Making noise about silence: Repression of repeated genes in animals

Current Opinion in Genetics and Development

Volumn 10, Issue 2, 2000, Pages 211-216

  Birchler, James A ^a   Pal Bhadra, Manika ^a   Bhadra, Utpal ^a  

^a UNIVERSITY OF MISSOURI   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED RNA;

CAENORHABDITIS ELEGANS; GENE DUPLICATION; GENE MUTATION; GENE REPRESSION; GENE SILENCING; GENETIC TRANSCRIPTION; NONHUMAN; PRIORITY JOURNAL; RETROPOSON; REVIEW; TANDEM REPEAT; TRANSPOSON; VIRUS;

ANIMALIA; CAENORHABDITIS ELEGANS; DROSOPHILA;

EID: 0034069076     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-437X(00)00065-4     Document Type: Review

References (47)

1. Matzke M.A., Primig M., Trnovsky J., Matzke A.J.M. Reversible methylation and inactivation of marker genes in sequentially transformed tobacco plants. EMBO J. 8:1989;643-649.
2. Napoli C., Lemieux C., Jorgenson R.A. Introduction of a chimeric chalcone synthase gene in petunia results in reversible cosuppression of homologous genes in trans. Plant Cell. 2:1990;279-289.
3. van der Krol A.R., Mur L.A., Beld M., Mol J.N., Stuitje A.R. Flavonoid genes in petunia: addition of a limited number of gene copies may lead to a suppression of gene expression. Plant Cell. 2:1990;291-299.
4. Assaad F.F., Tucker K.L., Signer E.R. Epigenetic repeated-induced gene silencing (RIGS) in Arabidopsis. Plant Mol Biol. 22:1993;1067-1085.
5. Dorer D.R., Henikoff S. Expansions of transgene repeats cause heterochromatin formation and gene silencing in Drosophila. Cell. 77:1994;993-1002.
6. Garrick D., Fiering S., Martin D.I., Whitelaw E. Repeat induced gene silencing in mammals. Nat Genet. 18:1998;56-59. The demonstration in mammalian species that tandem repeats at a single insertion site are silenced, whereas a single copy is active.
7. Sabl J.F., Henikoff S. Copy number and orientation determine the susceptibility of a gene to silencing by nearby heterochromatin in Drosophila. Genetics. 142:1996;447-458.
8. Fanti L., Dorer D.R., Berloco M., Henikoff S., Pimpinelli S. Heterochromatin protein 1 binds transgene arrays. Chromosoma. 107:1998;286-292.
9. Kelly W.G., Fire A. Chromatin silencing and the maintenance of a functional germline in Caenorhabditis elegans. Development. 125:1998;2451-2456.
10. Holdeman R., Nehrt S., Strome S. MES-2, a maternal protein essential for viability of the germline in Caenorhabditis elegans, is homologous to a Drosophila Polycomb group protein. Development. 125:1998;2457-2467.
11. Korf I., Fan Y., Strome S. The Polycomb group in Caenorhabditis elegans and maternal control of germline development. Development. 125:1998;2469-2478.
12. Tie F., Furuyama T., Harte P.J. The Drosophila Polycomb Group proteins ESC and E(Z) bind directly to each other and co-localize at multiple chromosomal sites. Development. 125:1998;3483-3496.
13. Pal-Bhadra M., Bhadra U., Birchler J.A. Cosuppression in Drosophila: gene silencing of Alcohol dehydrogenase by white-Adh transgenes is Polycomb dependent. Cell. 90:1997;479-490.
14. Pal-Bhadra M., Bhadra U., Birchler J.A. Cosuppression of nonhomologous transgenes in Drosophila involves mutually related endogenous sequences. Cell. 99:1999;35-46. The discovery that silencing of dispersed nonhomologous transgenes can be mediated via an endogenous gene with homology to different portions of the two types of transgenes. One region of the intermediary gene identified as required for the silencing interaction coincides with one of the transcriptional enhancers, which itself is not known to be transcribed.
15. Hagstrom K., Muller M., Schedl P. A Polycomb and GAGA dependent silencer adjoins the Fab-7 boundary in the Drosophila bithorax complex. Genetics. 146:1997;1365-1380.
16. Sigrist C.J., Pirrotta V. Chromatin insulator elements block the silencing of a target gene by the Drosophila polycomb response element (PRE) but allow trans interactions between PREs on different chromosomes. Genetics. 147:1997;209-221.
17. Muller M., Hagstrom K., Gyurkovics H., Pirrotta V., Schedl P. The Mcp element from the Drosophila melanogaster bithorax complex mediates long-distance regulatory interactions. Genetics. 153:1999;1333-1356. The finding that transgenes carrying a PRE from the bithorax segment identity gene can interact interchromosomally to produce silencing of an adjacent reporter gene in the transformed construct. See also [15,16].
18. Kassis J.A., VanSickle E.P., Sensabaugh S.M. A fragment of engrailed regulatory DNA can mediate transvection of the white gene in Drosophila. Genetics. 128:1991;751-761.
19. Brown J.L., Mucci D., Whiteley M., Dirksen M.L., Kassis J.A. The Drosophila Polycomb group gene pleiohomeotic encodes a DNA binding protein with homology to the transcription factor YY1. Mol Cell. 1:1998;1057-1064. The authors demonstrate that a 'pairing sensitive' silencing site in the regulatory region of the engrailed gene is the DNA binding site of a member of the Polycomb Group and the demonstration that a Pc-G member binds DNA directly. The YY1 transcriptional factor is involved in the control of many viral promoters raising the possibility of a connection between homology dependent silencing and the evolution of a host mechanism to suppress viral expression.
20. Mallin D.R., Myung J.S., Patton J.S., Geyer P.K. Polycomb group repression is blocked by the Drosophila suppressor of Hairy-wing[su(Hw)] insulator. Genetics. 148:1998;331-339.
21. Becker K.G., Swergold G.D., Ozato K., Thayer R.E. Binding of the ubiquitous nuclear transcription factor YY1 to a cis regulatory sequence in the human LINE-1 transposable element. Hum Mol Genet. 2:1993;1697-1702.
22. Margolis D.M., Somasundaran M., Green M.R. Human transcription factor YY1 represses human immunodeficiency virus type 1 transcription and virion production. J Virol. 68:1994;905-910.
23. Romerio F., Bagriel M.N., Margolis D.M. Repression of human immunodeficiency virus type 1 through the novel cooperation of human factors YY1 and LSF. J Virol. 71:1997;9375-9382.
24. Alkema M.J., Bronk M., Verhoeven E., Otte A., Van't Veer L., Berns A., Van Lohuizen M. Identification of Bmi1-interacting proteins as constituents of a multimeric mammalian Polycomb complex. Genes Dev. 11:1997;226-240.
25. Laible G., Wolf A., Dorn R., Reuter G., Nislow C., Lebersorger A., Popkin D., Pillus L., Jenuwein T. Mammalian homologues of the Polycomb-group gene Enhancer of zeste mediate gene silencing in Drosophila heterochromatin and at S. cerevisiae telomeres. EMBO J. 16:1997;3219-3232.
26. Schoorlemmer J., Marcos-Gutierrez C., Were F., Martinez R., Garcia E., Satijn D.P.E., Otte A.P., Vidal M. Ring1A is a transcriptional repressor that interacts with the Polycomb-M33 protein and is expressed at rhombomere boundaries in the mouse hindbrain. EMBO J. 16:1997;5930-5942.
27. ••] provides direct evidence that transposons are susceptible to dispersed gene-silencing processes.
28. ••], a demonstration that transgenes carrying fragments of retrotransposons can silence the endogenous copies, illustrating a connection between cosuppression of transgenes and silencing of transposons.
29. Fire A., Xu S., Montgomery M.K., Kotas S.A., Driver S.E., Mello C.C. Potent and specific genetic interference by double stranded RNA in Caenorhabditis elegans. Nature. 391:1998;806-811. The authors find that double-stranded RNA is much more effective than either sense or antisense in triggering degradation of the homologous endogenously produced mRNAs. This work served as a stimulus for the development of reverse genetic 'knock-down' techniques in several animal species.
30. Kennerdell J.R., Carthew R.W. Use of dsRNA-mediated genetic interference to demonstrate that frizzled and frizzled2 act in the wingless pathway. Cell. 95:1998;1017-1026.
31. Ngo H., Tschuli C., Gull K., Ullu E. Double-stranded RNA induces mRNA degradation in Trypanosoma brucei. Proc Natl Acad Sci USA. 95:1998;1487-1492.
32. Ruiz F., Vayssie L., Klotz C., Sperling L., Madeddu L. Homology-dependent gene silencing in Paramecium. Mol Biol Cell. 9:1998;931-943.
33. Bahramian M.B., Zarbl H. Transcriptional and post-transcriptional silencing of rodent alpha(I) collagen by a homologous transcriptionally self-silenced transgene. Mol Cell Biol. 19:1999;274-283. The demonstration of cosuppression of an endogenous gene by an homologous transgene in mammalian cells. High-copy numbers of a transgene are not expressed but their presence triggers a rapid degradation of the homologous endogenous RNA.
34. Lohmann J.U., Endl I., Bosch T.C. Silencing of developmental genes in hydra. Dev Biol. 214:1999;211-214.
35. Misquitta L., Paterson B.M. Targeted disruption of gene function in Drosophila by RNA interference (RNAi): a role for nautilus in embryonic somatic muscle formation. Proc Natl Acad Sci USA. 96:1999;1451-1456.
36. Sanchez-Alvarado A., Newmark P.A. Double-stranded RNA specifically disrupts gene expression during planarian regeneration. Proc Natl Acad Sci USA. 96:1999;5049-5054.
37. Montgomery M.K., Xu S., Fire A. RNA as a target of double-stranded RNA-mediated genetic interference in Caenorhabditis elegans. Proc Natl Acad Sci USA. 95:1998;15502-15507. An examination of the gene features needed for RNAi. Double-stranded RNAs homologous to promoters and introns are ineffective whereas exonic fragments lead to a potent degradation of homologous mRNAs.
38. Bosher J.M., Dufourcq P., Sookhareea S., Labouesse M. RNA interference can target pre-mRNA. Consequences for gene expression in a Caenorhabditis elegans operon. Genetics. 153:1999;1245-1256.
39. Tabara H., Sarkissian M., Kelly W.G., Fleenor J., Grishok A., Timmons L., Fire A., Mello C.C. The rde-1 gene, RNA interference, and transposon silencing in C. elegans. Cell. 99:1999;123-132. The authors describe mutations that are defective in RNA interference and demonstrate that they exhibit a mutator activity indicative of the mobilization of transposable elements. Two of these mutations are capable of relieving the silencing in the germline associated with tandem arrays.
40. Ketting R.F., Haverkamp T.H., van Luenen H.G.A.M., Plasterk H.A. mut-7 of C. elegans, required for transposon silencing and RNA interference, is a homolog of Werner Syndrome helicase and RnaseD. Cell. 99:1999;133-141. This report is a demonstration that mutator strains with high mobility of DNA-based transposable elements are defective for RNAi and that one of these mutator genes is predicted from sequence analysis to have RNase activity.
41. Wassenegger M., Heimes S., Riedel L., Sanger H.L. RNA-directed de novo methylation of genomic sequences in plants. Cell. 76:1994;567-576.
42. Mette M.F., van der Winden J., Matzke M.A., Matzke A.J. Production of aberrant promoter transcripts contributes to methylation and silencing of unlinked homologous promoters in trans. EMBO J. 18:1999;241-248.
43. zu Putlitz J., Wands J.R. Specific inhibition of hepatitis B virus replication by sense RNA. Antisense Nuclei Acid Drug Dev. 9:1999;241-252. The demonstration in animal species that post-transcriptional gene silencing can be effective against viral multiplication.
44. Tuschl T., Zamore P.D., Lehmann R., Bartel D.P., Sharp P.A. Targeted mRNA degradation by double-stranded RNA in vitro. Genes Dev. 13:1999;3191-3197.
45. Tavernarakis N., Wang S.L., Dorovkov M., Ryazanov A., Driscoll M. Heritable and inducible genetic interference by double-stranded RNA encoded by transgenes. Nat Genet. 24:2000;180-183.
46. Wargelius A., Ellingsen Fjose A. Double-stranded RNA induces specific development defects in zebrafish embryos. Biochem Biophys Res Comm. 263:1999;156-161.
47. Wianny F., Zernicka-Goetz M. Specific interference with gene function by double-stranded RNA in early mouse development. Nat Cell Biol. 2:2000;70-75.