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. 1995 Nov 11;23(21):4229–4233. doi: 10.1093/nar/23.21.4229

The chromo superfamily: new members, duplication of the chromo domain and possible role in delivering transcription regulators to chromatin.

E V Koonin 1, S Zhou 1, J C Lucchesi 1
PMCID: PMC307373  PMID: 7501439

Abstract

Using computer methods for detecting conserved amino acid sequence motifs, we show that the chromatin organization modifier (chromo) domain that has been previously identified in several proteins involved in transcription down-regulation is present in a much larger group of (putative) chromatin-binding proteins, some of which are positive rather than negative regulators of transcription. The most interesting new members of the chromo superfamily are Drosophila male-specific lethal (MSL-3) protein involved in the X chromosome gene dosage compensation in the males and human retinoblastoma-binding protein RBP-1. We show that the chromo domain is duplicated in several chromatin-binding proteins and use this observation to interpret recent results on chromatin binding obtained with chimeric chromo domain-containing proteins. We hypothesize that the chromo domain may be a vehicle that delivers both positive and negative transcription regulators to the sites of their action on chromatin.

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Selected References

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  1. Altschul S. F., Boguski M. S., Gish W., Wootton J. C. Issues in searching molecular sequence databases. Nat Genet. 1994 Feb;6(2):119–129. doi: 10.1038/ng0294-119. [DOI] [PubMed] [Google Scholar]
  2. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  3. Baker B. S., Gorman M., Marín I. Dosage compensation in Drosophila. Annu Rev Genet. 1994;28:491–521. doi: 10.1146/annurev.ge.28.120194.002423. [DOI] [PubMed] [Google Scholar]
  4. Boguski M. S., Lowe T. M., Tolstoshev C. M. dbEST--database for "expressed sequence tags". Nat Genet. 1993 Aug;4(4):332–333. doi: 10.1038/ng0893-332. [DOI] [PubMed] [Google Scholar]
  5. Chothia C. Proteins. One thousand families for the molecular biologist. Nature. 1992 Jun 18;357(6379):543–544. doi: 10.1038/357543a0. [DOI] [PubMed] [Google Scholar]
  6. Delmas V., Stokes D. G., Perry R. P. A mammalian DNA-binding protein that contains a chromodomain and an SNF2/SWI2-like helicase domain. Proc Natl Acad Sci U S A. 1993 Mar 15;90(6):2414–2418. doi: 10.1073/pnas.90.6.2414. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Dynlacht B. D. Retinoblastoma protein. Pol I gets repressed. Nature. 1995 Mar 9;374(6518):114–114. doi: 10.1038/374114a0. [DOI] [PubMed] [Google Scholar]
  8. Eissenberg J. C., Morris G. D., Reuter G., Hartnett T. The heterochromatin-associated protein HP-1 is an essential protein in Drosophila with dosage-dependent effects on position-effect variegation. Genetics. 1992 Jun;131(2):345–352. doi: 10.1093/genetics/131.2.345. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Epstein H., James T. C., Singh P. B. Cloning and expression of Drosophila HP1 homologs from a mealybug, Planococcus citri. J Cell Sci. 1992 Feb;101(Pt 2):463–474. doi: 10.1242/jcs.101.2.463. [DOI] [PubMed] [Google Scholar]
  10. Fattaey A. R., Helin K., Dembski M. S., Dyson N., Harlow E., Vuocolo G. A., Hanobik M. G., Haskell K. M., Oliff A., Defeo-Jones D. Characterization of the retinoblastoma binding proteins RBP1 and RBP2. Oncogene. 1993 Nov;8(11):3149–3156. [PubMed] [Google Scholar]
  11. Gorman M., Franke A., Baker B. S. Molecular characterization of the male-specific lethal-3 gene and investigations of the regulation of dosage compensation in Drosophila. Development. 1995 Feb;121(2):463–475. doi: 10.1242/dev.121.2.463. [DOI] [PubMed] [Google Scholar]
  12. Green P., Lipman D., Hillier L., Waterston R., States D., Claverie J. M. Ancient conserved regions in new gene sequences and the protein databases. Science. 1993 Mar 19;259(5102):1711–1716. doi: 10.1126/science.8456298. [DOI] [PubMed] [Google Scholar]
  13. James T. C., Elgin S. C. Identification of a nonhistone chromosomal protein associated with heterochromatin in Drosophila melanogaster and its gene. Mol Cell Biol. 1986 Nov;6(11):3862–3872. doi: 10.1128/mcb.6.11.3862. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Kaelin W. G., Jr, Krek W., Sellers W. R., DeCaprio J. A., Ajchenbaum F., Fuchs C. S., Chittenden T., Li Y., Farnham P. J., Blanar M. A. Expression cloning of a cDNA encoding a retinoblastoma-binding protein with E2F-like properties. Cell. 1992 Jul 24;70(2):351–364. doi: 10.1016/0092-8674(92)90108-o. [DOI] [PubMed] [Google Scholar]
  15. Koonin E. V., Tatusov R. L. Computer analysis of bacterial haloacid dehalogenases defines a large superfamily of hydrolases with diverse specificity. Application of an iterative approach to database search. J Mol Biol. 1994 Nov 18;244(1):125–132. doi: 10.1006/jmbi.1994.1711. [DOI] [PubMed] [Google Scholar]
  16. Lawrence C. E., Altschul S. F., Boguski M. S., Liu J. S., Neuwald A. F., Wootton J. C. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science. 1993 Oct 8;262(5131):208–214. doi: 10.1126/science.8211139. [DOI] [PubMed] [Google Scholar]
  17. Li X., Shou W., Kloc M., Reddy B. A., Etkin L. D. The association of Xenopus nuclear factor 7 with subcellular structures is dependent upon phosphorylation and specific domains. Exp Cell Res. 1994 Aug;213(2):473–481. doi: 10.1006/excr.1994.1225. [DOI] [PubMed] [Google Scholar]
  18. Lorentz A., Ostermann K., Fleck O., Schmidt H. Switching gene swi6, involved in repression of silent mating-type loci in fission yeast, encodes a homologue of chromatin-associated proteins from Drosophila and mammals. Gene. 1994 May 27;143(1):139–143. doi: 10.1016/0378-1119(94)90619-x. [DOI] [PubMed] [Google Scholar]
  19. Messmer S., Franke A., Paro R. Analysis of the functional role of the Polycomb chromo domain in Drosophila melanogaster. Genes Dev. 1992 Jul;6(7):1241–1254. doi: 10.1101/gad.6.7.1241. [DOI] [PubMed] [Google Scholar]
  20. Otterson G. A., Kratzke R. A., Lin A. Y., Johnston P. G., Kaye F. J. Alternative splicing of the RBP1 gene clusters in an internal exon that encodes potential phosphorylation sites. Oncogene. 1993 Apr;8(4):949–957. [PubMed] [Google Scholar]
  21. Paro R., Hogness D. S. The Polycomb protein shares a homologous domain with a heterochromatin-associated protein of Drosophila. Proc Natl Acad Sci U S A. 1991 Jan 1;88(1):263–267. doi: 10.1073/pnas.88.1.263. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Platero J. S., Hartnett T., Eissenberg J. C. Functional analysis of the chromo domain of HP1. EMBO J. 1995 Aug 15;14(16):3977–3986. doi: 10.1002/j.1460-2075.1995.tb00069.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Powers J. A., Eissenberg J. C. Overlapping domains of the heterochromatin-associated protein HP1 mediate nuclear localization and heterochromatin binding. J Cell Biol. 1993 Jan;120(2):291–299. doi: 10.1083/jcb.120.2.291. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Rice C. M., Fuchs R., Higgins D. G., Stoehr P. J., Cameron G. N. The EMBL data library. Nucleic Acids Res. 1993 Jul 1;21(13):2967–2971. doi: 10.1093/nar/21.13.2967. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Rost B., Sander C. Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol. 1993 Jul 20;232(2):584–599. doi: 10.1006/jmbi.1993.1413. [DOI] [PubMed] [Google Scholar]
  26. Saunders W. S., Chue C., Goebl M., Craig C., Clark R. F., Powers J. A., Eissenberg J. C., Elgin S. C., Rothfield N. F., Earnshaw W. C. Molecular cloning of a human homologue of Drosophila heterochromatin protein HP1 using anti-centromere autoantibodies with anti-chromo specificity. J Cell Sci. 1993 Feb;104(Pt 2):573–582. doi: 10.1242/jcs.104.2.573. [DOI] [PubMed] [Google Scholar]
  27. Schneider T. D., Stephens R. M. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 1990 Oct 25;18(20):6097–6100. doi: 10.1093/nar/18.20.6097. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Schuler G. D., Altschul S. F., Lipman D. J. A workbench for multiple alignment construction and analysis. Proteins. 1991;9(3):180–190. doi: 10.1002/prot.340090304. [DOI] [PubMed] [Google Scholar]
  29. Shaffer C. D., Wallrath L. L., Elgin S. C. Regulating genes by packaging domains: bits of heterochromatin in euchromatin? Trends Genet. 1993 Feb;9(2):35–37. doi: 10.1016/0168-9525(93)90171-D. [DOI] [PubMed] [Google Scholar]
  30. Singh P. B., Miller J. R., Pearce J., Kothary R., Burton R. D., Paro R., James T. C., Gaunt S. J. A sequence motif found in a Drosophila heterochromatin protein is conserved in animals and plants. Nucleic Acids Res. 1991 Feb 25;19(4):789–794. doi: 10.1093/nar/19.4.789. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Stokes D. G., Perry R. P. DNA-binding and chromatin localization properties of CHD1. Mol Cell Biol. 1995 May;15(5):2745–2753. doi: 10.1128/mcb.15.5.2745. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Szekely L., Uzvolgyi E., Jiang W. Q., Durko M., Wiman K. G., Klein G., Sumegi J. Subcellular localization of the retinoblastoma protein. Cell Growth Differ. 1991 Jun;2(6):287–295. [PubMed] [Google Scholar]
  33. Tschiersch B., Hofmann A., Krauss V., Dorn R., Korge G., Reuter G. The protein encoded by the Drosophila position-effect variegation suppressor gene Su(var)3-9 combines domains of antagonistic regulators of homeotic gene complexes. EMBO J. 1994 Aug 15;13(16):3822–3831. doi: 10.1002/j.1460-2075.1994.tb06693.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Weinberg R. A. The retinoblastoma protein and cell cycle control. Cell. 1995 May 5;81(3):323–330. doi: 10.1016/0092-8674(95)90385-2. [DOI] [PubMed] [Google Scholar]
  35. Wootton J. C. Non-globular domains in protein sequences: automated segmentation using complexity measures. Comput Chem. 1994 Sep;18(3):269–285. doi: 10.1016/0097-8485(94)85023-2. [DOI] [PubMed] [Google Scholar]
  36. Zink B., Paro R. In vivo binding pattern of a trans-regulator of homoeotic genes in Drosophila melanogaster. Nature. 1989 Feb 2;337(6206):468–471. doi: 10.1038/337468a0. [DOI] [PubMed] [Google Scholar]

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