Tandem zinc-finger gene families in mammals: Insights and unanswered questions

Mitochondrial DNA

Volumn 8, Issue 5, 1998, Pages 303-315

  Shannon, Mark ^a   Kim, Joomyeong ^a   Ashworth, Linda ^b   Branscomb, Elbert ^b   Stubbs, Lisa ^a  

^a OAK RIDGE NATIONAL LABORATORY   (United States)

^b LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

Author keywords

evolution; gene clusters; mammals; Review; zinc finger proteins

Indexed keywords

GENE CLUSTER; MAMMALIAN GENETICS;

AMINO ACID SEQUENCE; ANIMALS; CHROMOSOMES, HUMAN, PAIR 19; CONSERVED SEQUENCE; DNA-BINDING PROTEINS; EVOLUTION, MOLECULAR; HUMANS; MAMMALS; MICE; MOLECULAR SEQUENCE DATA; REPRESSOR PROTEINS; ZINC FINGERS;

EID: 0032407684     PISSN: 19401736     EISSN: 19401744     Source Type: Journal    
DOI: 10.3109/10425179809034075     Document Type: Article

References (59)

1. Abrink, M., Aveskogh, M. and Hellman, L. (1994) "Isolation of cDNA clones for 42 different Kruppel-related zinc finger proteins expressed in the human monoblast cell line U-937," DNA Cell Biol, 14,125-136.
2. Ashworth, L. K., Batzer, M. A., Brandriff, B., Branscomb, E., dejong, P., Garcia, E., Games, J. A., Gordon, L., Lamerdin, J., Lennon, G., Mohrenweiser, H., Olsen, A., Slezak, T. and Carrano, A. V. (1995a) "An integrated, metric physical map of human chromosome 19," Nature Genet, 11,422-27.
3. Ashworth, L. K., Alegria-Hartman, M, Burgin, M., Devlin, L., Carrano, A. V. and Batzer, M. A. (1995b) "Assembly of high-resolution bacterial artificial chromosome, Pl-derived bacterial artificial chromosome, and cosmid contigs," Anal Biochem, 224, 564-571.
4. Aubry, M., Marineau, C, Zhang, F. R., Zahed, L., Figlewicz, D., Delattre, O., Thomas, G., dejong, P. J., Julien, J-P. and Rouleau, G. A. (1992) "Cloning of six new genes with zinc finger motifs mapping to short and long arms of human acrocentric chromosome 22 (p and qll.2)," Genomics, 13,641-648.
5. w18 allele of the mouse tcl-4 complementation group," Genomics, 36,39-46. (Pubitemid 26277756)
6. Bellefroid, E. J., Poncelet, D. A., Lecocq, P. J., Revelant, O. and Martial, J. A. (1991) "The evolutionarily conserved Kruppel-associated box domain defines a subfamily of eukaryotic multifingered proteins," Proc Natl Acad Sci USA, 88,3608-3612. (Pubitemid 21916672)
7. Bellefroid, E. J., Marine, J-C, Ried, T., Lecocq, P. J., Riviere, M., Amemiya, C, Poncelet, D. A., Coulie, P. G., de Jong, P., Szpiere, C, Ward, D. C. and Martial, J. A. (1993) "Clustered organization of homologous KRAB zinc-finger genes with enhanced expression in human T lymphoid cells," EMBO J, 12,1363-1374. (Pubitemid 23112791)
8. Bellefroid, E. J., Marine, J-C, Matera, A. G., Bourguignon, C, Desai, T., Healy, K. C, Bray-Ward, P., Martial, J. A., Ihle, J. N. and Ward, D. C. (1995) "Emergence of the ZNF91 Kruppel-associated box-containing zinc finger gene family in the last common ancestor of Anthropoidea," Proc Natl Acad Sci USA, 92,10757-10761.
9. Bird, A. (1995) "Gene number, noise reduction and biological complexity," Trends Genet, 11,94-100.
10. Calabro, V., Pengue, G., Bartoli, P. C, Pagliuca, A., Featherstone, T. and Lania, L. (1995) "Positional cloning of cDNAs from the human chromosome 3p21-22 region identifies a clustered organization of zinc-finger genes" Hum Genet, 95,18-21.
11. Call, K. M., Glaser, T., Ito, C. Y., Buckler, A. J., Pelletier, J., Haber, D. A., Rose, E. A., Krai, A., Yeger, H., Lewis, W. H., Jones, C. and Housman, D. E. (1990) "Isolation and characterization of a zinc finger polypeptide gene at the human chromosome 11 Wilms' Tumor locus," Cell, 60,509-520.
12. Carroll, S. B. (1995) "Homeotic genes and the evolution of arthropods and chordates," Nature, 376,479-85. (Pubitemid 26455551)
13. Choo, Y. and Klug, A. (1994a) "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. (Pubitemid 24349646)
14. Choo, Y. and Klug, A. (1994b) "Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions," Proc Natl Acad Sci USA, 91, 11168-11172. (Pubitemid 24349647)
15. Constantinou-Deltas, C. D., Gilbert, J., Bartlett, R. J., Herbstreith, M., Roses, A. D. and Lee, J. E. (1992) "The identification and characterization of KRAB-domain-containing zinc finger proteins," Genomics, 12,581-589.
16. Constantinou-Deltas, C, Bashiardes, E., Patsalis, P. C, Hadjimarcou, M., Kroisel, P. M., Ioannou, P. A., Roses, A. D. and Lee, J. E. (1996) "Complete coding sequence, exonJintron arrangement and chromosome location of ZNF45, a KRAB-domain-containing gene," Cytogenet Cell Genet, 75,230-233. (Pubitemid 27104354)
17. Derry, J. M., Jess, U. and Francke, Y. (1995) "Cloning and characterization of a novel zinc finger gene in Xpll.2," Genomics, 30,361-365.
18. El-Baradi, T. and Pieler, T. (1991) "Zinc finger proteins: what we know and what we would like to know," Mech Devel, 35, 155-169.
19. Filippova, G. N., Fagerlie, S., Klenova, E. M., Myers, C, Dehner, Y., Goodwin, G., Neiman, P. E., Collins, S. J. and Lobanenkov, V. V. (1996) "An exceptionally conserved transcriptional repressor, CTCF, employs different combinations of zinc fingers to bind diverged promoter sequences of avian and mammalian c-myc oncogenes," Mol Cell Biol, 16, 2802-2813. (Pubitemid 26161284)
20. Friedman, J. R., Fredericks, W. J., Jensen, D. E., Speicher, D. W., Huang, X-P., Neilson, E. G. and Rauscher, F. J. III (1996) "KAP-1, a novel corepressor of the highly conserved KRAB repression domain," Genes Devel, 10, 2067-2078. (Pubitemid 26346114)
21. Fryxell, K. J. (1996) "The coevolution of gene family trees," Trends Genet, 12, 364-369. (Pubitemid 26294697)
22. Gilbert, S. F., Opitz, J. M. and Raff, R. A. (1996) "Resynthesiz- ing evolutionary and developmental biology," Devel Biol, 173,357-372. (Pubitemid 26064862)
23. Holland, P. W. H. and Garcia-Fernandez, J. (1996) "Hox genes and chordate evolution," Devel Biol, 173, 382-395. (Pubitemid 26064864)
24. Hoovers, J. M. N., Mannens, M., John, R., Bliek, J., van Heyningen, V., Porteous, D. J., Leschot, N. J., Westerveld, A. and Little, P. F. R. (1992) "High-resolution localization of 69 potential human zinc finger protein genes: A number are clustered," Genomics, 12, 254-263.
25. Huebner, K., Druck, T., Croce, C. M. and Thiesen, H-J. (1991) "Twenty-seven nonoverlapping zinc finger cDNAs from human T cells map to nine different chromosomes with apparent clustering," Am ] Hum Genet, 48,726-740. (Pubitemid 21891617)
26. Jackson, M. S., See, C. G., Mulligan, L. M. and Lauffart, B. F. (1996) "A 9.75-Mb map across the centromere of human chromosome 10," Genomics, 33,258-270. (Pubitemid 26132121)
27. Johnson, A. D. (1995) "The price of repression," Cell, 81, 655-658.
28. Kapfhamer, D., Sweet, H. O., Sufalko, D., Warren, S., Johnson, K. R. and Burmeister, M. (1996) "The neurological mouse mutations jittery and hesitant are allelic and map to the region of mouse chromosome 10 homologous to 19pl3.3," Genomics, 35,533-538. (Pubitemid 26270020)
29. Kim, S-S., Chen, Y-M., O'Leary, E., Witzgall, R, Vidal, M. and Bonventre, J. V. (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. (Pubitemid 27009595)
30. Lange, R., Christoph, A., Thiesen, H-J., Vopper, G., Johnson, K. R., Lemaire, L., Plomann, M., Cremer, H, Barthels, B. and Heinlein, U. A. O. (1995) "Developmentally regulated mouse gene NK10 encodes a zinc finger repressor protein with differential DNA-binding domains," DNA Cell Biol, 14,971-981.
31. Lichter, P., Bray, P., Ried, T., Dawid, I. B. and Ward, D. C. (1992) "Clustering of C2-H2 zinc finger motif sequences within telometric and fragile site regions of human chromosomes," Genomics, 13, 999-1007.
32. Margolin, J. F., Friedman, J. R., Meyer, W. K. H, Vissing, H., Thiesen, H-J. and Rauscher, F. J. III (1994) "Kruppel-associated boxes are potent transcriptional repression domains," Proc Natl Acad Sci USA, 91,4509-4513.
33. Marine, J-C, Gilbert, D. J., Bellefroid, E. J., Martial, J. A., Ihle, J. N., Copeland, N. G. and Jenkins, N. A. (1996) "Chromosomal location of fifteen unique mouse KRAB-containing zinc finger loci," Mammal Genome, 7,413-416. (Pubitemid 126441245)
34. Miller, J., McLachlan, A. D. and Klug, A. (1985) "Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes," EMBO J, 4,1609-1614.
35. Moosmann, P., Georgiev, O., LeDouarin, B., Bourquin, J-P. and Schaffner, W. (1996) "Transcriptional repression by RING finger protein TIFlf3 that interacts with the KRAB repressor domain of KOX1," Nucl Acids Res, 24,4849-4867.
36. Nieto, M. A., Sargent, M. G., Wilkinson, D. G. and Cooke, J. (1994) "Control of cell behavior during vertebrate development by Slug, a zinc finger gene," Science, 264,835-839. (Pubitemid 24193449)
37. Ohno, S. (1970) Evolution by Gene Duplication. (Springer-Verlag, Berlin, New York).
38. O'Neill, E. M., Ellis, M. C, Rubin, G. M. and Tijan, R. (1995) "Functional domain analysis of glass, a zinc-finger-containing transcription factor in Drosophila," Proc Natl Acad Sci USA, 92, 6557-6561.
39. Pengue, G. and Lania, L. (1996) "Kruppel-associated box-mediated repression of RNA polymerase II promoters is influenced by the arrangement of basal promoter elements," Proc Natl Acad Sci USA, 93,1015-1020.
40. Pengue, G., Calabro, V., Bartoli, P. C., Pagliuca, A. and Lania, L. (1994) "Repression of transcriptional activity at a distance by the evolutionarily conserved KRAB domain present in a subfamily of zinc finger genes," Nucl Acids Res, 22, 2908-2914.
41. Pieler, T. and Bellefroid, E. (1994) "Perspectives on zinc finger protein function and evolution-an update," Molecular Biology Reports, 20,1-8. (Pubitemid 2141445)
42. Rosati, M., Marino, M., Franze, A., Tramontano, A. and Grimaldi, G. (1991) "Members of the zinc finger protein gene family sharing a conserved N-terminal module," Nucl Acids Res, 19, 5661-5667. (Pubitemid 21912970)
43. Rosenberg, J. B., Schroder, C., Preiss, A., Kienlin, A., Cote, S., Riede, I. and Jackie, H. (1986) "Structural homology of the product of the Drosophila Kruppel gene with Xenopus transcription factor IIIA," Nature, 319, 336-339. (Pubitemid 16212953)
44. Rousseau-Merck, M-F., Hillion, J., Jonveaux, P., Couillin, P., Seite, P., Thiesen, H-J. and Berger, R. (1993) "Chromosomal localization of 9 KOX zinc finger genes: physical linkages suggest clustering of KOX genes on chromosomes 12, 16, and 19," Hum Genet, 92, 583-587. (Pubitemid 23356817)
45. Ruddle, F. H., Bentley, K. L., Murtha, M. T. and Risch, N. (1994) "Gene loss and gain in the evolution of vertebrates," Development, (1994 supplement), 155-161.
46. Saleh, M., Selleri, L' Little, P. F. R. and Evans, G. A. (1992) "Isolation and expression of linked zinc finger gene clusters on human chromosome llq," Genomics, 14, 970-978. (Pubitemid 23053035)
47. Schuh, R., Aider, W., Gaul, U., Cote, S., Preiss, A., Maier, D., Seifert, E., Nauber, U., Schroder, C, Kemier, R. and Jackie, H. (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.
48. Shannon, M., Ashworth, L. K, Mucenski, M., Lamerdin, J. E., Branscomb, E. and Stubbs, L. (1996) "Comparative analysis of a conserved zinc-finger gene cluster on human chromosome 19q and mouse chromosome 7," Genomics, 33, 112-120. (Pubitemid 26119402)
49. Stubbs, L., Carver, E. A., Shannon, M. E., Kim, J., Geisler, J., Generoso, E. E., Stanford, B. G., Dunn, W. C, Mohrenweiser, H., Zimmermann, W., Watt, S. M. and Ashworth, L. K. (1996) "Detailed comparative map of human chromosome 19q and related regions of the mouse genome," Genomics, 35,499-508. (Pubitemid 26270016)
50. Supp, D. M., Witte, D. P., Branford, W. W., Smith, E. P. and Potter, S. S. (1996) "Sp4, a member of the Spl-family of zinc finger transcription factors, is required for normal murine growth, viability, and male fertility," Devel Biol, 176,284-299. (Pubitemid 26202818)
51. Suzuki, M., Gerstein, M. and Yagi, H. (1994) "Stereochemical basis of DNA recognition by Zn fingers," Nucl Acids Res, 22, 3397-3405. (Pubitemid 24280633)
52. Tommerup, N. and Vissing, H. (1995) "Isolation and fine mapping of 16 novel human zinc finger-encoding cDNAs identify putative candidate genes for developmental and malignant disorders," Genomics, 27, 259-264.
53. Tunnacliffe, A., Lizhi, L., Moore, J. K., Lerversha, M. A., Jackson, M. S., Papi, L., Ferguson-Smith, M. A., Thiesen, H-J. and Ponder, B. A. J. (1993) "Duplicated KOX zinc finger gene clusters flank the centromere of human chromosome 10: evidence for a pericentric inversion during primate evolution," Nucl Acids Res, 21,1409-1417. (Pubitemid 23154372)
54. Valentine, J. W., Erwin, D. H. and Jablonski, D. (1996) "Developmental evolution of metazoan bodyplans: The fossil evidence," Devel Biol, 173,373-381. (Pubitemid 26064863)
55. Villa, A., Zucchi, I., Pilia, G, Strina, D., Susani, L., Morali, F., Patrosso, C, Frattini, A., Lucchini, F., Repetto, M., Sacco, M. G., Zoppe, M. and Vezzoni, P. (1993) "ZNF75: Isolation of a cDNA clone of the KRAB zinc finger gene subfamily mapped in YACs 1Mb telomeric of HPRT," Genomics, 18, 223-229. (Pubitemid 23339530)
56. Villa, A., Strina, B., Frattini, A' Faranda, S., Macchi, P., Finelli, P., Bozzi, F., Susani, L., Archidiacono, N., Rocchi, M. and Vezzoni, P. (1996) "The ZNF75 zinc finger gene subfamily: Isolation and mapping of the four members in humans and great apes," Genomics, 35,312-320. (Pubitemid 26250317)
57. Vissing, H, Meyer, W. K-H, Aagaard, L., Tommerup, N. and Thiesen, H-J. (1995) "Repression of transcriptional activity by heterologous KRAB domains present in zinc finger proteins," FEES Letters, 369,153-157.
58. Witzgall, R., O'Leary, E., Leaf, A., Onaldi, K. and Bonventre, J. V. (1994) "The Kruppel-associated box-A (KRAB-A) domain of zinc finger proteins mediates transcriptional repression," Proc Natl Acad Sci USA, 91, 4514-1518.
59. Zweidler-McKay, P. A., Grimes, H. L., Flubacher, M. M. and Tsichlis, P. N. (1996) "Gfi-1 encodes a nuclear zinc finger protein that binds DNA and functions as a transcriptional repressor," Mol Cell Biol, 16,4024-4034. (Pubitemid 26251201)