A study on the distribution of 37 well conserved families of C2H2 zinc finger genes in eukaryotes

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Seetharam, Arun ^a,b   Stuart, Gary W ^a  

^a INDIANA STATE UNIVERSITY   (United States)

^b PURDUE UNIVERSITY   (United States)

Author keywords

C2H2 Zinc Finger Genes; Family Expansion; HMM; Orthologs Detection; RBH

Indexed keywords

ZINC FINGER PROTEIN;

ACCURACY; ANALYTIC METHOD; ANIMAL; ARTICLE; AUTOMATION; BILATERIA; C2H2 ZINC FINGER GENE; COMPUTER PROGRAM; EUKARYOTE; EXCAVATA; FUNGUS; GENE DUPLICATION; GENE IDENTIFICATION; GENE LOSS; GENETIC CONSERVATION; HIDDEN MARKOV MODEL; HUMAN; MACHINE LEARNING; MULTIGENE FAMILY; NONHUMAN; PHYLOGENY; PLANT; PROTIST; RECIPROCAL BEST HIT; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE;

AMOEBOZOA; ANIMALS; CONSERVED SEQUENCE; EUKARYOTA; FUNGI; MARKOV CHAINS; PLANTS; ZINC FINGERS;

BILATERIA; EUKARYOTA; FUNGI; METAZOA; PROTISTA; VERTEBRATA;

EID: 84879242281     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-420     Document Type: Article

References (36)

1. Tadepally HD, Burger G, Aubry M. Evolution of C2H2-zinc finger genes and subfamilies in mammals: species-specific duplication and loss of clusters, genes and effector domains. BMC Evol Biol 2008, 8:176. 10.1186/1471-2148-8-176, 2443715, 18559114.
2. Rivera MC, Jain R, Moore JE, Lake JA. Genomic evidence for two functionally distinct gene classes. Proc Natl Acad Sci USA 1998, 95(11):6239-6244. 10.1073/pnas.95.11.6239, 27643, 9600949.
3. Eddy SR. Profile hidden Markov models. Bioinformatics 1998, 14(9):755-763. 10.1093/bioinformatics/14.9.755, 9918945.
4. Pennisi E. Drafting a tree. Science 2003, 300(5626):1694. 10.1126/science.300.5626.1694, 12805533.
5. Valentine JW, Collins AG. The significance of moulting in Ecdysozoan evolution. Evol Dev 2000, 2(3):152-156. 10.1046/j.1525-142x.2000.00043.x, 11252571.
6. Knight RD, Shimeld SM. Identification of conserved C2H2 zinc-finger gene families in the Bilateria. Genome Biol 2001, 2(5). RESEARCH0016.
7. Seetharam A, Bai Y, Stuart GW. A survey of well conserved families of C2H2 zinc-finger genes in Daphnia. BMC Genomics 2010, 11:276. 10.1186/1471-2164-11-276, 2889900, 20433734.
8. Soding J. Protein homology detection by HMM-HMM comparison. Bioinformatics 2005, 21(7):951-960. 10.1093/bioinformatics/bti125, 15531603.
9. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
10. Chen F, Mackey AJ, Vermunt JK, Roos DS. Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS One 2007, 2(4):e383. 10.1371/journal.pone.0000383, 1849888, 17440619.
11. Huntley S, Baggott DM, Hamilton AT, Tran-Gyamfi M, Yang S, Kim J, Gordon L, Branscomb E, Stubbs L. A comprehensive catalog of human KRAB-associated zinc finger genes: insights into the evolutionary history of a large family of transcriptional repressors. Genome Res 2006, 16(5):669-677. 10.1101/gr.4842106, 1457042, 16606702.
12. Hamilton AT, Huntley S, Kim J, Branscomb E, Stubbs L. Lineage-specific expansion of KRAB zinc-finger transcription factor genes: implications for the evolution of vertebrate regulatory networks. Cold Spring Harb Symp Quant Biol 2003, 68:131-140. 10.1101/sqb.2003.68.131, 15338611.
13. Nowick K, Fields C, Gernat T, Caetano-Anolles D, Kholina N, Stubbs L. Gain, loss and divergence in primate zinc-finger genes: a rich resource for evolution of gene regulatory differences between species. PLoS One 2011, 6(6):e21553. 10.1371/journal.pone.0021553, 3126818, 21738707.
14. Ding G, Lorenz P, Kreutzer M, Li Y, Thiesen HJ. SysZNF: the C2H2 zinc finger gene database. Nucleic Acids Res 2009, 37:D267-273. Database issue, 10.1093/nar/gkn782, 2686507, 18974185.
15. Chung HR, Lohr U, Jackle H. Lineage-specific expansion of the zinc finger associated domain ZAD. Mol Biol Evol 2007, 24(9):1934-1943. 10.1093/molbev/msm121, 17569752.
16. Ebersberger I, Strauss S, Von Haeseler A. HaMStR: profile hidden markov model based search for orthologs in ESTs. BMC Evol Biol 2009, 9:157. 10.1186/1471-2148-9-157, 2723089, 19586527.
17. Kramer A, Ferfoglia F, Huang CJ, Mulhaupt F, Nesic D, Tanackovic G. Structure-function analysis of the U2 snRNP-associated splicing factor SF3a. Biochem Soc Trans 2005, 33(Pt 3):439-442.
18. Tanackovic G, Kramer A. Human splicing factor SF3a, but not SF1, is essential for pre-mRNA splicing in vivo. Mol Biol Cell 2005, 16(3):1366-1377. 10.1091/mbc.E04-11-1034, 551499, 15647371.
19. Biard DS, Miccoli L, Despras E, Frobert Y, Creminon C, Angulo JF. Ionizing radiation triggers chromatin-bound kin17 complex formation in human cells. J Biol Chem 2002, 277(21):19156-19165. 10.1074/jbc.M200321200, 11880372.
20. Iuchi S, Kuldell N. Zinc finger proteins : from atomic contact to cellular function 2005, Georgetown, Tex. New York: Landes Bioscience Kluwer Academic/Plenum Publishers.
21. Holland LZ, Gibson-Brown JJ. The Ciona intestinalis genome: when the constraints are off. BioEssays 2003, 25(6):529-532. 10.1002/bies.10302, 12766941.
22. Vienne A, Pontarotti P. Metaphylogeny of 82 gene families sheds a new light on chordate evolution. Int J Biol Sci 2006, 2(2):32-37. 1458423, 16733531.
23. Delsuc F, Tsagkogeorga G, Lartillot N, Philippe H. Additional molecular support for the new chordate phylogeny. Genesis 2008, 46(11):592-604. 10.1002/dvg.20450, 19003928.
24. Lespinet O, Wolf YI, Koonin EV, Aravind L. The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res 2002, 12(7):1048-1059. 10.1101/gr.174302, 186617, 12097341.
25. Rubin G, Yandell M, Wortman J, Gabor Miklos G, Nelson C, Hariharan I, Fortini M, Li P, Apweiler R, Fleischmann W. Comparative genomics of the eukaryotes. Science 2000, 287:2204-2215. 10.1126/science.287.5461.2204, 2754258, 10731134.
26. Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, et al. Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science 1998, 282(5396):2022-2028. 3057080, 9851918.
27. Fumasoni I, Meani N, Rambaldi D, Scafetta G, Alcalay M, Ciccarelli FD. Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebrates. BMC Evol Biol 2007, 7:187. 10.1186/1471-2148-7-187, 2082429, 17916234.
28. Demuth JP, De Bie T, Stajich JE, Cristianini N, Hahn MW. The evolution of mammalian gene families. PLoS One 2006, 1:e85. 10.1371/journal.pone.0000085, 1762380, 17183716.
29. Emerson RO, Thomas JH. Adaptive evolution in zinc finger transcription factors. PLoS Genet 2009, 5(1):e1000325. 10.1371/journal.pgen.1000325, 2604467, 19119423.
30. Pruitt KD, Tatusova T, Klimke W, Maglott DR. NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res 2009, 37:D32-36. Database issue, 10.1093/nar/gkn721, 2686572, 18927115.
31. Boutet E, Lieberherr D, Tognolli M, Schneider M, Bairoch A. UniProtKB/Swiss-Prot. Methods Mol Biol 2007, 406:89-112.
32. Englbrecht CC, Schoof H, Bohm S. Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome. BMC Genomics 2004, 5(1):39. 10.1186/1471-2164-5-39, 481060, 15236668.
33. Haerty W, Artieri C, Khezri N, Singh RS, Gupta BP. Comparative analysis of function and interaction of transcription factors in nematodes: extensive conservation of orthology coupled to rapid sequence evolution. BMC Genomics 2008, 9:399. 10.1186/1471-2164-9-399, 2533025, 18752680.
34. Materna SC, Howard-Ashby M, Gray RF, Davidson EH. The C2H2 zinc finger genes of Strongylocentrotus purpuratus and their expression in embryonic development. Dev Biol 2006, 300(1):108-120. 10.1016/j.ydbio.2006.08.032, 16997293.
35. Johnson LS, Eddy SR, Portugaly E. Hidden Markov model speed heuristic and iterative HMM search procedure. BMC bioinformatics 2010, 11:431. 10.1186/1471-2105-11-431, 2931519, 20718988.
36. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23(21):2947-2948. 10.1093/bioinformatics/btm404, 17846036.