Analysis of a splice array experiment elucidates roles of chromatin elongation factor Spt4-5 in splicing

PLoS Computational Biology

Volumn 1, Issue 4, 2005, Pages 0276-0288

  Xiao, Yuanyuan ^a   Yang, Yee H ^a   Burckin, Todd A ^b   Shiue, Lily ^b   Hartzog, Grant A ^b   Segal, Mark R ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHIPS; GENE EXPRESSION REGULATION; GENOME; INDIUM COMPOUNDS; POLYMERASE CHAIN REACTION; STATISTICS; YEAST;

DNA MICROARRAY; ELONGATION FACTOR; FUNCTIONAL LINKS; GENES EXPRESSION; GENOMICS; HYBRIDISATION; ROBUST MODELING; STATISTIC MODELING; WILD TYPES; YEAST SACCHAROMYCES CEREVISIAE;

TRANSCRIPTION;

MESSENGER RNA; NONHISTONE PROTEIN; NUCLEAR PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN; SPT4 PROTEIN, S CEREVISIAE; SPT5 TRANSCRIPTIONAL ELONGATION FACTOR; TRANSCRIPTION ELONGATION FACTOR;

ARTICLE; BIOLOGICAL MODEL; CHROMATIN; DNA MICROARRAY; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; METABOLISM; MUTATION; RNA SPLICING; SACCHAROMYCES CEREVISIAE;

CHROMATIN; CHROMOSOMAL PROTEINS, NON-HISTONE; DATABASES, GENETIC; GENE EXPRESSION REGULATION, FUNGAL; MODELS, GENETIC; MUTATION; NUCLEAR PROTEINS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA SPLICING; RNA, MESSENGER; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTIONAL ELONGATION FACTORS;

EID: 55449110096     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0010039     Document Type: Article

References (45)

1. Maniatis T, Task B (2002) Alternative pre-mRNA splicing and proteome expansion in metazoans. Nature 418: 236-243.
2. Maniatis T, Reed R (2002) An extensive network of coupling among gene expression machines. Nature 416: 499-506.
3. Proudfoot NJ, Furger A, Dye MJ (2002) Integrating mRNA processing with transcription. Cell 108: 501-512.
4. Burckin TA, Nagel R, Mandel-Gutfreund Y, Shiue L, Clark TA, et al. (2005) Exploring functional relationships between components of the transcription, splicing and mRNA export machinery by gene expression machinery. Nat Struct Mol Biol 12: 175-182.
5. Schwer B, Shuman S (1996) Conditional inactivation of mRNA capping enzyme affects yeast pre-mRNA splicing in vivo. RNA 2: 574-583.
6. Fresco LD, Buratowski S (1996) Conditional mutants of the yeast mRNA capping enzyme show that the cap enhances, but is not required for, mRNA splicing. RNA 2: 584-596.
7. Howe KJ, Kane CM, Ares M Jr. (2003) Perturbation of transcription elongation influences the fidelity of internal exon inclusion in Saccharomyces cerevisiae. RNA 9: 993-1006.
8. de la Mata M, Alonso CR, Kadener S, Fededa JP, Blaustein M, et al. (2003) A slow RNA ploymerase II affects alternative splicing in vivo. Mol Cell 12: 525-532.
9. Fehlbaum P, Guihal C, Bracco L, Cochet O (2005) A microarray configuration to quantify expression levels and relative abundance of splice variants. Nucleic Acids Res 33: e47.
10. Johnson JM, Castle J, Garrett-Engele P, Kan Z, Loerch PM, et al. (2003) Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science 302: 2141-2144.
11. Pan Q, Shai O, Misquitta C, Zhang W, Saltzman AL, et al. (2004) Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Mol Cell 16: 929-941.
12. Barrass JD, Beggs JD (2003) Splicing goes global. Trends Genet 19: 295-298.
13. Lopez PJ, Seraphin B (1999) Genomic-scale quantitative analysis of yeast pre-mRNA splicing: Implications for splice-site recognition. RNA 5: 1135-1137.
14. Ares M Jr., Grate L, Pauling MH (1999) A handful of intron-containing genes produces the lion's share of yeast mRNA. RNA 5: 1138-1139.
15. Clark TA, Sugnet CW, Ares M Jr. (2002) Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays. Science 296: 907-910.
16. Hartzog GA, Speer JL, Lindstrom DL (2002) Transcript elongation on a nucleoprotein template. Biochim Biophys Acta 1577: 276-286.
17. Lindstrom DL, Squazzo SL, Muster N, Burckin TA, Wachter KC, et al. (2003) Dual roles for Spt5 in pre-mRNA processing and transcription elongation revealed by identification of Spt5-associated proteins. Mol Cell Biol 23: 1368-1378.
18. Pei Y, Shuman S (2002) Interactions between fission yeast mRNA capping enzymes and elongation factor Spt5. J Biol Chem 277: 19639-19648.
19. Wen Y, Shatkin AJ (1999) Transcription elongation factor hSPT5 stimulates mRNA capping. Genes Dev 13: 1774-1779.
20. Mandai SS, Chu C, Wada T, Handa H, Shatkin AJ, et al. (2004) Functional interactions of RNA-capping enzyme with factors that positively and negatively regulate promoter escape by RNA polymerase II. Proc Natl Acad Sci U S A 101: 7572-7577.
21. Dudoit S, Yang YH, Callow MJ, Speed TP (2002) Statistical methods for indentifying differentially expressed genes in replicated cDNA microarray experiments. Statistica Sinica 12: 111-139.
22. Kerr MK, Martin M, Churchill GA (2000) Analysis of variance for gene expression microarray data. J Comput Biol 7: 819-837.
23. Wolfinger RD, Gibson G, Wolfinger ED, Bennett L, Hamadeh H, et al. (2001) Assessing gene significance from cDNA microarray expression data via mixed models. J Comput Biol 8: 625-637.
24. Efron E, Tibshirani R, Storey J, Tusher VG (2001) Empirical bayes analysis of a microarray experiment. J Am Stat Assoc 96: 1151-1160.
25. Lee ML, Lu W, Whitmore GA, Beier D (2002) Models for microarray gene expression data. J Biopharm Stat 12: 1-19.
26. Newton MA, Kendziorski CM, Richmond CS, Blattner FR, Tsui KW (2001) On differential variability of expression ratios: Improving statistical inference about gene expression changes from microarray data. J Comput Biol 8: 37-52.
27. Kendziorski CM, Newton MA, Lan H, Gould MN (2003) On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles. Stat Med 22: 3899-3914.
28. Lönnstedt I, Speed TP (2001) Replicated microarray data. Statistica Sinica 12: 31-46.
29. Smyth GK (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3: Article 3.
30. Baldi P, Long AD (2001) A Bayesian framework for the analysis of microarray expression data: Regularized t-test and statistical inferences of gene changes. Bioinformatics 17: 509-519.
31. Newton MA, Noueiry A, Sarkar D, Ahlquist P (2004) Detecting differential gene expression with a semiparametric hierarchical mixture method. Biostatistics 5: 155-176.
32. Yang YH, Xiao Y, Segal MR (2005) Identifying differentially expressed genes from microarray experiments via statistic synthesis. Bioinformatics 21: 1084-1093.
33. Hartzog GA, Wada T, Handa H, Winston F (1998) Evidence that Spt4, Spt5, and Spt6 control transcription elongation by RNA polymerase II in Saccharomyces cerevisiae. Genes Dev 12: 357-369.
34. Chen Y, Dougherty ER, Bittner ML (1997) Ratio-based decisions and the quantitative analysis of cDNA microarray images. J Biomed Opt 2: 364-374.
35. Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 98: 5116-5121.
36. Spingola M, Grate L, Haussler D, Ares M Jr. (1999) Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae. RNA 5: 221-234.
37. Wade JT, Hall DB, Struhl K (2004) The transcription factor Ifh1 is a key regulator of yeast ribosomal protein genes. Nature 432: 1054-1058.
38. Lindstrom DL, Hartzog GA (2001) Genetic interactions of Spt4-Spt5 and TFIIS with the RNA polymerase II CTD and CTD modifying enzymes in Saccharomyces cerevisiae. Genetics 159: 487-497.
39. Kim DK, InuKai N, Yamada T, Furuya A, Sato H, et al. (2003) Structure-function analysis of human Spt4: Evidence that hSpt4 and hSpt5 exert their roles in transcriptional elongation as parts of the DSIF complex. Genes Cells 8: 371-378.
40. Nogues G, Kadener S, Cramer P, de la Mata M, Fededa JP, et al. (2003) Control of alternative pre-mRNA splicing by RNA Pol II elongation: Faster is not always better. IUBMB Life 55: 235-241.
41. Winston F, Dollard C, Ricupero-Hovasse SL (1995) Construction of a set of convenient Saccharomyces cerevisiae strains that are isogenic to S288C. Yeast 11: 53-55.
42. Zavanelli MI, Ares M Jr. (1991) Efficient association of U2 snRNPs with pre-mRNA requires an essential U2 RNA structural element. Genes Dev 5: 2521-2533.
43. Yang YH, Dudoit S, Luu P, Lin DM, Peng V, et al. (2002) Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 30: e15.
44. Holstege FC, Jennings EG, Wyrick JJ, Lee TI, Hengartner CJ, et al. (1998) Dissecting the regulatory circuitry of aeukaryotic genome. Cell 95: 717-728.
45. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, et al. (2003) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31: e15.