Transcription of the Major Neurospora crassa microRNA-Like Small RNAs Relies on RNA Polymerase III

PLoS Genetics

Volumn 9, Issue 1, 2013, Pages

  Yang, Qiuying ^a   Li, Liande ^a   Xue, Zhihong ^a   Ye, Qiaohong ^a   Zhang, Lin ^b   Li, Shaojie ^c   Liu, Yi ^a  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^b SUN YAT SEN UNIVERSITY   (China)

^c INSTITUTE OF MICROBIOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DNA DIRECTED RNA POLYMERASE III; MICRORNA; MICRORNA LIKE SMALL RNA; RIBONUCLEASE; RIBONUCLEASE Z; RNA POLYMERASE II; TRANSFER RNA; UNCLASSIFIED DRUG;

ARTICLE; BIOGENESIS; CONTROLLED STUDY; DNA SEQUENCE; ENZYME ACTIVITY; ENZYME INHIBITION; ENZYME SYNTHESIS; GENE LOCUS; GENE SILENCING; GENETIC CONSERVATION; NEUROSPORA CRASSA; NONHUMAN; NUCLEOTIDE SEQUENCE; PROMOTER REGION; RNA SYNTHESIS; RNA TRANSCRIPTION;

BASE SEQUENCE; ENDORIBONUCLEASES; GENE EXPRESSION REGULATION, FUNGAL; GENE SILENCING; MICRORNAS; MOLECULAR SEQUENCE DATA; NEUROSPORA CRASSA; PROMOTER REGIONS, GENETIC; RNA POLYMERASE II; RNA POLYMERASE III; RNA, FUNGAL;

EID: 84873508731     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1003227     Document Type: Article

References (47)

1. Bartel DP, (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
2. Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, et al. (2003) A uniform system for microRNA annotation. RNA 9: 277-279.
3. Lee RC, Feinbaum RL, Ambros V, (1993) The C. elegans heterochromatic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843-854.
4. Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T, (2001) Identification of novel genes coding for small expressed RNAs. Science 294: 853-858.
5. Lee RC, Ambros V, (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294: 862-864.
6. Llave C, Kasschau KD, Rector MA, Carrington JC, (2002) Endogenous and silencing-associated small RNAs in plants. Plant Cell 14: 1605-1619.
7. Molnar A, Schwach F, Studholme DJ, Thuenemann EC, Baulcombe DC, (2007) miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii. Nature 447: 1126-1129.
8. Zhao T, Li G, Mi S, Li S, Hannon GJ, et al. (2007) A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii. Genes Dev 21: 1190-1203.
9. Lee Y, Kim M, Han J, Yeom KH, Lee S, et al. (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J 23: 4051-4060.
10. Cai X, Hagedorn CH, Cullen BR, (2004) Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA 10: 1957-1966.
11. Kim VN, Han J, Siomi MC, (2009) Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol 10: 126-139.
12. Yang JS, Lai EC, (2011) Alternative miRNA biogenesis pathways and the interpretation of core miRNA pathway mutants. Mol Cell 43: 892-903.
13. Dieci G, Fiorino G, Castelnuovo M, Teichmann M, Pagano A, (2007) The expanding RNA polymerase III transcriptome. Trends Genet 23: 614-622.
14. White RJ, (2011) Transcription by RNA polymerase III: more complex than we thought. Nat Rev Genet 12: 459-463.
15. Oler AJ, Alla RK, Roberts DN, Wong A, Hollenhorst PC, et al. (2010) Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors. Nat Struct Mol Biol 17: 620-628.
16. Raha D, Wang Z, Moqtaderi Z, Wu L, Zhong G, et al. (2010) Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc Natl Acad Sci U S A 107: 3639-3644.
17. Orioli A, Pascali C, Pagano A, Teichmann M, Dieci G, (2012) RNA polymerase III transcription control elements: themes and variations. Gene 493: 185-194.
18. Haussecker D, Huang Y, Lau A, Parameswaran P, Fire AZ, et al. (2010) Human tRNA-derived small RNAs in the global regulation of RNA silencing. RNA 16: 673-695.
19. Bogerd HP, Karnowski HW, Cai X, Shin J, Pohlers M, et al. (2010) A mammalian herpesvirus uses noncanonical expression and processing mechanisms to generate viral MicroRNAs. Mol Cell 37: 135-142.
20. Diebel KW, Smith AL, van Dyk LF, (2010) Mature and functional viral miRNAs transcribed from novel RNA polymerase III promoters. RNA 16: 170-185.
21. Kincaid RP, Burke JM, Sullivan CS, (2012) RNA virus microRNA that mimics a B-cell oncomiR. Proc Natl Acad Sci U S A 109: 3077-3082.
22. Lee HC, Li L, Gu W, Xue Z, Crosthwaite SK, et al. (2010) Diverse pathways generate microRNA-like RNAs and Dicer-independent small interfering RNAs in fungi. Mol Cell 38: 803-814.
23. Xue Z, Yuan H, Guo J, Liu Y, (2012) Reconstitution of an Argonaute-Dependent Small RNA Biogenesis Pathway Reveals a Handover Mechanism Involving the RNA Exosome and the Exonuclease QIP. Mol Cell.
24. Braglia P, Percudani R, Dieci G, (2005) Sequence context effects on oligo(dT) termination signal recognition by Saccharomyces cerevisiae RNA polymerase III. J Biol Chem 280: 19551-19562.
25. Wu L, Pan J, Thoroddsen V, Wysong DR, Blackman RK, et al. (2003) Novel small-molecule inhibitors of RNA polymerase III. Eukaryot Cell 2: 256-264.
26. Werner M, Thuriaux P, Soutourina J, (2009) Structure-function analysis of RNA polymerases I and III. Curr Opin Struct Biol 19: 740-745.
27. Schramm L, Hernandez N, (2002) Recruitment of RNA polymerase III to its target promoters. Genes Dev 16: 2593-2620.
28. Hartmann RK, Gossringer M, Spath B, Fischer S, Marchfelder A, (2009) The making of tRNAs and more- RNase P and tRNase Z. Prog Mol Biol Transl Sci 85: 319-368.
29. Phizicky EM, Hopper AK, (2010) tRNA biology charges to the front. Genes Dev 24: 1832-1860.
30. Walker SC, Engelke DR, (2006) Ribonuclease P: the evolution of an ancient RNA enzyme. Crit Rev Biochem Mol Biol 41: 77-102.
31. Borchert GM, Lanier W, Davidson BL, (2006) RNA polymerase III transcribes human microRNAs. Nat Struct Mol Biol 13: 1097-1101.
32. Listerman I, Bledau AS, Grishina I, Neugebauer KM, (2007) Extragenic accumulation of RNA polymerase II enhances transcription by RNA polymerase III. PLoS Genet 3: e212 doi:10.1371/journal.pgen.0030212.
33. Ghildiyal M, Zamore PD, (2009) Small silencing RNAs: an expanding universe. Nat Rev Genet 10: 94-108.
34. Cheng P, He Q, He Q, Wang L, Liu Y, (2005) Regulation of the Neurospora circadian clock by an RNA helicase. Genes Dev 19: 234-241.
35. Maiti M, Lee HC, Liu Y, (2007) QIP, a putative exonuclease, interacts with the Neurospora Argonaute protein and facilitates conversion of duplex siRNA into single strands. Genes Dev 21: 590-600.
36. Zheng L, Baumann U, Reymond JL, (2004) An efficient one-step site-directed and site-saturation mutagenesis protocol. Nucleic Acids Res 32: e115.
37. Choudhary S, Lee HC, Maiti M, He Q, Cheng P, et al. (2007) A double-stranded-RNA response program important for RNA interference efficiency. Mol Cell Biol 27: 3995-4005.
38. Aronson BD, Johnson KA, Loros JJ, Dunlap JC, (1994) Negative feedback defining a circadian clock: autoregulation of the clock gene frequency. Science 263: 1578-1584.
39. Catalanotto C, Azzalin G, Macino G, Cogoni C, (2002) Involvement of small RNAs and role of the qde genes in the gene silencing pathway in Neurospora. Genes Dev 16: 790-795.
40. Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, et al. (2009) Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res 37: e123.
41. Li R, Li Y, Kristiansen K, Wang J, (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24: 713-714.
42. Trapnell C, Pachter L, Salzberg SL, (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111.
43. Langmead B, Trapnell C, Pop M, Salzberg SL, (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
44. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28: 511-515.
45. Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L, (2011) Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol 12: R22.
46. Roberts A, Pimentel H, Trapnell C, Pachter L, (2011) Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics 27: 2325-2329.
47. Thorvaldsdottir H, Robinson JT, Mesirov JP, (2012) Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform.