Determinants of Heterochromatic siRNA Biogenesis and Function

Molecular Cell

Volumn 53, Issue 2, 2014, Pages 262-276

  Yu, Ruby ^a   Jih, Gloria ^a   Iglesias, Nahid ^a   Moazed, Danesh ^a  

^a HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DICER; HISTONE H3; LYSINE; MESSENGER RNA; REPETITIVE DNA; RIBONUCLEASE; SMALL INTERFERING RNA;

3' UNTRANSLATED REGION; ARTICLE; BIOGENESIS; CATALYSIS; GENE FUNCTION; GENE LOCUS; GENETIC ASSOCIATION; HETEROCHROMATIN; METHYLATION; NONHUMAN; NUCLEOTIDE SEQUENCE; SCHIZOSACCHAROMYCES POMBE; TRANSCRIPTION INITIATION;

ENDORIBONUCLEASES; GENE EXPRESSION REGULATION; HETEROCHROMATIN; HISTONES; METHYLATION; POLYADENYLATION; RIBONUCLEASE III; RNA 3' POLYADENYLATION SIGNALS; RNA INTERFERENCE; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, SMALL INTERFERING; SCHIZOSACCHAROMYCES; SCHIZOSACCHAROMYCES POMBE PROTEINS;

EID: 84892879874     PISSN: 10972765     EISSN: 10974164     Source Type: Journal    
DOI: 10.1016/j.molcel.2013.11.014     Document Type: Article

References (42)

1. Allshire R.C., Javerzat J.P., Redhead N.J., Cranston G. Position effect variegation at fission yeast centromeres. Cell 1994, 76:157-169.
2. Bayne E.H., Portoso M., Kagansky A., Kos-Braun I.C., Urano T., Ekwall K., Alves F., Rappsilber J., Allshire R.C. Splicing factors facilitate RNAi-directed silencing in fission yeast. Science 2008, 322:602-606.
3. Bayne E.H., White S.A., Kagansky A., Bijos D.A., Sanchez-Pulido L., Hoe K.L., Kim D.U., Park H.O., Ponting C.P., Rappsilber J., Allshire R.C. Stc1: a critical link between RNAi and chromatin modification required for heterochromatin integrity. Cell 2010, 140:666-677.
4. Birse C.E., Lee B.A., Hansen K., Proudfoot N.J. Transcriptional termination signals for RNA polymerase II in fission yeast. EMBO J. 1997, 16:3633-3643.
5. Bühler M., Verdel A., Moazed D. Tethering RITS to a nascent transcript initiates RNAi- and heterochromatin-dependent gene silencing. Cell 2006, 125:873-886.
6. Bühler M., Haas W., Gygi S.P., Moazed D. RNAi-dependent and -independent RNA turnover mechanisms contribute to heterochromatic gene silencing. Cell 2007, 129:707-721.
7. Bühler M., Spies N., Bartel D.P., Moazed D. TRAMP-mediated RNA surveillance prevents spurious entry of RNAs into the Schizosaccharomyces pombe siRNA pathway. Nat. Struct. Mol. Biol. 2008, 15:1015-1023.
8. Cam H.P., Sugiyama T., Chen E.S., Chen X., FitzGerald P.C., Grewal S.I. Comprehensive analysis of heterochromatin- and RNAi-mediated epigenetic control of the fission yeast genome. Nat. Genet. 2005, 37:809-819.
9. Colmenares S.U., Buker S.M., Buhler M., Dlakić M., Moazed D. Coupling of double-stranded RNA synthesis and siRNA generation in fission yeast RNAi. Mol. Cell 2007, 27:449-461.
10. Djupedal I., Kos-Braun I.C., Mosher R.A., Söderholm N., Simmer F., Hardcastle T.J., Fender A., Heidrich N., Kagansky A., Bayne E., et al. Analysis of small RNA in fission yeast; centromeric siRNAs are potentially generated through a structured RNA. EMBO J. 2009, 28:3832-3844.
11. Dumesic P.A., Natarajan P., Chen C., Drinnenberg I.A., Schiller B.J., Thompson J., Moresco J.J., Yates J.R., Bartel D.P., Madhani H.D. Stalled spliceosomes are a signal for RNAi-mediated genome defense. Cell 2013, 152:957-968.
12. Dutrow N., Nix D.A., Holt D., Milash B., Dalley B., Westbroek E., Parnell T.J., Cairns B.R. Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping. Nat. Genet. 2008, 40:977-986.
13. Ekwall K. Epigenetic control of centromere behavior. Annu. Rev. Genet. 2007, 41:63-81.
14. Emmerth S., Schober H., Gaidatzis D., Roloff T., Jacobeit K., Bühler M. Nuclear retention of fission yeast dicer is a prerequisite for RNAi-mediated heterochromatin assembly. Dev. Cell 2010, 18:102-113.
15. Funabiki H., Hagan I., Uzawa S., Yanagida M. Cell cycle-dependent specific positioning and clustering of centromeres and telomeres in fission yeast. J. Cell Biol. 1993, 121:961-976.
16. Gerace E.L., Halic M., Moazed D. The methyltransferase activity of Clr4Suv39h triggers RNAi independently of histone H3K9 methylation. Mol. Cell 2010, 39:360-372.
17. Ghildiyal M., Zamore P.D. Small silencing RNAs: an expanding universe. Nat. Rev. Genet. 2009, 10:94-108.
18. Goldstein A.L., McCusker J.H. Three new dominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae. Yeast 1999, 15:1541-1553.
19. Halic M., Moazed D. Dicer-independent primal RNAs trigger RNAi and heterochromatin formation. Cell 2010, 140:504-516.
20. Hong E.J., Villén J., Gerace E.L., Gygi S.P., Moazed D. A cullin E3 ubiquitin ligase complex associates with Rik1 and the Clr4 histone H3-K9 methyltransferase and is required for RNAi-mediated heterochromatin formation. RNA Biol. 2005, 2:106-111.
21. Huang J., Moazed D. Association of the RENT complex with nontranscribed and coding regions of rDNA and a regional requirement for the replication fork block protein Fob1 in rDNA silencing. Genes Dev. 2003, 17:2162-2176.
22. Iida T., Nakayama J., Moazed D. siRNA-mediated heterochromatin establishment requires HP1 and is associated with antisense transcription. Mol. Cell 2008, 31:178-189.
23. Kawakami K., Hayashi A., Nakayama J., Murakami Y. A novel RNAi protein, Dsh1, assembles RNAi machinery on chromatin to amplify heterochromatic siRNA. Genes Dev. 2012, 26:1811-1824.
24. Leeds P., Peltz S.W., Jacobson A., Culbertson M.R. The product of the yeast UPF1 gene is required for rapid turnover of mRNAs containing a premature translational termination codon. Genes Dev. 1991, 5(12A):2303-2314.
25. Maundrell K. nmt1 of fission yeast. A highly transcribed gene completely repressed by thiamine. J. Biol. Chem. 1990, 265:10857-10864.
26. Moazed D. Small RNAs in transcriptional gene silencing and genome defence. Nature 2009, 457:413-420.
27. Moreno S., Klar A., Nurse P. Molecular genetic analysis of fission yeast Schizosaccharomyces pombe. Methods Enzymol. 1991, 194:795-823.
28. Motamedi M.R., Verdel A., Colmenares S.U., Gerber S.A., Gygi S.P., Moazed D. Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs. Cell 2004, 119:789-802.
29. Noma K., Sugiyama T., Cam H., Verdel A., Zofall M., Jia S., Moazed D., Grewal S.I. RITS acts in cis to promote RNA interference-mediated transcriptional and post-transcriptional silencing. Nat. Genet. 2004, 36:1174-1180.
30. Ozsolak F., Kapranov P., Foissac S., Kim S.W., Fishilevich E., Monaghan A.P., John B., Milos P.M. Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell 2010, 143:1018-1029.
31. Proudfoot N.J. Ending the message: poly(A) signals then and now. Genes Dev. 2011, 25:1770-1782.
32. Reinhart B.J., Bartel D.P. Small RNAs correspond to centromere heterochromatic repeats. Science 2002, 297:1831.
33. Rhind N., Chen Z., Yassour M., Thompson D.A., Haas B.J., Habib N., Wapinski I., Roy S., Lin M.F., Heiman D.I., et al. Comparative functional genomics of the fission yeasts. Science 2011, 332:930-936.
34. Richard P., Manley J.L. Transcription termination by nuclear RNA polymerases. Genes Dev. 2009, 23:1247-1269.
35. Sabin L.R., Delás M.J., Hannon G.J. Dogma derailed: the many influences of RNA on the genome. Mol. Cell 2013, 49:783-794.
36. Sadaie M., Iida T., Urano T., Nakayama J. A chromodomain protein, Chp1, is required for the establishment of heterochromatin in fission yeast. EMBO J. 2004, 23:3825-3835.
37. Sigova A., Rhind N., Zamore P.D. A single Argonaute protein mediates both transcriptional and posttranscriptional silencing in Schizosaccharomyces pombe. Genes Dev. 2004, 18:2359-2367.
38. Simmer F., Buscaino A., Kos-Braun I.C., Kagansky A., Boukaba A., Urano T., Kerr A.R., Allshire R.C. Hairpin RNA induces secondary small interfering RNA synthesis and silencing in trans in fission yeast. EMBO Rep. 2010, 11:112-118.
39. Sugiyama T., Cam H., Verdel A., Moazed D., Grewal S.I. RNA-dependent RNA polymerase is an essential component of a self-enforcing loop coupling heterochromatin assembly to siRNA production. Proc. Natl. Acad. Sci. USA 2005, 102:152-157.
40. Verdel A., Jia S., Gerber S., Sugiyama T., Gygi S., Grewal S.I., Moazed D. RNAi-mediated targeting of heterochromatin by the RITS complex. Science 2004, 303:672-676.
41. Volpe T.A., Kidner C., Hall I.M., Teng G., Grewal S.I., Martienssen R.A. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 2002, 297:1833-1837.
42. Wong K.H., Struhl K. The Cyc8-Tup1 complex inhibits transcription primarily by masking the activation domain of the recruiting protein. Genes Dev. 2011, 25:2525-2539.