Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebrates

BMC Evolutionary Biology

Volumn 7, Issue , 2007, Pages

  Fumasoni, Irene ^a   Meani, Natalia ^a   Rambaldi, Davide ^a   Scafetta, Gaia ^a   Alcalay, Myriam ^a   Ciccarelli, Francesca D ^a  

^a EUROPEAN INSTITUTE OF ONCOLOGY   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CARCINOGENESIS; COMPARATIVE STUDY; FAMILY EXPANSION; FAMILY PLANNING; GENE REARRANGEMENT; MOLECULAR EVOLUTION; PARALOGY; PRDM GENE; RNA SPLICING; TRANSCRIPTION REGULATION; TUMOR SUPPRESSOR GENE; VERTEBRATE; AMINO ACID SEQUENCE; ANIMAL; GENE DUPLICATION; GENE EXPRESSION REGULATION; GENETICS; HUMAN; MULTIGENE FAMILY; PHYLOGENY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE;

METAZOA; PRIMATES; VERTEBRATA;

PRIMER DNA; REPRESSOR PROTEIN; TRANSCRIPTION FACTOR;

AMINO ACID SEQUENCE; ANIMALS; DNA PRIMERS; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENE EXPRESSION REGULATION; GENE REARRANGEMENT; HUMANS; MULTIGENE FAMILY; PHYLOGENY; REPRESSOR PROTEINS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; SPECIES SPECIFICITY; TRANSCRIPTION FACTORS; VERTEBRATES;

EID: 36348939746     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-7-187     Document Type: Article

References (44)

1. Comparative Genomics of the Eukaryotes. GM Rubin MD Yandell JR Wortman GL Gabor Miklos CR Nelson IK Hariharan ME Fortini PW Li R Apweiler W Fleischmann, Science 2000 287 5461 2204 2215 10.1126/science.287.5461.2204 10731134
2. Comparison of the Complete Protein Sets of Worm and Yeast: Orthology and Divergence. SA Chervitz L Aravind G Sherlock CA Ball EV Koonin SS Dwight MA Harris K Dolinski S Mohr T Smith, Science 1998 282 5396 2022 2028 10.1126/science.282.5396.2022 9851918
3. The Role of Lineage-Specific Gene Family Expansion in the Evolution of Eukaryotes. O Lespinet YI Wolf EV Koonin L Aravind, Genome Res 2002 12 7 1048 1059 12097341 10.1101/gr.174302
4. Protein Family Expansions and Biological Complexity. C Vogel C Chothia, PLoS Computational Biology 2006 2 5 e48 16733546 10.1371/journal.pcbi.0020048
5. Initial sequencing and analysis of the human genome. Consortium IHGS, Nature 2001 409 6822 860 921 10.1038/35057062 11237011
6. Evolution by gene duplication. S Ohno, Berlin-Heidelberg-New York: Springer-Verlang 1970
7. Preservation of duplicate genes by complementary, degenerative mutations. A Force M Lynch FB Pickett A Amores YL Yan J Postlethwait, Genetics 1999 151 4 1531 1545 10101175
8. On the possibility of constructive neutral evolution. A Stoltzfus, J Mol Evol 1999 49 2 169 181 10.1007/PL00006540 10441669
9. The probability of duplicate gene preservation by subfunctionalization. M Lynch A Force, Genetics 2000 154 1 459 473 10629003
10. Blimp-1, a novel zinc finger-containing protein that can drive the maturation of B lymphocytes into immunoglobulin-secreting cells. CA Turner Jr DH Mack MM Davis, Cell 1994 77 2 297 306 10.1016/0092-8674(94)90321-2 8168136
11. BLIMP1 regulates cell growth through repression of p53 transcription. J Yan J Jiang CA Lim Q Wu H-H Ng K-C Chin, PNAS 2007 104 6 1841 1846 17264218 10.1073/pnas.0605562104
12. PRDM5 is silenced in human cancers and has growth suppressive activities. Q Deng S Huang, Oncogene 2004 23 28 4903 4910 10.1038/sj.onc.1207615 15077163
13. RIZ1, but not the alternative RIZ2 product of the same gene, is underexpressed in breast cancer, and forced RIZ1 expression causes G2-M cell cycle arrest and/or apoptosis. L He JX Yu L Liu IM Buyse MS Wang QC Yang A Nakagawara GM Brodeur YE Shi S Huang, Cancer Res 1998 58 19 4238 4244 9766644
14. Histone methyltransferases, diet nutrients and tumour suppressors. S Huang, Nat Rev Cancer 2002 2 6 469 476 10.1038/nrc819 12189389
15. Re-SET-ting heterochromatin by histone methyltransferases. T Jenuwein, Trends Cell Biol 2001 11 6 266 273 10.1016/S0962-8924(01)02001-3 11356363
16. A histone H3 methyltransferase controls epigenetic events required for meiotic prophase. K Hayashi K Yoshida Y Matsui, Nature 2005 438 7066 374 378 10.1038/nature04112 16292313
17. Inactivation of a histone methyltransferase by mutations in human cancers. KC Kim L Geng S Huang, Cancer Res 2003 63 22 7619 7623 14633678
18. Blimp1 associates with Prmt5 and directs histone arginine methylation in mouse germ cells. K Ancelin UC Lange P Hajkova R Schneider AJ Bannister T Kouzarides MA Surani, Nat Cell Biol 2006 8 6 623 630 10.1038/ncb1413 16699504
19. PRISM/PRDM6, a transcriptional repressor that promotes the proliferative gene program in smooth muscle cells. CA Davis M Haberland MA Arnold LB Sutherland OG McDonald JA Richardson G Childs S Harris GK Owens EN Olson, Mol Cell Biol 2006 26 7 2626 2636 16537907 10.1128/MCB.26.7.2626-2636.2006
20. hamlet, a Binary Genetic Switch Between Single- and Multiple- Dendrite Neuron Morphology. AW Moore LY Jan YN Jan, Science 2002 297 5585 1355 1358 10.1126/science.1072387 12193790
21. A Genetic Screen for Dominant Modifiers of a cyclin E Hypomorphic Mutation Identifies Novel Regulators of S-Phase Entry in Drosophila. A Brumby J Secombe J Horsfield M Coombe N Amin D Coates R Saint H Richardson, Genetics 2004 168 1 227 251 15454540 10.1534/genetics.104.026617
22. Tumor formation and inactivation of RIZ1, an Rb-binding member of a nuclear protein-methyltransferase superfamily. G Steele-Perkins W Fang XH Yang M Van Gele T Carling J Gu IM Buyse JA Fletcher J Liu R Bronson, Genes Dev 2001 15 17 2250 2262 11544182 10.1101/gad.870101
23. Leukemogenesis of the EVI1/MEL1 gene family. K Morishita, Int J Hematol 2007 85 4 279 286 10.1532/IJH97.06174 17483069
24. Meisetz, a novel histone tri-methyltransferase, regulates meiosis-specific epigenesis. K Hayashi Y Matsui, Cell Cycle 2006 5 6 615 620 16582607
25. Meisetz and the birth of the KRAB motif. Z Birtle CP Ponting, Bioinformatics 2006 22 23 2841 2845 10.1093/bioinformatics/btl498 17032681
26. PRDI-BF1 recruits the histone H3 methyltransferase G9a in transcriptional silencing. I Gyory J Wu G Fejer E Seto KL Wright, Nat Immunol 2004 5 3 299 308 10.1038/ni1046 14985713
27. Highly expressed genes in yeast evolve slowly. C Pal B Papp LD Hurst, Genetics 2001 158 2 927 931 11430355
28. Why highly expressed proteins evolve slowly. DA Drummond JD Bloom C Adami CO Wilke FH Arnold, PNAS 2005 102 40 14338 14343 16176987 10.1073/pnas. 0504070102
29. Complex genomic rearrangements lead to novel primate gene function. FD Ciccarelli C von Mering M Suyama ED Harrington E Izaurralde P Bork, Genome Res 2005 15 3 343 351 15710750 10.1101/gr.3266405
30. Primate segmental duplications: crucibles of evolution, diversity and disease. JA Bailey EE Eichler, Nat Rev Genet 2006 7 7 552 564 10.1038/nrg1895 16770338
31. How were introns inserted into nuclear genes? JH Rogers, Trends Genet 1989 5 7 213 216 10.1016/0168-9525(89)90084-X 2551082
32. Late changes in spliceosomal introns define clades in vertebrate evolution. B Venkatesh Y Ning S Brenner, Proc Natl Acad Sci USA 1999 96 18 10267 10271 10468597 10.1073/pnas.96.18.10267
33. High rate of recent intron gain and loss in simultaneously duplicated Arabidopsis genes. DG Knowles A McLysaght, Mol Biol Evol 2006 23 8 1548 1557 10.1093/molbev/msl017 16720694
34. mRNA surveillance: the perfect persist. E Wagner J Lykke-Andersen, J Cell Sci 2002 115 15 3033 3038 12118059
35. Functional divergence of proteins through frameshift mutations. J Raes Y Van de Peer, Trends in Genetics 2005 21 8 428 431 10.1016/j.tig.2005.05.013 15951050
36. Basic local alignment search tool. SF Altschul W Gish W Miller EW Myers DJ Lipman, J Mol Biol 1990 215 403 410 2231712
37. SMART 5: domains in the context of genomes and networks. I Letunic RR Copley B Pils S Pinkert J Schultz P Bork, Nucl Acids Res 2006 34 suppl_1 D257 260 10.1093/nar/gkj079
38. PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames. E Birney JD Thompson TJ Gibson, Nucleic Acids Res 1996 24 14 2730 2739 8759004 10.1093/nar/24.14.2730
39. BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments. M Suyama D Torrents P Bork, Bioinformatics 2004 20 12 1968 1970 10.1093/bioinformatics/bth172 15037510
40. MUSCLE: multiple sequence alignment with high accuracy and high throughput. RC Edgar, Nucl Acids Res 2004 32 5 1792 1797 15034147 10.1093/nar/gkh340
41. Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis. J Castresana, Mol Biol Evol 2000 17 4 540 552 10742046
42. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. S Guindon O Gascuel, Syst Biol 2003 52 5 696 704 10.1080/10635150390235520 14530136
43. MrBayes 3: Bayesian phylogenetic inference under mixed models. F Ronquist JP Huelsenbeck, Bioinformatics 2003 19 12 1572 1574 10.1093/bioinformatics/ btg180 12912839
44. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. I Letunic P Bork, Bioinformatics 2007 23 1 127 128 10.1093/bioinformatics/btl529 17050570