RNA splicing and debranching viewed through analysis of RNA lariats

Molecular Genetics and Genomics

Volumn 286, Issue 5-6, 2011, Pages 395-410

  Cheng, Zhi ^a,b   Menees, Thomas M ^a  

^a UNIVERSITY OF MISSOURI KANSAS CITY   (United States)

^b CEDARS SINAI MEDICAL CENTER   (United States)

Author keywords

Debranching enzyme Dbr1; Intron RNA lariats; MRNA splicing; Polynucleotide phosphorylase; Yeast Ty1 retrotransposon

Indexed keywords

RNA;

ALTERNATIVE RNA SPLICING; ARTICLE; CONTROLLED STUDY; INTRON; NONHUMAN; PRIORITY JOURNAL; PROCESS DEVELOPMENT; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; RNA CLEAVAGE; RNA DEGRADATION; RNA SEQUENCE; RNA SPLICING; RNA TRANSCRIPTION; SACCHAROMYCES CEREVISIAE;

EXORIBONUCLEASES; GENE EXPRESSION; INTRONS; NUCLEIC ACID CONFORMATION; RNA; RNA NUCLEOTIDYLTRANSFERASES; RNA SPLICING; RNA STABILITY; RNA, FUNGAL; SACCHAROMYCES CEREVISIAE;

SACCHAROMYCES CEREVISIAE;

EID: 84855657292     PISSN: 16174615     EISSN: 16174623     Source Type: Journal    
DOI: 10.1007/s00438-011-0635-y     Document Type: Article

References (73)

1. Abelson J (2008) Is the spliceosome a ribonucleoprotein enzyme? Nat Struct Mol Biol 15(12):1235-1237
2. Alani E, Cao L, Kleckner N (1987) A method for gene disruption that allows repeated use of URA3 selection in the construction of multiply disrupted yeast strains. Genetics 116(4):541-545
3. Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K (2003) Current protocols in molecular biology on CD-ROM. Current Protocols Inc., Brooklyn
4. Berezikov E, Chung WJ, Willis J, Cuppen E, Lai EC (2007) Mammalian mirtron genes. Mol Cell 28(2):328-336 (Pubitemid 47600007)
5. Bushman FD, Malani N, Fernandes J, D'Orso I, Cagney G, Diamond TL, Zhou H, Hazuda DJ, Espeseth AS, Konig R, Bandyopadhyay S, Ideker T, Goff SP, Krogan NJ, Frankel AD, Young JA, Chanda SK (2009) Host cell factors in HIV replication: Metaanalysis of genome-wide studies. PLoS Pathog 5(5):e1000437
6. Chapman KB, Boeke JD (1991) Isolation and characterization of the gene encoding yeast debranching enzyme. Cell 65:483-492 (Pubitemid 121002058)
7. Cheng Z, Menees TM (2004) RNA branching and debranching in the yeast retrovirus-like element Ty1. Science 303:240-243 (Pubitemid 38057576)
8. Cloonan N, Forrest AR, Kolle G, Gardiner BB, Faulkner GJ, Brown MK, Taylor DF, Steptoe AL, Wani S, Bethel G, Robertson AJ, Perkins AC, Bruce SJ, Lee CC, Ranade SS, Peckham HE, Manning JM, McKernan KJ, Grimmond SM (2008) Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 5(7):613-619 (Pubitemid 351911866)
9. Conklin JF, Goldman A, Lopez AJ (2005) Stabilization and analysis of intron lariats in vivo. Methods 37(4):368-375 (Pubitemid 41682507)
10. Coombes CE, Boeke JD (2005) An evaluation of detection methods for large lariat RNAs. RNA 11(3):323-331 (Pubitemid 40270824)
11. Daniels DL, Michels WJ Jr, Pyle AM (1996) Two competing pathways for self-splicing by group II introns: A quantitative analysis of in vitro reaction rates and products. J Mol Biol 256(1):31-49 (Pubitemid 26104208)
12. Engleman A (2010) Reverse transcription and integration. In: Kurth R, Bannert N (eds) Retroviruses: Molecular biology, genomics, and pathogenesis. Caister Academic Press, Norfolk, pp 129-159
13. Falaleeva MV, Chetverina HV, Ugarov VI, Uzlova EA, Chetverin AB (2008) Factors influencing RNA degradation by Thermus thermophilus polynucleotide phosphorylase. FEBS J 275(9):2214-2226 (Pubitemid 351569560)
14. Filipowicz W, Pogacic V (2002) Biogenesis of small nucleolar ribonucleoproteins. Curr Opin Cell Biol 14(3):319-327 (Pubitemid 34626970)
15. Gallwitz D, Sures I (1980) Structure of a split yeast gene: Complete nucleotide sequence of the actin gene in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 77(5):2546-2550 (Pubitemid 10049818)
16. Gao K, Masuda A, Matsuura T, Ohno K (2008) Human branch point consensus sequence is yUnAy. Nucleic Acids Res 36(7):2257-2267 (Pubitemid 351575093)
17. Garcia-Martinez J, Aranda A, Perez-Ortin JE (2004) Genomic run-on evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms. Mol Cell 15(2):303-313 (Pubitemid 38950977)
18. Goff SP (2007) Retroviridae: The retroviruses and their replication. In: Knipe DM, Howley PM (eds) Fields virology. Lipincott, Williams, and Wilkins, Philadelphia, pp 1999-2069
19. Gray M, Kupiec M, Honigberg SM (2004) Site-specific genomic (SSG) and random domain-localized (RDL) mutagenesis in yeast. BMC Biotechnol 4:7
20. Griffith JL, Coleman LE, Raymond AS, Goodson SG, Pittard WS, Tsui C, Devine SE (2003) Functional genomics reveals relationships between the retrovirus-like Ty1 element and its host Saccharomyces cerevisiae. Genetics 164(3):867-879 (Pubitemid 36935666)
21. Guarneros G, Portier C (1990) Different specificities of ribonuclease II and polynucleotide phosphorylase in 30mRNA decay. Biochimie 72(11):771-777
22. Hallegger M, Llorian M, Smith CW (2010) Alternative splicing: Global insights. FEBS J 277(4):856-866
23. Hill JE, Myers AM, Koerner TJ, Tzagoloff A (1986) Yeast/E. coli shuttle vectors with multiple unique restriction sites. Yeast 2(3):163-167
24. Holstege FC, Jennings EG, Wyrick JJ, Lee TI, Hengartner CJ, Green MR, Golub TR, Lander ES, Young RA (1998) Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95(5):717-728 (Pubitemid 28544132)
25. Irwin B, Aye M, Baldi P, Beliakova-Bethell N, Cheng H, Dou Y, Liou W, Sandmeyer S (2005) Retroviruses and yeast retrotransposons use overlapping sets of host genes. Genome Res 15(5):641-654 (Pubitemid 41043634)
26. Juneau K, Palm C, Miranda M, Davis RW (2007) High-density yeasttiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing. Proc Natl Acad Sci USA 104(5):1522-1527 (Pubitemid 46214623)
27. Kaiser C, Michaelis S, Mitchell A (1994) Methods in yeast genetics. CSHL Press, Cold Spring Harbor
28. Karst SM, Rutz M-L, Menees TM (2000) The yeast retrotransposons Ty1 and Ty3 required the RNA lariat debranching enzyme, Dbr1p, for efficient accumulation of reverse transcripts. Bio-Chem Biophys Res Comm 268:112-117 (Pubitemid 30116619)
29. Kataoka N, Fujita M, Ohno M (2009) Functional association of the Microprocessor complex with the spliceosome. Mol Cell Biol 29(12):3243-3254
30. Khalid MF, Damha MJ, Shuman S, Schwer B (2005) Structurefunction analysis of yeast RNA debranching enzyme (Dbr1), a manganese-dependent phosphodiesterase. Nucleic Acids Res 33(19):6349-6360 (Pubitemid 41742572)
31. Kim YK, Kim VN (2007) Processing of intronic microRNAs. EMBO J 26(3):775-783
32. Kiss T, Fayet E, Jady BE, Richard P, Weber M (2006) Biogenesis and intranuclear trafficking of human box C/D and H/ACA RNPs. Cold Spring Harb Symp Quant Biol 71:407-417
33. Lestrade L, Weber MJ (2006) snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Res 34(database issue):D158-162
34. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133(3):523-536
35. Loeb JD, Kerentseva TA, Pan T, Sepulveda-Becerra M, Liu H (1999) Saccharomyces cerevisiae G1 cyclins are differentially involved in invasive and pseudohyphal growth independent of the filamentation mitogen-activated protein kinase pathway. Genetics 153(4):1535-1546
36. Lopez PJ, Seraphin B (2000) YIDB: The Yeast Intron DataBase. Nucleic Acids Res 28(1):85-86 (Pubitemid 30047721)
37. Martin A, Schneider S, Schwer B (2002) Prp43 is an essential RNAdependent ATPase required for release of lariat-intron from the spliceosome. J Biol Chem 277(20):17743-17750 (Pubitemid 34967580)
38. McLaren RS, Newbury SF, Dance GS, Causton HC, Higgins CF (1991) mRNA degradation by processive 3'-5' exoribonucleases in vitro and the implications for prokaryotic mRNA decay in vivo. J Mol Biol 221(1):81-95 (Pubitemid 121003560)
39. Miller C, Schwalb B, Maier K, Schulz D, Dumcke S, Zacher B, Mayer A, Sydow J, Marcinowski L, Dolken L, Martin DE, Tresch A, Cramer P (2011) Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol 7:458
40. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNASeq. Nat Methods 5(7):621-628 (Pubitemid 351911867)
41. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320(5881):1344-1349 (Pubitemid 351929471)
42. Nam K, Hudson RH, Chapman KB, Ganeshan K, Damha MJ, Boeke JD (1994) Yeast lariat debranching enzyme. Substrate and sequence specificity. J Biol Chem 269(32):20613-20621
43. Ng R, Abelson J (1980) Isolation and sequence of the gene for actin in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 77(7):3912-3916 (Pubitemid 10015490)
44. Nilsen TW, Graveley BR (2010) Expansion of the eukaryotic proteome by alternative splicing. Nature 463(7280):457-463
45. Okamura K, Hagen JW, Duan H, Tyler DM, Lai EC (2007) The mirtron pathway generates microRNA-class regulatory RNAs in Drosophila. Cell 130(1):89-100 (Pubitemid 47031325)
46. Ooi SL, Samarsky DA, Fournier MJ, Boeke JD (1998) Intronic snoRNA biosynthesis in Saccharomyces cerevisiae depends on the lariat-debranching enzyme: Intron length effects and activity of a precursor snoRNA. RNA 4(9):1096-1110 (Pubitemid 28413456)
47. Ooi SL, Dann C 3rd, Nam K, Leahy DJ, Damha MJ, Boeke JD (2001) RNA lariat debranching enzyme. Methods Enzymol 342:233-248 (Pubitemid 32911946)
48. Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40(12):1413-1415
49. Pastuszak AW, Joachimiak MP, Blanchette M, Rio DC, Brenner SE, Frankel AD (2010) An SF1 affinity model to identify branch point sequences in human introns. Nucleic Acids Res 39(6): 2344-2356
50. Pelechano V, Perez-Ortin JE (2010) There is a steady-state transcriptome in exponentially growing yeast cells. Yeast 27(7):413-422
51. Pratico ED, Silverman SK (2007) Ty1 reverse transcriptase does not read through the proposed 2', 5'-branched retrotransposition intermediate in vitro. RNA 13(9):1528-1536 (Pubitemid 47347423)
52. Preker PJ, Guthrie C (2006) Autoregulation of the mRNA export factor Yra1p requires inefficient splicing of its pre-mRNA. RNA 12(6):994-1006 (Pubitemid 43788118)
53. Preker PJ, Kim KS, Guthrie C (2002) Expression of the essential mRNA export factor Yra1p is autoregulated by a splicingdependent mechanism. RNA 8(8):969-980
54. Rodriguez A, Griffiths-Jones S, Ashurst JL, Bradley A (2004) Identification of mammalian microRNA host genes and transcription units. Genome Res 14(10A):1902-1910 (Pubitemid 39386503)
55. Rodriguez-Navarro S, Strasser K, Hurt E (2002) An intron in the YRA1 gene is required to control Yra1 protein expression and mRNA export in yeast. EMBO Rep 3(5):438-442 (Pubitemid 34567431)
56. Ruby JG, Jan CH, Bartel DP (2007) Intronic microRNA precursors that bypass Drosha processing. Nature 448(7149):83-86 (Pubitemid 47037009)
57. Salem LA, Boucher CL, Menees TM (2003) Relationship between RNA lariat debranching and yeast Ty1 element retrotransposition. J Virol 77:12795-12806 (Pubitemid 37430674)
58. Schmittgen TD, Livak KJ (2008) Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc 3(6):1101-1108 (Pubitemid 351818697)
59. Sikorski RS, Hieter P (1989) A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122(1):19-27
60. Smale ST (2009). Nuclear run-on assay. Cold Spring Harb Protoc 2009(11): Pdb prot5329
61. Smith DJ, Query CC, Konarska MM (2008) "Nought may endure but mutability": Spliceosome dynamics and the regulation of splicing. Mol Cell 30(6):657-666 (Pubitemid 351815122)
62. Spingola M, Grate L, Haussler D, Ares M Jr (1999) Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae. RNA 5(2):221-234 (Pubitemid 29079282)
63. Storici F, Lewis LK, Resnick MA (2001) In vivo site-directed mutagenesis using oligonucleotides. Nat Biotechnol 19(8): 773-776 (Pubitemid 32729542)
64. Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, Schmidt D, O'Keeffe S, Haas S, Vingron M, Lehrach H, Yaspo ML(2008) A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321(5891):956-960
65. Suzuki H, Zuo Y, Wang J, Zhang MQ, Malhotra A, Mayeda A (2006) Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing. Nucleic Acids Res 34(8):e63
66. Tang GQ, Maxwell ES (2008) Xenopus microRNA genes are predominantly located within introns and are differentially expressed in adult frog tissues via post-transcriptional regulation. Genome Res 18(1):104-112
67. Vincent HA, Deutscher MP (2006) Substrate recognition and catalysis by the exoribonuclease RNase R. J Biol Chem 281(40):29769-29775 (Pubitemid 44536986)
68. Vogel J, Borner T (2002) Lariat formation and a hydrolytic pathway in plant chloroplast group II intron splicing. EMBO J 21(14): 3794-3803 (Pubitemid 34787052)
69. Vogel J, Hess WR, Borner T (1997) Precise branch point mapping and quantification of splicing intermediates. Nucleic Acids Res 25(10):2030-2031 (Pubitemid 27303401)
70. Wahl MC, Will CL, Luhrmann R (2009) The spliceosome: Design principles of a dynamic RNP machine. Cell 136(4):701-718
71. Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, Goodhead I, Penkett CJ, Rogers J, Bahler J (2008) Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453(7199):1239-1243 (Pubitemid 351913597)
72. Ye Y, De Leon J, Yokoyama N, Naidu Y, Camerini D (2005) DBR1 siRNA inhibition of HIV-1 replication. Retrovirology 2:63
73. Zhang Z, Hesselberth JR, Fields S (2007) Genome-wide identification of spliced introns using a tiling microarray. Genome Res 17(4):503-509 (Pubitemid 46556454)