Function and evolution of C2H2 zinc finger arrays

Sub-Cellular Biochemistry

Volumn 52, Issue , 2011, Pages 75-94

  Stubbs, Lisa ^a   Sun, Younguk ^b   Caetano Anolles, Derek ^b  

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

^b NONE

Author keywords

[No Author keywords available]

Indexed keywords

EUKARYOTA; METAZOA; VERTEBRATA;

DNA BINDING PROTEIN; TRANSCRIPTION FACTOR; ZINC FINGER PROTEIN;

AMINO ACID SEQUENCE; ANIMAL; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; VERTEBRATE;

AMINO ACID SEQUENCE; ANIMALS; DNA-BINDING PROTEINS; EVOLUTION, MOLECULAR; MOLECULAR SEQUENCE DATA; TRANSCRIPTION FACTORS; VERTEBRATES; ZINC FINGERS;

EID: 84880221731     PISSN: 03060225     EISSN: None     Source Type: Journal    
DOI: 10.1007/978-90-481-9069-0_4     Document Type: Article

References (83)

1. Miller J, McLachlan AD, Klug A (1985) Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J 4:1609-1614
2. Ollo R, Maniatis T (1987) Drosophila Krüppel gene product produced in a baculovirus expression system is a nuclear phosphoprotein that binds to DNA. Proc Natl Acad Sci USA 84:5700-5704
3. Bouhouche N, Syvanen M, Kado CI (2000) The origin of prokaryotic C2H2 zinc finger regulators. Trends Microbiol 8:77-81
4. Frankel AD, Berg JM, Pabo CO (1987) Metal-dependent folding of a single zinc finger from transcription factor IIIA. Proc Natl Acad Sci USA 84:4841-4845
5. Lee MS, Gippert GP, Soman KV, Case DA, Wright PE (1989) Three-dimensional solution structure of a single zinc finger DNA-binding domain. Science 245:635-637
6. Pavletich NP, Pabo CO (1991) Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A. Science 252:809-817
7. Arya GH, Lodico MJ, Ahmad OI, Amin R, Tomkiel JE (2006) Molecular characterization of teflon, a gene required for meiotic autosome segregation in male Drosophila melanogaster. Genetics 174:125-134
8. 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
9. Myers S, Bowden R, Tumian A, Bontrop RE, Freeman C, MacFie TS, McVean G, Donnelly P (2010) Drive against hotspot motifs in primates implicates the PRDM9 gene in meiotic recombination. Science 327:876-879
10. Parvanov ED, Petkov PM, Paigen K (2010) Prdm9 controls activation of mammalian recombination hotspots. Science 327:835
11. Phillips CM, Dernburg AF (2006) A family of zinc-finger proteins is required for chromosome-specific pairing and synapsis during meiosis in C. elegans. Dev Cell 11:817-829
12. Dickson J, Gowher H, Strogantsev R, Gaszner M, Hair A, Felsenfeld G, West AG (2010) VEZF1 elements mediate protection from DNA methylation. PLoS Genet 6:e1000804
13. Li X, Ito M, Zhou F, Youngson N, Zuo X, Leder P, Ferguson-Smith AC (2008) A maternalzygotic effect gene, Zfp57, maintains both maternal and paternal imprints. Dev Cells 15: 547-557
14. Englbrecht CC, Schoof H, Bohm S (2004) Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome. BMC Genomics 5:39
15. Choo Y, Klug A (1994) Toward a code for the interactions of zinc fingers with DNA: selection of randomized fingers displayed on phage. Proc Natl Acad Sci USA 91:11163-11167
16. Wuttke DS, Foster MP, Case DA, Gottesfeld JM, Wright PE (1997) Solution structure of the first three zinc fingers of TFIIIA bound to the cognate DNA sequence: determinants of affinity and sequence specificity. J Mol Biol 273:183-206
17. Elrod-Erickson M, Pabo CO (1999) Binding studies with mutants of Zif268. Contribution of individual side chains to binding affinity and specificity in the Zif268 zinc finger-DNA complex. J Biol Chem 274:19281-19285
18. Elrod-Erickson M, Rould MA, Nekludova L, Pabo CO (1996) Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions. Structure 4:1171-1180
19. Kaplan T, Friedman N, Margalit H (2005) Ab initio prediction of transcription factor targets using structural knowledge. PLoS Comput Biol 1:e1
20. Liu J, Stormo GD (2008) Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors. Bioinformatics 24:1850-1857
21. Persikov AV, Osada R, Singh M (2009) Predicting DNA recognition by Cys2His2 zinc finger proteins. Bioinformatics 25:22-29
22. Klug A (2010) The discovery of zinc fingers and their applications in gene regulation and genome manipulation. Annu Rev Biochem 79:213-231
23. Rizkallah R, Hurt MM (2009) Regulation of the transcription factor YY1 in mitosis through phosphorylation of its DNA-binding domain. Mol Biol Cell 20:4766-4776
24. Bird AJ, Zhao H, Luo H, Jensen LT, Srinivasan C, Evans-Galea M, Winge DR, Eide DJ (2000) A dual role for zinc fingers in both DNA binding and zinc sensing by the Zap1 transcriptional activator. EMBO J 19:3704-3713
25. Hoffmann A, Barz T, Spengler D (2006) Multitasking C2H2 zinc fingers link Zac DNA binding to coordinated regulation of p300-histone acetyltransferase activity. Mol Cell Biol 26:5544-5557
26. Hoffmann A, Ciani E, Boeckardt J, Holsboer F, Journot L, Spengler D (2003) Transcriptional activities of the zinc finger protein Zac are differentially controlled by DNA binding. Mol Cell Biol 23:988-1003
27. Hata A, Seoane J, Lagna G, Montalvo E, Hemmati-Brivanlou A, Massague J (2000) OAZ uses distinct DNA- and protein-binding zinc fingers in separate BMP-Smad and Olf signaling pathways. Cell 100:229-240
28. Brayer KJ, Segal DJ (2008) Keep your fingers off my DNA: protein-protein interactions mediated by C2H2 zinc finger domains. Cell Biochem Biophys 50:111-131
29. Johnson DS, Mortazavi A, Myers RM, Wold B (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316:1497-1502
30. Frietze S, Lan X, Jin VX, Farnham PJ (2010) Genomic targets of the KRAB and SCAN domain-containing zinc finger protein 263. J Biol Chem 285:1393-1403
31. Kim TH, Abdullaev ZK, Smith AD, Ching KA, Loukinov DI, Green RD, Zhang MQ, Lobanenkov VV, Ren B (2007) Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 128:1231-1245
32. Smith ST, Wickramasinghe P, Olson A, et al. (2009) Genome wide ChIP-chip analyses reveal important roles for CTCF in Drosophila genome organization. Dev Biol 328:518-528
33. Knight RD, Shimeld SM (2001) Identification of conserved C2H2 zinc-finger gene families in the Bilateria. Genome Biol 2:RESEARCH0016
34. Pearson R, Fleetwood J, Eaton S, Crossley M, Bao S (2008) Kruppel-like transcription factors: a functional family. Int J Biochem Cell Biol 40:1996-2001
35. Albagli O, Dhordain P, Deweindt C, Lecocq G, Leprince D (1995) The BTB/POZ domain: a new protein-protein interaction motif common to DNA- and actin-binding proteins. Cell Growth Differ 6:1193-1198
36. Kelly KF, Daniel JM (2006) POZ for effect - POZ-ZF transcription factors in cancer and development. Trends Cell Biol 16:578-587
37. Jauch R, Bourenkov GP, Chung HR, Urlaub H, Reidt U, Jäckle H, Wahl MC (2003) The zinc finger-associated domain of the Drosophila transcription factor grauzone is a novel zinccoordinating protein-protein interaction module. Structure 11:1393-1402
38. Chung HR, Löhr U, Jäckle H (2007) Lineage-specific expansion of the zinc finger associated domain ZAD. Mol Biol Evol 24:1934-1943
39. Chung HR, Schafer U, Jäckle H, Böhm S (2002) Genomic expansion and clustering of ZAD containing C2H2 zinc-finger genes in Drosophila. EMBO Rep 3:1158-1162
40. Edelstein LC, Collins T (2005) The SCAN domain family of zinc finger transcription factors. Gene 359:1-17
41. Emerson RO, Thomas JH (2009) Adaptive evolution in zinc finger transcription factors. PLoS Genet 5:e1000325
42. Huntley S, Baggott DM, Hamilton AT, Tran-Gyamfi M, Yang S, Kim J, Gordon L, Branscomb E, Stubbs L (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
43. Abrink M, Ortiz JA, Mark C, Sanchez C, Looman C, Hellman L, Chambon P, Losson R (2001) Conserved interaction between distinct Krüppel-associated box domains and the transcriptional intermediary factor 1 beta. Proc Natl Acad Sci USA 98:1422-1426
44. Friedman JR, Fredericks WJ, Jensen DE, Speicher DW, Huang XP, Neilson EG, Rauscher FJ 3rd. (1996) KAP-1, a novel corepressor for the highly conserved KRAB repression domain. Genes Dev 10:2067-2078
45. Lorenz P, Koczan D, Thiesen HJ (2001) Transcriptional repression mediated by the KRAB domain of the human C2H2 zinc finger protein Kox1/ZNF10 does not require histone deacetylation. Biol Chem 382:637-644
46. Margolin JF, Friedman JR, Meyer WK, Vissing H, Thiesen HJ, Rauscher FJ 3rd. (1994) Kruppel-associated boxes are potent transcriptional repression domains. Proc Natl Acad Sci USA 91:4509-4513
47. Witzgall R, O’Leary E, Leaf A, Onaldi D, Bonventre JV (1994) The Krüppel-associated box-A (KRAB-A) domain of zinc finger proteins mediates transcriptional repression. Proc Natl Acad Sci USA 91:4514-4518
48. Birtle Z, Ponting CP (2006) Meisetz and the birth of the KRAB motif. Bioinformatics 22:2841-2845
49. Thomas JH, Emerson RO, Shendure J (2009) Extraordinary molecular evolution in the PRDM9 fertility gene. PLoS One 4:e8505
50. Baudat F, Buard J, Grey C, de Massy B (2010) [Prdm9, a key control of mammalian recombination hotspots]. Med Sci (Paris) 26:468-470
51. 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
52. Krebs CJ, Larkins LK, Khan SM, Robins DM (2005) Expansion and diversification of KRAB zinc-finger genes within a cluster including Regulator of sex-limitation 1 and 2. Genomics 85:752-761
53. Nowick K, Hamilton AT, Zhang H, Stubbs L (2010) Rapid sequence and expression divergence suggests selection for novel function in primate-specific KRAB-ZNF genes. Mol Biol Evol 27:2606-2617
54. Cooper GM, Nickerson DA, Eichler EE (2007) Mutational and selective effects on copynumber variants in the human genome. Nat Genet 39:S22-29
55. Stankiewicz P, Lupski JR (2010) Structural variation in the human genome and its role in disease. Annu Rev Med 61:437-455
56. 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
57. Nowick K, Stubbs L (2010) Lineage-specific transcription factors and the evolution of gene regulatory networks. Brief Funct Genomics 9:65-78
58. Shannon M, Ashworth LK, Mucenski ML, Lamerdin JE, Branscomb E, Stubbs L (1996) Comparative analysis of a conserved zinc finger gene cluster on human chromosome 19q and mouse chromosome 7. Genomics 33:112-120
59. Hamilton AT, Huntley S, Tran-Gyamfi M, Baggott DM, Gordon L, Stubbs L (2006) Evolutionary expansion and divergence in the ZNF91 subfamily of primate-specific zinc finger genes. Genome Res 16:584-594
60. 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
61. Hardwick RJ, Tretyakov MV, Dubrova YE (2009) Age-related accumulation of mutations supports a replication-dependent mechanism of spontaneous mutation at tandem repeat DNA Loci in mice. Mol Biol Evol 26:2647-2654
62. Nietfeld W, Conrad S, van Wijk I, Giltay R, Bouwmeester T, Knochel W, Pieler T (1993) Evidence for a clustered genomic organization of FAX-zinc finger protein encoding transcription units in Xenopus laevis. J Mol Biol 230:400-412
63. Kim SS, Chen YM, O’Leary E, Witzgall R, Vidal M, Bonventre JV (1996) A novel member of the RING finger family, KRIP-1, associates with the KRAB-A transcriptional repressor domain of zinc finger proteins. Proc Natl Acad Sci USA 93:15299-15304
64. Moosmann P, Georgiev O, Le Douarin B, Bourquin JP, Schaffner W (1996) Transcriptional repression by RING finger protein TIF1 beta that interacts with the KRAB repressor domain of KOX1. Nucleic Acids Res 24:4859-4867
65. Duan J, Xia Q, Cheng D, Zha X, Zhao P, Xiang Z (2008) Species-specific expansion of C2H2 zinc-finger genes and their expression profiles in silkworm, Bombyx mori. Insect Biochem Mol Biol 38:1121-1129
66. Badis G, Berger MF, Philippakis AA, et al. (2009) Diversity and complexity in DNA recognition by transcription factors. Science 324:1720-1723
67. Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346:818-822
68. Oliphant AR, Brandl CJ, Struhl K (1989) Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein. Mol Cell Biol 9:2944-2949
69. Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505-510
70. Noyes MB, Meng X, Wakabayashi A, Sinha S, Brodsky MH, Wolfe SA (2008) A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Nucleic Acids Res 36:2547-2560
71. Dekelver RC, Choi VM, Moehle EA, et al. (2010) Functional genomics, proteomics, and regulatory DNA analysis in isogenic settings using zinc finger nuclease-driven transgenesis into a safe harbor locus in the human genome. Genome Res 20:1133-1142
72. Kim HJ, Lee HJ, Kim H, Cho SW, Kim JS (2009) Targeted genome editing in human cells with zinc finger nucleases constructed via modular assembly. Genome Res 19:1279-1288
73. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K (2007) High-resolution profiling of histone methylations in the human genome. Cell 129: 823-837
74. Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J, Loh YH, Yeo HC, Yeo ZX, Narang V, Govindarajan KR, Leong B, Shahab A, Ruan Y, Bourque G, Sung WK, Clarke ND, Wei CL, Ng HH (2008) Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133:1106-1117
75. Delwel R, Funabiki T, Kreider BL, Morishita K, Ihle JN (1993) Four of the seven zinc fingers of the Evi-1 myeloid-transforming gene are required for sequence-specific binding to GA(C/T)AAGA(T/C)AAGATAA. Mol Cell Biol 13:4291-4300
76. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunesekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A (2010) The PFAM protein families database. Nucl Acids Res 38 (Database Issue):D211-D222
77. Materna SC, Howard-Ashby M, Gray RF, Davidson EH (2006) The C2H2 zinc finger genes of Strongylocentrotus purpuratus and their expression in embryonic development. Devel Biol 300:108-120
78. Portales-Casamar E, Kirov S, Lim J, Lithwick S, Swanson MI, Ticoll A, Snoddy J, Wasserman WW (2007) PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation. Genome Biol 8:R207
79. Riechmann JL, Heard J, Martin G, Reuber L, Jiang CZ, Keddie J, Adam L, Pineda O, Ratcliffe OJ, Samaha RR, Creelman R, Pilgrim M, Broun P, Zhang JZ, Ghandehari D, Sherman BK, Yu GL (2000) Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290:2105-2110
80. Schaub M, Myslinski E, Schuster C, Krol A, Carbon P (1997) Staf, a promiscuous activator for enhanced transcription by RNA polymerases II and III. EMBO J 16:173-181
81. Shrivastava A, Calame K (1994) An analysis of genes regulated by the multi-functional transcriptional regulator Yin Yang-1. Nucl Acids Res 22:5151-5155
82. Thiagalingam A, De Bustros A, Borges M, Jasti R, Compton D, Diamond L, Mabry M, Ball DW, Baylin SB, Nelkin BD (1996) RREB-1, a novel zinc finger protein, is involved in the differentiation response to Ras in human medullary thyroid carcinomas. Mol Cell Biol 16:5335-5345
83. Tsai RY, Reed RR (1998) Identification of DNA recognition sequences and protein interaction domains of the multiple-Zn-finger protein Roaz. Mol Cell Biol 18:6447-6456