• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of rnaThe RNA SocietyeTOC AlertsSubscriptionsJournal HomeCSHL PressRNA
RNA. Feb 1999; 5(2): 221–234.
PMCID: PMC1369754

Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae.

Abstract

Introns have typically been discovered in an ad hoc fashion: introns are found as a gene is characterized for other reasons. As complete eukaryotic genome sequences become available, better methods for predicting RNA processing signals in raw sequence will be necessary in order to discover genes and predict their expression. Here we present a catalog of 228 yeast introns, arrived at through a combination of bioinformatic and molecular analysis. Introns annotated in the Saccharomyces Genome Database (SGD) were evaluated, questionable introns were removed after failing a test for splicing in vivo, and known introns absent from the SGD annotation were added. A novel branchpoint sequence, AAUUAAC, was identified within an annotated intron that lacks a six-of-seven match to the highly conserved branchpoint consensus UACUAAC. Analysis of the database corroborates many conclusions about pre-mRNA substrate requirements for splicing derived from experimental studies, but indicates that splicing in yeast may not be as rigidly determined by splice-site conservation as had previously been thought. Using this database and a molecular technique that directly displays the lariat intron products of spliced transcripts (intron display), we suggest that the current set of 228 introns is still not complete, and that additional intron-containing genes remain to be discovered in yeast. The database can be accessed at http://www.cse.ucsc.edu/research/compbi o/yeast_introns.html.

Full Text

The Full Text of this article is available as a PDF (682K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Leu JY, Chua PR, Roeder GS. The meiosis-specific Hop2 protein of S. cerevisiae ensures synapsis between homologous chromosomes. Cell. 1998 Aug 7;94(3):375–386. [PubMed]
  • Ares M, Jr, Weiser B. Rearrangement of snRNA structure during assembly and function of the spliceosome. Prog Nucleic Acid Res Mol Biol. 1995;50:131–159. [PubMed]
  • Bachellerie JP, Michot B, Nicoloso M, Balakin A, Ni J, Fournier MJ. Antisense snoRNAs: a family of nucleolar RNAs with long complementarities to rRNA. Trends Biochem Sci. 1995 Jul;20(7):261–264. [PubMed]
  • Baronas-Lowell DM, Warner JR. Ribosomal protein L30 is dispensable in the yeast Saccharomyces cerevisiae. Mol Cell Biol. 1990 Oct;10(10):5235–5243. [PMC free article] [PubMed]
  • Barta I, Iggo R. Autoregulation of expression of the yeast Dbp2p 'DEAD-box' protein is mediated by sequences in the conserved DBP2 intron. EMBO J. 1995 Aug 1;14(15):3800–3808. [PMC free article] [PubMed]
  • Berglund JA, Chua K, Abovich N, Reed R, Rosbash M. The splicing factor BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAAC. Cell. 1997 May 30;89(5):781–787. [PubMed]
  • Brys A, Schwer B. Requirement for SLU7 in yeast pre-mRNA splicing is dictated by the distance between the branchpoint and the 3' splice site. RNA. 1996 Jul;2(7):707–717. [PMC free article] [PubMed]
  • Chapman KB, Boeke JD. Isolation and characterization of the gene encoding yeast debranching enzyme. Cell. 1991 May 3;65(3):483–492. [PubMed]
  • Charpentier B, Rosbash M. Intramolecular structure in yeast introns aids the early steps of in vitro spliceosome assembly. RNA. 1996 Jun;2(6):509–522. [PMC free article] [PubMed]
  • Cui Y, Hagan KW, Zhang S, Peltz SW. Identification and characterization of genes that are required for the accelerated degradation of mRNAs containing a premature translational termination codon. Genes Dev. 1995 Feb 15;9(4):423–436. [PubMed]
  • Dick T, Surana U, Chia W. Molecular and genetic characterization of SLC1, a putative Saccharomyces cerevisiae homolog of the metazoan cytoplasmic dynein light chain 1. Mol Gen Genet. 1996 Apr 24;251(1):38–43. [PubMed]
  • Dujon B. The yeast genome project: what did we learn? Trends Genet. 1996 Jul;12(7):263–270. [PubMed]
  • Fouser LA, Friesen JD. Mutations in a yeast intron demonstrate the importance of specific conserved nucleotides for the two stages of nuclear mRNA splicing. Cell. 1986 Apr 11;45(1):81–93. [PubMed]
  • Fouser LA, Friesen JD. Effects on mRNA splicing of mutations in the 3' region of the Saccharomyces cerevisiae actin intron. Mol Cell Biol. 1987 Jan;7(1):225–230. [PMC free article] [PubMed]
  • Frank D, Guthrie C. An essential splicing factor, SLU7, mediates 3' splice site choice in yeast. Genes Dev. 1992 Nov;6(11):2112–2124. [PubMed]
  • Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, et al. Life with 6000 genes. Science. 1996 Oct 25;274(5287):546–567. [PubMed]
  • Goguel V, Rosbash M. Splice site choice and splicing efficiency are positively influenced by pre-mRNA intramolecular base pairing in yeast. Cell. 1993 Mar 26;72(6):893–901. [PubMed]
  • Grohmann L, Graack HR, Kruft V, Choli T, Goldschmidt-Reisin S, Kitakawa M. Extended N-terminal sequencing of proteins of the large ribosomal subunit from yeast mitochondria. FEBS Lett. 1991 Jun 17;284(1):51–56. [PubMed]
  • Hawkins JD. A survey on intron and exon lengths. Nucleic Acids Res. 1988 Nov 11;16(21):9893–9908. [PMC free article] [PubMed]
  • Howe KJ, Ares M., Jr Intron self-complementarity enforces exon inclusion in a yeast pre-mRNA. Proc Natl Acad Sci U S A. 1997 Nov 11;94(23):12467–12472. [PMC free article] [PubMed]
  • Hughey R, Krogh A. Hidden Markov models for sequence analysis: extension and analysis of the basic method. Comput Appl Biosci. 1996 Apr;12(2):95–107. [PubMed]
  • Jacquier A, Rodriguez JR, Rosbash M. A quantitative analysis of the effects of 5' junction and TACTAAC box mutants and mutant combinations on yeast mRNA splicing. Cell. 1985 Dec;43(2 Pt 1):423–430. [PubMed]
  • Jacquier A, Rosbash M. RNA splicing and intron turnover are greatly diminished by a mutant yeast branch point. Proc Natl Acad Sci U S A. 1986 Aug;83(16):5835–5839. [PMC free article] [PubMed]
  • Kaiser P, Seufert W, Höfferer L, Kofler B, Sachsenmaier C, Herzog H, Jentsch S, Schweiger M, Schneider R. A human ubiquitin-conjugating enzyme homologous to yeast UBC8. J Biol Chem. 1994 Mar 25;269(12):8797–8802. [PubMed]
  • Kalogeropoulos A. Automatic intron detection in nuclear DNA sequences of Saccharomyces cerevisiae. Yeast. 1995 May;11(6):555–565. [PubMed]
  • Kandels-Lewis S, Séraphin B. Involvement of U6 snRNA in 5' splice site selection. Science. 1993 Dec 24;262(5142):2035–2039. [PubMed]
  • Kitakawa M, Graack HR, Grohmann L, Goldschmidt-Reisin S, Herfurth E, Wittmann-Liebold B, Nishimura T, Isono K. Identification and characterization of the genes for mitochondrial ribosomal proteins of Saccharomyces cerevisiae. Eur J Biochem. 1997 Apr 15;245(2):449–456. [PubMed]
  • Köhrer K, Domdey H. Splicing and spliceosome formation of the yeast MATa1 transcript require a minimum distance from the 5' splice site to the internal branch acceptor site. Nucleic Acids Res. 1988 Oct 25;16(20):9457–9475. [PMC free article] [PubMed]
  • Koonin EV. Similarities in RNA helicases. Nature. 1991 Jul 25;352(6333):290–290. [PubMed]
  • Krogh A, Brown M, Mian IS, Sjölander K, Haussler D. Hidden Markov models in computational biology. Applications to protein modeling. J Mol Biol. 1994 Feb 4;235(5):1501–1531. [PubMed]
  • Lesser CF, Guthrie C. Mutational analysis of pre-mRNA splicing in Saccharomyces cerevisiae using a sensitive new reporter gene, CUP1. Genetics. 1993 Apr;133(4):851–863. [PMC free article] [PubMed]
  • Lesser CF, Guthrie C. Mutations in U6 snRNA that alter splice site specificity: implications for the active site. Science. 1993 Dec 24;262(5142):1982–1988. [PubMed]
  • Li B, Vilardell J, Warner JR. An RNA structure involved in feedback regulation of splicing and of translation is critical for biological fitness. Proc Natl Acad Sci U S A. 1996 Feb 20;93(4):1596–1600. [PMC free article] [PubMed]
  • Libri D, Stutz F, McCarthy T, Rosbash M. RNA structural patterns and splicing: molecular basis for an RNA-based enhancer. RNA. 1995 Jun;1(4):425–436. [PMC free article] [PubMed]
  • Lisowsky T. Removal of an intron with unique 3' branch site creates an amino-terminal protein sequence directing the scERV1 gene product to mitochondria. Yeast. 1996 Dec;12(15):1501–1510. [PubMed]
  • Logghe M, Molemans F, Fiers W, Contreras R. The two genes encoding yeast ribosomal protein S8 reside on different chromosomes, and are closely linked to the hsp70 stress protein genes SSA3 and SSA4. Yeast. 1994 Aug;10(8):1093–1100. [PubMed]
  • Long M, de Souza SJ, Gilbert W. The yeast splice site revisited: new exon consensus from genomic analysis. Cell. 1997 Dec 12;91(6):739–740. [PubMed]
  • Louis EJ, Haber JE. The structure and evolution of subtelomeric Y' repeats in Saccharomyces cerevisiae. Genetics. 1992 Jul;131(3):559–574. [PMC free article] [PubMed]
  • Luca FC, Winey M. MOB1, an essential yeast gene required for completion of mitosis and maintenance of ploidy. Mol Biol Cell. 1998 Jan;9(1):29–46. [PMC free article] [PubMed]
  • Luukkonen BG, Séraphin B. The role of branchpoint-3' splice site spacing and interaction between intron terminal nucleotides in 3' splice site selection in Saccharomyces cerevisiae. EMBO J. 1997 Feb 17;16(4):779–792. [PMC free article] [PubMed]
  • Malone RE, Pittman DL, Nau JJ. Examination of the intron in the meiosis-specific recombination gene REC114 in Saccharomyces. Mol Gen Genet. 1997 Jul;255(4):410–419. [PubMed]
  • Miller AM. The yeast MATa1 gene contains two introns. EMBO J. 1984 May;3(5):1061–1065. [PMC free article] [PubMed]
  • Mitra G, Warner JR. A yeast ribosomal protein gene whose intron is in the 5' leader. J Biol Chem. 1984 Jul 25;259(14):9218–9224. [PubMed]
  • Mizuta K, Hashimoto T, Otaka E. Yeast ribosomal proteins: XIII. Saccharomyces cerevisiae YL8A gene, interrupted with two introns, encodes a homolog of mammalian L7. Nucleic Acids Res. 1992 Mar 11;20(5):1011–1016. [PMC free article] [PubMed]
  • Mizuta K, Hashimoto T, Otaka E. The evolutionary relationships between homologs of ribosomal YL8 protein and YL8-like proteins. Curr Genet. 1995 Jun;28(1):19–25. [PubMed]
  • Myslinski E, Ségault V, Branlant C. An intron in the genes for U3 small nucleolar RNAs of the yeast Saccharomyces cerevisiae. Science. 1990 Mar 9;247(4947):1213–1216. [PubMed]
  • Nam K, Hudson RH, Chapman KB, Ganeshan K, Damha MJ, Boeke JD. Yeast lariat debranching enzyme. Substrate and sequence specificity. J Biol Chem. 1994 Aug 12;269(32):20613–20621. [PubMed]
  • Newman A. Specific accessory sequences in Saccharomyces cerevisiae introns control assembly of pre-mRNAs into spliceosomes. EMBO J. 1987 Dec 1;6(12):3833–3839. [PMC free article] [PubMed]
  • O'Keefe RT, Norman C, Newman AJ. The invariant U5 snRNA loop 1 sequence is dispensable for the first catalytic step of pre-mRNA splicing in yeast. Cell. 1996 Aug 23;86(4):679–689. [PubMed]
  • Parker R, Guthrie C. A point mutation in the conserved hexanucleotide at a yeast 5' splice junction uncouples recognition, cleavage, and ligation. Cell. 1985 May;41(1):107–118. [PubMed]
  • Patterson B, Guthrie C. A U-rich tract enhances usage of an alternative 3' splice site in yeast. Cell. 1991 Jan 11;64(1):181–187. [PubMed]
  • Philippsen P, Stotz A, Scherf C. DNA of Saccharomyces cerevisiae. Methods Enzymol. 1991;194:169–182. [PubMed]
  • Portman DS, O'Connor JP, Dreyfuss G. YRA1, an essential Saccharomyces cerevisiae gene, encodes a novel nuclear protein with RNA annealing activity. RNA. 1997 May;3(5):527–537. [PMC free article] [PubMed]
  • Qu LH, Henry Y, Nicoloso M, Michot B, Azum MC, Renalier MH, Caizergues-Ferrer M, Bachellerie JP. U24, a novel intron-encoded small nucleolar RNA with two 12 nt long, phylogenetically conserved complementarities to 28S rRNA. Nucleic Acids Res. 1995 Jul 25;23(14):2669–2676. [PMC free article] [PubMed]
  • Rain JC, Legrain P. In vivo commitment to splicing in yeast involves the nucleotide upstream from the branch site conserved sequence and the Mud2 protein. EMBO J. 1997 Apr 1;16(7):1759–1771. [PMC free article] [PubMed]
  • Reiss G, te Heesen S, Gilmore R, Zufferey R, Aebi M. A specific screen for oligosaccharyltransferase mutations identifies the 9 kDa OST5 protein required for optimal activity in vivo and in vitro. EMBO J. 1997 Mar 17;16(6):1164–1172. [PMC free article] [PubMed]
  • Rodriguez-Medina JR, Rymond BC. Prevalence and distribution of introns in non-ribosomal protein genes of yeast. Mol Gen Genet. 1994 Jun 3;243(5):532–539. [PubMed]
  • Rothstein R. Targeting, disruption, replacement, and allele rescue: integrative DNA transformation in yeast. Methods Enzymol. 1991;194:281–301. [PubMed]
  • Ruskin B, Green MR. An RNA processing activity that debranches RNA lariats. Science. 1985 Jul 12;229(4709):135–140. [PubMed]
  • Ruskin B, Green MR. RNA lariat debranching enzyme as tool for analyzing RNA structure. Methods Enzymol. 1990;181:180–188. [PubMed]
  • Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlich HA. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science. 1988 Jan 29;239(4839):487–491. [PubMed]
  • Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. [PMC free article] [PubMed]
  • Schneider JC, Guarente L. The untranslated leader of nuclear COX4 gene of Saccharomyces cerevisiae contains an intron. Nucleic Acids Res. 1987 Apr 24;15(8):3515–3529. [PMC free article] [PubMed]
  • Séraphin B, Kretzner L, Rosbash M. A U1 snRNA:pre-mRNA base pairing interaction is required early in yeast spliceosome assembly but does not uniquely define the 5' cleavage site. EMBO J. 1988 Aug;7(8):2533–2538. [PMC free article] [PubMed]
  • Séraphin B, Rosbash M. Mutational analysis of the interactions between U1 small nuclear RNA and pre-mRNA of yeast. Gene. 1989 Oct 15;82(1):145–151. [PubMed]
  • Séraphin B, Rosbash M. Exon mutations uncouple 5' splice site selection from U1 snRNA pairing. Cell. 1990 Nov 2;63(3):619–629. [PubMed]
  • Siliciano PG, Guthrie C. 5' splice site selection in yeast: genetic alterations in base-pairing with U1 reveal additional requirements. Genes Dev. 1988 Oct;2(10):1258–1267. [PubMed]
  • Smith CW, Chu TT, Nadal-Ginard B. Scanning and competition between AGs are involved in 3' splice site selection in mammalian introns. Mol Cell Biol. 1993 Aug;13(8):4939–4952. [PMC free article] [PubMed]
  • Staley JP, Guthrie C. Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell. 1998 Feb 6;92(3):315–326. [PubMed]
  • Stearns T, Hoyt MA, Botstein D. Yeast mutants sensitive to antimicrotubule drugs define three genes that affect microtubule function. Genetics. 1990 Feb;124(2):251–262. [PMC free article] [PubMed]
  • Teigelkamp S, Newman AJ, Beggs JD. Extensive interactions of PRP8 protein with the 5' and 3' splice sites during splicing suggest a role in stabilization of exon alignment by U5 snRNA. EMBO J. 1995 Jun 1;14(11):2602–2612. [PMC free article] [PubMed]
  • Thompson-Jäger S, Domdey H. Yeast pre-mRNA splicing requires a minimum distance between the 5' splice site and the internal branch acceptor site. Mol Cell Biol. 1987 Nov;7(11):4010–4016. [PMC free article] [PubMed]
  • Uemura H, Pandit S, Jigami Y, Sternglanz R. Mutations in GCR3, a gene involved in the expression of glycolytic genes in Saccharomyces cerevisiae, suppress the temperature-sensitive growth of hpr1 mutants. Genetics. 1996 Apr;142(4):1095–1103. [PMC free article] [PubMed]
  • Umen JG, Guthrie C. The second catalytic step of pre-mRNA splicing. RNA. 1995 Nov;1(9):869–885. [PMC free article] [PubMed]
  • Vilardell J, Warner JR. Ribosomal protein L32 of Saccharomyces cerevisiae influences both the splicing of its own transcript and the processing of rRNA. Mol Cell Biol. 1997 Apr;17(4):1959–1965. [PMC free article] [PubMed]
  • Villa T, Ceradini F, Presutti C, Bozzoni I. Processing of the intron-encoded U18 small nucleolar RNA in the yeast Saccharomyces cerevisiae relies on both exo- and endonucleolytic activities. Mol Cell Biol. 1998 Jun;18(6):3376–3383. [PMC free article] [PubMed]
  • Vincent A, Liebman SW. The yeast omnipotent suppressor SUP46 encodes a ribosomal protein which is a functional and structural homolog of the Escherichia coli S4 ram protein. Genetics. 1992 Oct;132(2):375–386. [PMC free article] [PubMed]
  • Wilson W, Malim MH, Mellor J, Kingsman AJ, Kingsman SM. Expression strategies of the yeast retrotransposon Ty: a short sequence directs ribosomal frameshifting. Nucleic Acids Res. 1986 Sep 11;14(17):7001–7016. [PMC free article] [PubMed]
  • Woolford JL., Jr Nuclear pre-mRNA splicing in yeast. Yeast. 1989 Nov-Dec;5(6):439–457. [PubMed]
  • Zavanelli MI, Ares M., Jr Efficient association of U2 snRNPs with pre-mRNA requires an essential U2 RNA structural element. Genes Dev. 1991 Dec;5(12B):2521–2533. [PubMed]
  • Zhang X, Schwer B. Functional and physical interaction between the yeast splicing factors Slu7 and Prp18. Nucleic Acids Res. 1997 Jun 1;25(11):2146–2152. [PMC free article] [PubMed]

Articles from RNA are provided here courtesy of The RNA Society

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...