Gain, loss and divergence in primate Zinc-Finger genes: A rich resource for evolution of gene regulatory differences between species

PLoS ONE

Volumn 6, Issue 6, 2011, Pages

  Nowick, Katja ^a,b,c   Fields, Christopher ^a   Gernat, Tim ^a   Caetano Anolles, Derek ^a,b   Kholina, Nadezda ^a,b   Stubbs, Lisa ^a,b  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^c UNIVERSITY OF LEIPZIG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

KRUPPEL TYPE ZINC FINGER PROTEIN; UNCLASSIFIED DRUG; ZINC FINGER PROTEIN;

ARTICLE; CHIMPANZEE; CONTROLLED STUDY; GENE; GENE DELETION; GENE DUPLICATION; GENE IDENTIFICATION; GENE LOCUS; GENE LOSS; GENE REGULATORY NETWORK; GENETIC CONSERVATION; GENETIC GAIN; GENETIC RESOURCE; GENETIC VARIABILITY; GENOME ANALYSIS; HUMAN; KRUPPEL TYPE ZINC FINGER GENE; MACACA; MOLECULAR EVOLUTION; NONHUMAN; ORANG UTAN; PREDICTION; PROTEIN DNA BINDING; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; VALIDATION PROCESS; ANIMAL; GENETICS; PRIMATE;

MACACA MULATTA; PAN; PONGO PYGMAEUS; PRIMATES;

ANIMALS; EVOLUTION, MOLECULAR; HUMANS; PRIMATES; ZINC FINGERS;

EID: 79959668884     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0021553     Document Type: Article

References (43)

1. Oliver PL, Goodstadt L, Bayes JJ, Birtle Z, Roach KC, et al. (2009) Accelerated evolution of the Prdm9 speciation gene across diverse metazoan taxa. PLoS Genet 5: e1000753.
2. Nowick K, Stubbs L, (2010) Lineage-specific transcription factors and the evolution of gene regulatory networks. Brief Funct Genomics 9: 65-78.
3. Hecht J, Stricker S, Wiecha U, Stiege A, Panopoulou G, et al. (2008) Evolution of a core gene network for skeletogenesis in chordates. PLoS Genet 4: e1000025.
4. Enard W, Przeworski M, Fisher SE, Lai CS, Wiebe V, et al. (2002) Molecular evolution of FOXP2, a gene involved in speech and language. Nature 418: 869-872.
5. Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM, (2009) A census of human transcription factors: function, expression and evolution. Nat Rev Genet 10: 252-263.
6. Urrutia R, (2003) KRAB-containing zinc-finger repressor proteins. Genome Biol 4: 231.
7. Margolin JF, Friedman JR, Meyer WK, Vissing H, Thiesen HJ, et al. (1994) Kruppel-associated boxes are potent transcriptional repression domains. Proc Natl Acad Sci U S A 91: 4509-4513.
8. Collins T, Stone JR, Williams AJ, (2001) All in the family: the BTB/POZ, KRAB, and SCAN domains. Mol Cell Biol 21: 3609-3615.
9. Huntley S, Baggott DM, Hamilton AT, Tran-Gyamfi M, Yang S, et al. (2006) A comprehensive catalog of human KRAB-associated zinc finger genes: Insights into the evolutionary history of a large family of transcriptional repressors. Genome Res 16: 669-677.
10. Bellefroid EJ, Marine JC, Ried T, Lecocq PJ, Riviere M, et al. (1993) Clustered organization of homologous KRAB zinc-finger genes with enhanced expression in human T lymphoid cells. Embo J 12: 1363-1374.
11. Looman C, Abrink M, Mark C, Hellman L, (2002) KRAB zinc finger proteins: An analysis of the molecular mechanisms governing their increase in numbers and complexity during evolution. Mol Biol Evol 19: 2118-2130.
12. Nowick K, Hamilton AT, Zhang H, Stubbs L, (2010) Rapid sequence and expression divergence suggest selection for novel function in primate-specific KRAB-ZNF genes. Mol Biol Evol 27: 2606-2617.
13. Nowick K, Gernat T, Almaas E, Stubbs L, (2009) Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in brain. Proc Natl Acad Sci U S A 106: 22358-22363.
14. Tadepally HD, Burger G, Aubry M, (2008) Evolution of C2H2-zinc finger genes and subfamilies in mammals: species-specific duplication and loss of clusters, genes and effector domains. BMC Evol Biol 8: 176.
15. Thomas JH, Emerson RO, (2009) Evolution of C2H2-zinc finger genes revisited. BMC Evol Biol 9: 51.
16. Shannon M, Hamilton AT, Gordon L, Branscomb E, Stubbs L, (2003) Differential expansion of zinc-finger transcription factor loci in homologous human and mouse gene clusters. Genome Res 13: 1097-1110.
17. Hamilton AT, Huntley S, Kim J, Branscomb E, Stubbs L, (2003) Lineage-specific expansion of KRAB zinc-finger transcription factor genes: Implications for the evolution of vertebrate regulatory networks. Cold Spring Harb Symp Quant Biol 68: 131-140.
18. Emerson RO, Thomas JH, (2009) Adaptive evolution in zinc finger transcription factors. PLoS Genet 5: e1000325.
19. Li L, Stoeckert CJ Jr, Roos DS, (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13: 2178-2189.
20. Perry GH, Tchinda J, McGrath SD, Zhang J, Picker SR, et al. (2006) Hotspots for copy number variation in chimpanzees and humans. Proc Natl Acad Sci U S A 103: 8006-8011.
21. Marques-Bonet T, Kidd JM, Ventura M, Graves TA, Cheng Z, et al. (2009) A burst of segmental duplications in the genome of the African great ape ancestor. Nature 457: 877-881.
22. Wolfe SA, Grant RA, Elrod-Erickson M, Pabo CO, (2001) Beyond the "recognition code": structures of two Cys2His2 zinc finger/TATA box complexes. Structure 9: 717-723.
23. Nowick K, Huntley S, Stubbs L, (2009) Rapid expansion and divergence suggest a central and distinct role for KRAB-ZNF genes in vertebrate evolution. In: Yoshida K, editors. Focus on Zinc Finger Protein Research: Research Signpost pp. 13-29.
24. Hamilton AT, Huntley S, Tran-Gyamfi M, Baggott DM, Gordon L, et al. (2006) Evolutionary expansion and divergence in the ZNF91 subfamily of primate-specific zinc finger genes. Genome Res 16: 584-594.
25. Thomas JH, Emerson RO, Shendure J, (2009) Extraordinary molecular evolution in the PRDM9 fertility gene. PLoS One 4: e8505.
26. Kaplan T, Friedman N, Margalit H, (2005) Ab initio prediction of transcription factor targets using structural knowledge. PLoS Comput Biol 1: e1.
27. Prufer K, Muetzel B, Do HH, Weiss G, Khaitovich P, et al. (2007) FUNC: a package for detecting significant associations between gene sets and ontological annotations. BMC Bioinformatics 8: 41.
28. Mason S, Piper M, Gronostajski RM, Richards LJ, (2009) Nuclear factor one transcription factors in CNS development. Mol Neurobiol 39: 10-23.
29. Kim MY, Reyna J, Chen LS, Zeichner-David M, (2009) Role of the transcription factor NFIC in odontoblast gene expression. J Calif Dent Assoc 37: 875-881.
30. Yang X, Kilgallen S, Andreeva V, Spicer DB, Pinz I, et al. (2010) Conditional expression of Spry1 in neural crest causes craniofacial and cardiac defects. BMC Dev Biol 10: 48.
31. Eloy-Trinquet S, Wang H, Edom-Vovard F, Duprez D, (2009) Fgf signaling components are associated with muscles and tendons during limb development. Dev Dyn 238: 1195-1206.
32. Urs S, Venkatesh D, Tang Y, Henderson T, Yang X, et al. (2010) Sprouty1 is a critical regulatory switch of mesenchymal stem cell lineage allocation. FASEB J 24: 3264-3273.
33. Uittenbogaard M, Chiaramello A, (2002) Expression of the bHLH transcription factor Tcf12 (ME1) gene is linked to the expansion of precursor cell populations during neurogenesis. Brain Res Gene Expr Patterns 1: 115-121.
34. Parvanov ED, Petkov PM, Paigen K, (2010) Prdm9 controls activation of mammalian recombination hotspots. Science 327: 835.
35. Baudat F, Buard J, Grey C, Fledel-Alon A, Ober C, et al. (2010) PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice. Science 327: 836-840.
36. Myers S, Bowden R, Tumian A, Bontrop RE, Freeman C, et al. (2010) Drive against hotspot motifs in primates implicates the PRDM9 gene in meiotic recombination. Science 327: 876-879.
37. Lewis SE, Searle SM, Harris N, Gibson M, Lyer V, et al. (2002) Apollo: a sequence annotation editor. Genome Biol 3: RESEARCH0082.
38. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, et al. (2002) The generic genome browser: a building block for a model organism system database. Genome Res 12: 1599-1610.
39. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, et al. (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Res 12: 1611-1618.
40. McKay SJ, Vergara IA, Stajich JE, (2010) Using the Generic Synteny Browser (GBrowse_syn). Curr Protoc Bioinformatics Chapter 9: Unit 9 12.
41. Needleman SB, Wunsch CD, (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48: 443-453.
42. Yang Z, (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13: 555-556.
43. Martin A, Ochagavia ME, Rabasa LC, Miranda J, Fernandez-de-Cossio J, et al. (2010) BisoGenet: a new tool for gene network building, visualization and analysis. BMC Bioinformatics 11: 91.