KRAB zinc finger proteins: An analysis of the molecular mechanisms governing their increase in numbers and complexity during evolution

Molecular Biology and Evolution

Volumn 19, Issue 12, 2002, Pages 2118-2130

  Looman, Camilla ^a   Åbrink, Magnus ^b   Mark, Charlotta ^c   Hellman, Lars ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^c MEDICAL PRODUCTS AGENCY   (Sweden)

Author keywords

Evolution; KRAB; Kr ppel zinc finger

Indexed keywords

MESSENGER RNA; PROTEIN KRAB; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; ZINC FINGER PROTEIN; DNA BINDING PROTEIN; REPRESSOR PROTEIN; ZNF350 PROTEIN, HUMAN;

ARTICLE; HUMAN; MOLECULAR EVOLUTION; MOUSE; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; PROTEIN ANALYSIS; UNINDEXED SEQUENCE; ALGORITHM; AMINO ACID SEQUENCE; CHEMISTRY; GENETICS; MOLECULAR GENETICS; SEQUENCE HOMOLOGY;

MAMMALIA; METAZOA;

ALGORITHMS; AMINO ACID SEQUENCE; DNA-BINDING PROTEINS; MOLECULAR SEQUENCE DATA; PHYLOGENY; REPRESSOR PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; ZINC FINGERS;

EID: 0036899102     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a004037     Document Type: Article

References (45)

1. Abrink, M., J. A. Ortiz, C. Mark, C. Sanchez, C. Looman, L. Hellman, P. Chambon, and R. Losson. 2001. Conserved interaction between distinct Kruppel-associated box domains and the transcriptional intermediary factor 1 beta. Proc. Natl. Acad. Sci. USA 98:1422-1426.
2. Adams, M. D., S. E. Celniker, R. A. Holt et al. (195 coauthors). 2000. The genome sequence of Drosophila melanogaster. Science 287:2185-2195.
3. Bellefroid, E. J., D. A. Poncelet, P. J. Lecocq, O. Revelant, and J. A. Martial. 1991. The evolutionarily conserved Kruppel-associated box domain defines a subfamily of eukaryotic multifingered proteins. Proc. Natl. Acad. Sci. USA 88:3608-3612.
4. Benn, A., M. Antoine, H. Beug, and J. Niessing. 1991. Primary structure and expression of a chicken cDNA encoding a protein with zinc-finger motifs. Gene 106:207-212.
5. Collins, T., J. R. Stone, and A. J. Williams. 2001. All in the family: the BTB/POZ, KRAB and SCAN domains. Mol. Cell. Biol. 21:3609-3615.
6. Dehal, P., P. Predki, A. S. Olsen et al. (21 co-authors). 2001. Human chromosome 19 and related regions in mouse: Conservative and lineage-specific evolution. Science 293:104-111.
7. Eichler, E. E., S. M. Hoffman, A. A. Adamson, L. A. Gordon, P. McCready, J. E. Lamerdin, and H. W. Mohrenweiser. 1998. Complex beta-satellite repeat structures and the expansion of the zinc finger gene cluster in 19p12. Genome Res. 8:791-808.
8. Friedman, J. R., W. J. Fredericks, D. E. Jensen, D. W. Speicher, X. P. Huang, E. G. Neilson, and F. J. R Rauscher. 1996. KAP-1, a novel corepressor for the highly conserved KRAB repression domain. Genes Dev. 10:2067-2078.
9. Goffeau, A. 1997. The yeast genome directory. Nature 387:1-105.
10. Honer, C., P. Chen, M. J. Toth, and C. Schumacher. 2001. Identification of SCAN domains in four gene families. Biochim. Biophys. Acta 16:441-448.
11. Jackson, M. S., C. G. See, L. M. Mulligan, and B. F. Lauffart. 1996. A 9. 75-Mb map across the centromere of human chromosome 10. Genomics 33:258-270.
12. Kim, S. S., Y. M. Chen, E. O'Leary, R. Witzgall, M. Vidal, and J. V. Bonventre. 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.
13. Klug, A., and D. Rhodes. 1987. Zinc fingers: A novel protein motif for nucleic acid recognition. Trends Biochem. Sci. 12:464-469.
14. Knight, R. D., and S. M. Shimeld. 2001. Identification of conserved C2H2 zinc-finger gene families in the Bilateria. Genome Biol. 2:research 1-8.
15. Kumar, S., K. Tamura, I. B. Jakobsen, and M. Nei. 2001. MEGA2: Molecular evolutionary genetics analysis software. Bioinformatics 17:1244-1245.
16. Lee, M. S., G. P. Gippert, K. V. Soman, D. A. Case, and P. E. Wright. 1989. Three-dimensional solution structure of a single zinc finger DNA-binding domain. Science 245:635-637.
17. Lorenz, P., D. Koczan, and H. J. Thiesen, 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.
18. Lovering, R., and J. Trowsdale. 1991. A gene encoding 22 highly related zinc fingers is expressed in lymphoid cell lines. Nucleic Acids Res. 19:2921-2928.
19. Lynch, M., and J. S. Conery. 2000. The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155.
20. Margolin, J. F., J. R. Friedman, W. K. Meyer, H. Vissing, H. J. Thiesen, and F. J. R. Rauscher. 1994. Kruppel-associated boxes are potent transcriptional repression domains. Proc. Natl. Acad. Sci. USA 91:4509-4513.
21. Mark, C., M. Abrink, and L. Hellman. 1999. Comparative analysis of KRAB zinc finger proteins in rodents and man: Evidence for several evolutionarily distinct subfamilies of KRAB zinc finger genes. DNA Cell Biol. 18:381-396.
22. McPherson, J. D., M. Marra, L. Hillier et al. (104 co-authors). 2001. A physical map of the human genome. Nature 409:934-941.
23. Miller, J., A. D. McLachlan, and A. Klug. 1985. Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J. 4:1609-1614.
24. Moosmann, P., O. Georgiev, B. Le Douarin, J. P. Bourquin, and W. Schaffner. 1996. Transcriptional repression by RING finger protein TIF1 beta that interacts with the KRAB repressor domain of KOX1. Nucleic Acids Res. 24:4859-4867.
25. Nielsen, A. L., J. A. Ortiz, J. You, A. M. Oulad, R. Khechumian, A. Gansmuller, P. Chambon, and R. Losson. 1999. Interaction with members of the heterochromatin protein 1 (HP1) family and histone deacetylation are differentially involved in transcriptional silencing by members of the TIF1 family. EMBO J. 18:6385-6395.
26. Parraga, G., S. J. Horvath, A. Eisen, W. E. Taylor, L. Hood, E. T Young, and R. E. Klevit. 1988. Zinc-dependent structure of a single-finger domain of yeast ADR1. Science 241:1489-1492.
27. Pavletich, N. P., and C. O. Pabo. 1991. Zinc finger-DNA recognition: Crystal structure of a Zif268-DNA complex at 2.1 A. Science 252:809-817.
28. Rosati, M., M. Marino, A. Franze, A. Tramontano, and G. Grimaldi. 1991. Members of the zinc finger protein gene family sharing a conserved N-terminal module. Nucleic Acids Res. 19:5661-5667.
29. Ruiz i Altaba, A., H. Perry-O'Keefe, and D. A. Melton. 1987. Xfin: An embryonic gene encoding a multifingered protein in Xenopus. EMBO J. 6:3065-3070.
30. Ryan, R. F., D. C. Schultz, K. Ayyanathan, P. B. Singh, J. R. Friedman, W. J. Fredericks, and F. R. Rauscher. 1999. KAP-1 corepressor protein interacts and colocalizes with heterochromatic and euchromatic HP1 proteins: A potential role for Kruppel-associated box-zinc finger proteins in heterochromatin-mediated gene silencing. Mol. Cell. Biol. 19:4366-4378.
31. Sander, T. L., A. L. Haas, M. J. Peterson, and J. F. Morris. 2000. Identification of a novel SCAN box-related protein that interacts with MZF1B. The leucine-rich SCAN box mediates hetero- and homoprotein associations. J. Biol. Chem. 28:12857-12867.
32. Schuh, R., W. Aicher, U. Gaul et al. (11 co-authors). 1986. A conserved family of nuclear proteins containing structural elements of the finger protein encoded by Kruppel, a Drosophila segmentation gene. Cell 47:1025-1032.
33. Schumacher, C., H. Wang, C. Honer et al. (11 co-authors). 2000. The SCAN domain mediates selective oligomerization. J. Biol. Chem. 275:17173-17179.
34. Shannon, M., J. Kim, L. Ashworth, E. Branscomb, and L. Stubbs. 1998. Tandem zinc-finger gene families in mammals: Insights and unanswered questions. DNA Seq. 8:303-315.
35. Takashima, H., H. Nishio, H. Wakao, M. Nishio, K. Koizumi, A. Oda, T. Koike, and K. Sawada. 2001. Molecular cloning and characterization of a KRAB-containing zinc finger protein, ZNF317, and its isoforms. Biochem. Biophys. Res. Commun. 288:771-779.
36. The Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815.
37. The C. Elegans Sequencing Consortium. 1998. Genome sequence of the nematode C. elegans: A platform for investigating biology. Science 282:2012-2018.
38. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. Clustal W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
39. Tunnacliffe, A., L. Liu, J. K. Moore, M. A. Leversha, M. S. Jackson, L. Papi, M. A. Ferguson-Smith, H. J. Thiesen, and B. A. Ponder. 1993. Duplicated KOX zinc finger gene clusters flank the centromere of human chromosome 10: Evidence for a pericentric inversion during primate evolution. Nucleic Acids Res. 21:1409-1417.
40. Underhill, C., M. S. Qutob, S. P. Yee, and J. Torchia. 2000. A novel nuclear receptor corepressor complex, N-CoR, contains components of the mammalian SWI/SNF complex and the corepressor KAP-1. J. Biol. Chem. 275:40463-40470.
41. Venter, J. C., M. D. Adams, E. W. Myers et al. (274 coauthors). 2001. The sequence of the human genome. Science 291:1304-1351.
42. Vissing, H., W. K. Meyer, L. Aagaard, N. Tommerup, and H. J. Thiesen. 1995. Repression of transcriptional activity by heterologous KRAB domains present in zinc finger proteins. FEBS Lett. 369:153-157.
43. Williams, A. J., S. C. Blacklow, and T. Collins. 1999. The zinc finger-associated SCAN box is a conserved oligomerization domain. Mol. Cell Biol. 19:8526-8535.
44. Witzgall, R., E. O'leary, A. Leaf, D. Onaldi, and J. V. Bonventre. 1994. The Kruppel-associated box-A (KRAB-A) domain of zinc finger proteins mediates transcriptional repression. Proc. Natl. Acad. Sci. USA 91:4514-4518.
45. Wolfe, S. A., L. Nekludova, and C. O. Pabo. 2000. DNA recognition by Cys2His2 zinc finger proteins. Annu. Rev. Biophys. Biomol. Struct. 29:183-212.