Complex evolutionary history and diverse domain organization of SET proteins suggest divergent regulatory interactions

New Phytologist

Volumn 195, Issue 1, 2012, Pages 248-263

  Zhang, Liangsheng ^a   Ma, Hong ^a,b  

^a FUDAN UNIVERSITY   (China)

^b FUDAN UNIVERSITY   (China)

Author keywords

Animals and plants; Gene duplication; Lysine methylation; Meiosis; SET domain genes

Indexed keywords

CHAPERONE; SET PROTEIN, HUMAN; TRANSCRIPTION FACTOR; VEGETABLE PROTEIN;

EUKARYOTE; GENE; GENETIC ANALYSIS; GENOME; GENOMICS; PHYLOGENETICS; PROTEIN; RECRUITMENT (POPULATION DYNAMICS);

ANIMAL; ARTICLE; EVOLUTION; GENE DUPLICATION; GENE EXPRESSION REGULATION; GENETICS; INVERTEBRATE; MEIOSIS; MOLECULAR EVOLUTION; PHYLOGENY; PLANT GENOME; PROTEIN TERTIARY STRUCTURE; VERTEBRATE;

ANIMALS; BIOLOGICAL EVOLUTION; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENE EXPRESSION REGULATION; GENOME, PLANT; HISTONE CHAPERONES; INVERTEBRATES; MEIOSIS; PHYLOGENY; PLANT PROTEINS; PROTEIN STRUCTURE, TERTIARY; TRANSCRIPTION FACTORS; VERTEBRATES;

ANIMALIA; EMBRYOPHYTA; EUKARYOTA; VERTEBRATA;

EID: 84861482924     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/j.1469-8137.2012.04143.x     Document Type: Article

References (64)

1. Alvarez-Venegas R, Sadder M, Tikhonov A, Avramova Z. 2007. Origin of the bacterial SET domain genes: vertical or horizontal? Molecular Biology and Evolution 24: 482-497.
2. Baudat F, Buard J, Grey C, Fledel-Alon A, Ober C, Przeworski M, Coop G, de Massy B. 2010. PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice. Science 327: 836-840.
3. Baumbusch LO, Thorstensen T, Krauss V, Fischer A, Naumann K, Assalkhou R, Schulz I, Reuter G, Aalen RB. 2001. The Arabidopsis thaliana genome contains at least 29 active genes encoding SET domain proteins that can be assigned to four evolutionarily conserved classes. Nucleic Acids Research 29: 4319-4333.
4. Berger SL. 2007. The complex language of chromatin regulation during transcription. Nature 447: 407-412.
5. Berr A, McCallum EJ, Menard R, Meyer D, Fuchs J, Dong A, Shen WH. 2010. Arabidopsis SET DOMAIN GROUP2 is required for H3K4 trimethylation and is crucial for both sporophyte and gametophyte development. Plant Cell 22: 3232-3248.
6. Borde V, Robine N, Lin W, Bonfils S, Geli V, Nicolas A. 2009. Histone H3 lysine 4 trimethylation marks meiotic recombination initiation sites. EMBO Journal 28: 99-111.
7. Catchen JM, Conery JS, Postlethwait JH. 2009. Automated identification of conserved synteny after whole-genome duplication. Genome Research 19: 1497-1505.
8. Chalmel F, Rolland AD, Niederhauser-Wiederkehr C, Chung SS, Demougin P, Gattiker A, Moore J, Patard JJ, Wolgemuth DJ, Jegou B et al. 2007. The conserved transcriptome in human and rodent male gametogenesis. Proceedings of the National Academy of Sciences, USA 104: 8346-8351.
9. Chen Y, Souaiaia T, Chen T. 2009. PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. Bioinformatics 25: 2514-2521.
10. Dambacher S, Hahn M, Schotta G. 2010. Epigenetic regulation of development by histone lysine methylation. Heredity 105: 24-37.
11. Dehal P, Boore JL. 2005. Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biology 3: e314.
12. Dillon SC, Zhang X, Trievel RC, Cheng X. 2005. The SET-domain protein superfamily: protein lysine methyltransferases. Genome Biology 6: 227.
13. Eddy SR. 1998. Profile hidden Markov models. Bioinformatics 14: 755-763.
14. Edgar RC. 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 113.
15. Feng Q, Wang H, Ng HH, Erdjument-Bromage H, Tempst P, Struhl K, Zhang Y. 2002. Methylation of H3-lysine 79 is mediated by a new family of HMTases without a SET domain. Current Biology 12: 1052-1058.
16. Filichkin SA, Priest HD, Givan SA, Shen R, Bryant DW, Fox SE, Wong WK, Mockler TC. 2010. Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Research 20: 45-58.
17. Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL et al. 2008. The Pfam protein families database. Nucleic Acids Research 36: D281-D288.
18. Fumasoni I, Meani N, Rambaldi D, Scafetta G, Alcalay M, Ciccarelli FD. 2007. Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebrates. BMC Evolutionary Biology 7: 187.
19. Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. System Biology 52: 696-704.
20. Guo L, Yu Y, Law JA, Zhang X. 2010. SET DOMAIN GROUP2 is the major histone H3 lysine 4 trimethyltransferase in Arabidopsis. Proceedings of the National Academy of Sciences, USA 107: 18557-18562.
21. Huang J, Perez-Burgos L, Placek BJ, Sengupta R, Richter M, Dorsey JA, Kubicek S, Opravil S, Jenuwein T, Berger SL. 2006. Repression of p53 activity by Smyd2-mediated methylation. Nature 444: 629-632.
22. Huang Y, Liu C, Shen WH, Ruan Y. 2011. Phylogenetic analysis and classification of the Brassica rapa SET-domain protein family. BMC Plant Biology 11: 175.
23. Itoh N, Ornitz DM. 2004. Evolution of the Fgf and Fgfr gene families. Trends in Genetics 20: 563-569.
24. Jenuwein T, Laible G, Dorn R, Reuter G. 1998. SET domain proteins modulate chromatin domains in eu- and heterochromatin. Cellular and Molecular Life Sciences 54: 80-93.
25. Jiao Y, Meyerowitz EM. 2010. Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control. Molecular Systems Biology 6: 419.
26. Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, Tomsho LP, Hu Y, Liang H, Soltis PS et al. 2011. Ancestral polyploidy in seed plants and angiosperms. Nature 473: 97-100.
27. Jin J, Xie XY, Chen C, Park JG, Stark C, James DA, Olhovsky M, Linding R, Mao YY, Pawson T. 2009. Eukaryotic protein domains as functional units of cellular evolution. Science Signaling 2: ra76.
28. Jones RS, Gelbart WM. 1993. The Drosophila Polycomb-group gene Enhancer of zeste contains a region with sequence similarity to trithorax. Molecular and Cellular Biology 13: 6357-6366.
29. Kim DW, Kim KB, Kim JY, Seo SB. 2011. Characterization of a novel histone H3K36 methyltransferase setd3 in zebrafish. Bioscience, Biotechnology, and Biochemistry 75: 289-294.
30. Leinhart K, Brown M. 2011. SET/MYND lysine methyltransferases regulate gene transcription and protein activity. Genes 2: 210-218.
31. Levy D, Kuo AJ, Chang Y, Schaefer U, Kitson C, Cheung P, Espejo A, Zee BM, Liu CL, Tangsombatvisit S et al. 2011. Lysine methylation of the NF-kappaB subunit RelA by SETD6 couples activity of the histone methyltransferase GLP at chromatin to tonic repression of NF-kappaB signaling. Nature Immunology 12: 29-36.
32. Liu C, Lu F, Cui X, Cao X. 2010. Histone methylation in higher plants. Annual Review of Plant Biology 61: 395-420.
33. Maere S, De Bodt S, Raes J, Casneuf T, Van Montagu M, Kuiper M, Van de Peer Y. 2005. Modeling gene and genome duplications in eukaryotes. Proceedings of the National Academy of Sciences, USA 102: 5454-5459.
34. Margueron R, Li GH, Sarma K, Blais A, Zavadil J, Woodcock CL, Dyniacht BD, Reinberg D. 2008. Ezh1 and Ezh2 maintain repressive chromatin through different mechanisms. Molecular Cell 32: 503-518.
35. Nam J, Kim J, Lee S, An G, Ma H, Nei M. 2004. Type I MADS-box genes have experienced faster birth-and-death evolution than type II MADS-box genes in angiosperms. Proceedings of the National Academy of Sciences, USA 101: 1910-1915.
36. Ng DWK, Wang T, Chandrasekharan MB, Aramayo R, Kertbundit S, Hall TC. 2007. Plant SET domain-containing proteins: structure, function and regulation. Biochimica et Biophysica Acta 1769: 316-329.
37. Nimura K, Ura K, Kaneda Y. 2010. Histone methyltransferases: regulation of transcription and contribution to human disease. Journal of Molecular Medicine 88: 1213-1220.
38. Ohno S. 1970. Evolution by gene duplication. New York, NY, USA: Springer Verlag.
39. Oliver PL, Goodstadt L, Bayes JJ, Birtle Z, Roach KC, Phadnis N, Beatson SA, Lunter G, Malik HS, Ponting CP. 2009. Accelerated evolution of the Prdm9 speciation gene across diverse metazoan taxa. PLoS Genetics 5: e1000753.
40. Parvanov ED, Petkov PM, Paigen K. 2010. Prdm9 controls activation of mammalian recombination hotspots. Science 327: 835.
41. Pires N, Dolan L. 2010. Origin and diversification of basic-helix-loop-helix proteins in plants. Molecular Biology and Evolution 27: 862-874.
42. Ravi V, Lam K, Tay BH, Tay A, Brenner S, Venkatesh B. 2009. Elephant shark (Callorhinchus milii) provides insights into the evolution of Hox gene clusters in gnathostomes. Proceedings of the National Academy of Sciences, USA 106: 16327-16332.
43. Sakai H, Mizuno H, Kawahara Y, Wakimoto H, Ikawa H, Kawahigashi H, Kanamori H, Matsumoto T, Itoh T, Gaut BS. 2011. Retrogenes in rice (Oryza sativa L. ssp. japonica) exhibit correlated expression with their source genes. Genome Biology and Evolution 3: 1357-1368.
44. Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Scholkopf B, Weigel D, Lohmann JU. 2005. A gene expression map of Arabidopsis thaliana development. Nature Genetics 37: 501-506.
45. Spillane C, Schmid KJ, Laoueille-Duprat S, Pien S, Escobar-Restrepo JM, Baroux C, Gagliardini V, Page DR, Wolfe KH, Grossniklaus U. 2007. Positive darwinian selection at the imprinted MEDEA locus in plants. Nature 448: 349-352.
46. Springer NM, Napoli CA, Selinger DA, Pandey R, Cone KC, Chandler VL, Kaeppler HF, Kaeppler SM. 2003. Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots. Plant Physiology 132: 907-925.
47. Stassen MJ, Bailey D, Nelson S, Chinwalla V, Harte PJ. 1995. The Drosophila trithorax proteins contain a novel variant of the nuclear receptor type DNA binding domain and an ancient conserved motif found in other chromosomal proteins. Mechanisms of Development 52: 209-223.
48. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G et al. 2004. A gene atlas of the mouse and human protein-encoding transcriptomes. Proceedings of the National Academy of Sciences, USA 101: 6062-6067.
49. Sun XJ, Xu PF, Zhou T, Hu M, Fu CT, Zhang Y, Jin Y, Chen Y, Chen SJ, Huang QH et al. 2008. Genome-wide survey and developmental expression mapping of zebrafish SET domain-containing genes. PLoS ONE 3: e1499.
50. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28: 2731-2739.
51. Tang H, Bowers JE, Wang X, Ming R, Alam M, Paterson AH. 2008a. Synteny and collinearity in plant genomes. Science 320: 486-488.
52. Tang H, Wang X, Bowers JE, Ming R, Alam M, Paterson AH. 2008b. Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genome Research 18: 1944-1954.
53. Tang X, Zhang ZY, Zhang WJ, Zhao XM, Li X, Zhang D, Liu QQ, Tang WH. 2010. Global gene profiling of laser-captured pollen mother cells indicates molecular pathways and gene subfamilies involved in rice meiosis. Plant Physiology 154: 1855-1870.
54. Theodosiou A, Arhondakis S, Baumann M, Kossida S. 2009. Evolutionary scenarios of Notch proteins. Molecular Biology and Evolution 26: 1631-1640.
55. Thorstensen T, Grini PE, Aalen RB. 2011. SET domain proteins in plant development. Biochimica et Biophysica Acta 1809: 407-420.
56. Trievel RC, Flynn EM, Houtz RL, Hurley JH. 2003. Mechanism of multiple lysine methylation by the SET domain enzyme Rubisco LSMT. Nature Structural & Molecular Biology 10: 545-552.
57. Tschiersch B, Hofmann A, Krauss V, Dorn R, Korge G, Reuter G. 1994. The protein encoded by the Drosophila position-effect variegation suppressor gene Su(var)3-9 combines domains of antagonistic regulators of homeotic gene complexes. EMBO Journal 13: 3822-3831.
58. Van de Peer Y, Maere S, Meyer A. 2009. The evolutionary significance of ancient genome duplications. Nature Reviews Genetics 10: 725-732.
59. Veerappan CS, Avramova Z, Moriyama EN. 2008. Evolution of SET-domain protein families in the unicellular and multicellular Ascomycota fungi. BMC Evolutionary Biology 8: 190.
60. Vogel C, Chothia C. 2006. Protein family expansions and biological complexity. PLoS Computational Biology 2: e48.
61. Xu G, Ma H, Nei M, Kong H. 2009. Evolution of F-box genes in plants: different modes of sequence divergence and their relationships with functional diversification. Proceedings of the National Academy of Sciences, USA 106: 835-840.
62. Yang H, Lu P, Wang Y, Ma H. 2011. The transcriptome landscape of Arabidopsis male meiocytes from high-throughput sequencing: the complexity and evolution of the meiotic process. Plant Journal 65: 503-516.
63. Zhang LS, Ma CR, Ji Q, Wang YF. 2009. Genome-wide identification, classification and expression analyses of SET domain gene family in Arabidopsis and rice. Yi Chuan 31: 186-198.
64. Zhu X, Ma H, Chen Z. 2011. Phylogenetics and evolution of Su(var)3-9 SET genes in land plants: rapid diversification in structure and function. BMC Evolutionary Biology 11: 63.