Article

References (40)

1. Gellert M. V(D)J recombination: RAG proteins, repair factors, and regulation. Annu Rev Biochem 71 (2002) 101-132
2. Bassing C.H., Swat W., and Alt F.W. The mechanism and regulation of chromosomal V(D)J recombination. Cell 109 Suppl (2002) S45-S55
3. Lewis S.M. The mechanism of V(D)J joining: lessons from molecular, immunological, and comparative analyses. Adv Immunol 56 (1994) 27-150
4. Fugmann S.D., Lee A.I., Shockett P.E., Villey I.J., and Schatz D.G. The RAG proteins and V(D)J recombination: complexes, ends, and transposition. Annu Rev Immunol 18 (2000) 495-527
5. Grawunder U., and Harfst E. How to make ends meet in V(D)J recombination. Curr Opin Immunol 13 2 (2001) 186-194
6. Hesslein D.G., and Schatz D.G. Factors and forces controlling V(D)J recombination. Adv Immunol 78 (2001) 169-232
7. Landree M.A., Wibbenmeyer J.A., and Roth D.B. Mutational analysis of RAG1 and RAG2 identifies three catalytic amino acids in RAG1 critical for both cleavage steps of V(D)J recombination. Genes Dev 13 23 (1999) 3059-3069
8. Kim D.R., Dai Y., Mundy C.L., Yang W., and Oettinger M.A. Mutations of acidic residues in RAG1 define the active site of the V(D)J recombinase. Genes Dev 13 23 (1999) 3070-3080
9. Fugmann S.D., Villey I.J., Ptaszek L.M., and Schatz D.G. Identification of two catalytic residues in RAG1 that define a single active site within the RAG1/RAG2 protein complex. Mol Cell 5 1 (2000) 97-107
10. Akamatsu Y., and Oettinger M.A. Distinct roles of RAG1 and RAG2 in binding the V(D)J recombination signal sequences. Mol Cell Biol 18 8 (1998) 4670-4678
11. Difilippantonio M.J., McMahan C.J., Eastman Q.M., Spanopoulou E., and Schatz D.G. RAG1 mediates signal sequence recognition and recruitment of RAG2 in V(D)J recombination. Cell 87 2 (1996) 253-262
12. Swanson P.C., and Desiderio S. V(D)J recombination signal recognition: distinct, overlapping DNA-protein contacts in complexes containing RAG1 with and without RAG2. Immunity 9 1 (1998) 115-125
13. Swanson P.C., and Desiderio S. RAG-2 promotes heptamer occupancy by RAG-1 in the assembly of a V(D)J initiation complex. Mol Cell Biol 19 5 (1999) 3674-3683
14. Sadofsky M.J., Hesse J.E., and Gellert M. Definition of a core region of RAG-2 that is functional in V(D)J recombination. Nucleic Acids Res 22 10 (1994) 1805-1809
15. Cuomo C.A., and Oettinger M.A. Analysis of regions of RAG-2 important for V(D)J recombination. Nucleic Acids Res 22 10 (1994) 1810-1814
16. Lin W.C., and Desiderio S. Cell cycle regulation of V(D)J recombination-activating protein RAG-2. Proc Natl Acad Sci USA 91 7 (1994) 2733-2737
17. Lin W.C., and Desiderio S. Regulation of V(D)J recombination activator protein RAG-2 by phosphorylation. Science 260 5110 (1993) 953-959
18. Latham J.A., and Dent S.Y. Cross-regulation of histone modifications. Nat Struct Mol Biol 14 11 (2007) 1017-1024
19. Margueron R., Trojer P., and Reinberg D. The key to development: interpreting the histone code?. Curr Opin Genet Dev 15 2 (2005) 163-176
20. Taverna S.D., Li H., Ruthenburg A.J., Allis C.D., and Patel D.J. How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat Struct Mol Biol 14 11 (2007) 1025-1040
21. Ruthenburg A.J., Allis C.D., and Wysocka J. Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark. Mol Cell 25 1 (2007) 15-30
22. Callebaut I., and Mornon J.P. The V(D)J recombination activating protein RAG2 consists of a six-bladed propeller and a PHD fingerlike domain, as revealed by sequence analysis. Cell Mol Life Sci 54 8 (1998) 880-891
23. Shi X., Hong T., Walter K.L., et al. ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression. Nature 442 7098 (2006) 96-99
24. Liu Y., Subrahmanyam R., Chakraborty T., Sen R., and Desiderio S. A plant homeodomain in Rag-2 that binds hypermethylated lysine 4 of histone H3 is necessary for efficient antigen-receptor-gene rearrangement. Immunity 27 4 (2007) 561-571
25. Elkin S.K., Ivanov D., Ewalt M., et al. A PHD finger motif in the C terminus of RAG2 modulates recombination activity. J Biol Chem 280 31 (2005) 28701-28710
26. Ramon-Maiques S., Kuo A.J., Carney D., et al. The plant homeodomain finger of RAG2 recognizes histone H3 methylated at both lysine-4 and arginine-2. Proc Natl Acad Sci USA 104 48 (2007) 18993-18998
27. Matthews A.G., Kuo A.J., Ramon-Maiques S., et al. RAG2 PHD finger couples histone H3 lysine 4 trimethylation with V(D)J recombination. Nature 450 7172 (2007) 1106-1110
28. Fugmann S.D., Messier C., Novack L.A., Cameron R.A., and Rast J.P. An ancient evolutionary origin of the Rag1/2 gene locus. Proc Natl Acad Sci USA 103 10 (2006) 3728-3733
29. Kapitonov V.V., and Jurka J. RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons. PLoS Biol 3 6 (2005) e181
30. Rodgers K.K., Villey I.J., Ptaszek L., et al. A dimer of the lymphoid protein RAG1 recognizes the recombination signal sequence and the complex stably incorporates the high mobility group protein HMG2. Nucleic Acids Res 27 14 (1999) 2938-2946
31. Spanopoulou E., Zaitseva F., Wang F.H., et al. The homeodomain region of Rag-1 reveals the parallel mechanisms of bacterial and V(D)J recombination. Cell 87 2 (1996) 263-276
32. Dignam J.D. Preparation of extracts from higher eukaryotes. Methods Enzymol 182 (1990) 194-203
33. Radhakrishna H., and Donaldson J.G. ADP-ribosylation factor 6 regulates a novel plasma membrane recycling pathway. J Cell Biol 139 1 (1997) 49-61
34. Mellor J. It takes a PHD to read the histone code. Cell 126 1 (2006) 22-24
35. Morshead K.B., Ciccone D.N., Taverna S.D., Allis C.D., and Oettinger M.A. Antigen receptor loci poised for V(D)J rearrangement are broadly associated with BRG1 and flanked by peaks of histone H3 dimethylated at lysine 4. Proc Natl Acad Sci USA 100 20 (2003) 11577-11582
36. Perkins E.J., Kee B.L., and Ramsden D.A. Histone 3 lysine 4 methylation during the pre-B to immature B-cell transition. Nucleic Acids Res 32 6 (2004) 1942-1947
37. Goldmit M., Ji Y., Skok J., et al. Epigenetic ontogeny of the Igk locus during B cell development. Nat Immunol 6 2 (2005) 198-203
38. Barski A., Cuddapah S., Cui K., et al. High-resolution profiling of histone methylations in the human genome. Cell 129 4 (2007) 823-837
39. Ooi S.K., Qiu C., Bernstein E., et al. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448 7154 (2007) 714-717
40. Karagianni P., Amazit L., Qin J., and Wong J. ICBP90, a novel methyl K9 H3 binding protein linking protein ubiquitination with heterochromatin formation. Mol Cell Biol 28 2 (2008) 705-717