Genome-wide study of NAGNAG alternative splicing in Arabidopsis

Planta

Volumn 239, Issue 1, 2014, Pages 127-138

  Shi, Yanjing ^a   Sha, Guangli ^b   Sun, Xiaoyong ^c  

^a QINGDAO UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^b Qingdao Academy of Agricultural Sciences   (China)

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

Author keywords

"Fine tune" mechanism; Alternative acceptor site; Nomenclature tree; RNA Seq

Indexed keywords

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ALTERNATIVE RNA SPLICING; ARABIDOPSIS; ARTICLE; EXON; EXPRESSED SEQUENCE TAG; GENE EXPRESSION REGULATION; GENE ONTOLOGY; GENETIC ASSOCIATION; GENETICS; MICROBIOLOGY; PLANT GENOME; RNA SPLICING;

3' UNTRANSLATED REGIONS; 5' UNTRANSLATED REGIONS; ALTERNATIVE SPLICING; ARABIDOPSIS; EXONS; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION REGULATION, PLANT; GENE ONTOLOGY; GENOME, PLANT; GENOME-WIDE ASSOCIATION STUDY; RNA SPLICE SITES;

EID: 84891599115     PISSN: 00320935     EISSN: 14322048     Source Type: Journal    
DOI: 10.1007/s00425-013-1965-2     Document Type: Article

References (36)

1. Akerman M, Mandel-Gutfreund Y (2006) Alternative splicing regulation at tandem 3′ splice sites. Nucleic Acids Res 34: 23-31.
2. Bradley RK, Merkin J, Lambert NJ, Burge CB (2012) Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution. PLoS Biol 10: e1001229.
3. Busch A, Hertel KJ (2012) Extensive regulation of NAGNAG alternative splicing: new tricks for the spliceosome? Genome Biol 13: 143.
4. Campbell MA, Haas BJ, Hamilton JP, Mount SM, Buell CR (2006) Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. BMC Genomics 7: 327.
5. Chamary JV, Hurst LD (2005) Biased codon usage near intron-exon junctions: selection on splicing enhancers, splice-site recognition or something else? Trends Genet 21: 256-259.
6. Chern TM, van Nimwegen E, Kai C, Kawai J, Carninci P, Hayashizaki Y, Zavolan M (2006) A simple physical model predicts small exon length variations. PLoS Genet 2: e45.
7. Condorelli G, Bueno R, Smith RJ (1994) Two alternatively spliced forms of the human insulin-like growth factor I receptor have distinct biological activities and internalization kinetics. J Biol Chem 269: 8510-8516.
8. Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14: 1188-1190.
9. Fox-Walsh KL, Dou Y, Lam BJ, Hung SP, Baldi PF, Hertel KJ (2005) The architecture of pre-mRNAs affects mechanisms of splice-site pairing. Proc Natl Acad Sci USA 102: 16176-16181.
10. Galante PA, Sakabe NJ, Kirschbaum-Slager N, de Souza SJ (2004) Detection and evaluation of intron retention events in the human transcriptome. RNA 10: 757-765.
11. Hiller M, Huse K, Szafranski K, Jahn N, Hampe J, Schreiber S, Backofen R, Platzer M (2004) Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity. Nat Genet 36: 1255-1257.
12. Hiller M, Szafranski K, Backofen R, Platzer M (2006a) Alternative splicing at NAGNAG acceptors: simply noise or noise and more? PLoS Genet 2: e207.
13. Hiller M, Huse K, Szafranski K, Rosenstiel P, Schreiber S, Backofen R, Platzer M (2006b) Phylogenetically widespread alternative splicing at unusual GYNGYN donors. Genome Biol 7: R65.
14. Hiller M, Szafranski K, Huse K, Backofen R, Platzer M (2008) Selection against tandem splice sites affecting structured protein regions. BMC Evol Biol 8: 89.
15. Hu Z, Ma B, Wolfson H, Nussinov R (2000) Conservation of polar residues as hot spots at protein interfaces. Proteins 39: 331-342.
16. Huang DW, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nature Protoc 4: 44-57.
17. Leinonen R, Sugawara H, Shumway M (2011) The sequence read archive. Nucleic Acids Res 39(Suppl 1): D19-D21.
18. Li L, Howe GA (2001) Alternative splicing of prosystemin pre-mRNA produces two isoforms that are active as signals in the wound response pathway. Plant Mol Biol 46: 409-419.
19. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) 1000 Genome Project Data Processing Subgroup (2009) The sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25: 2078-2079.
20. Lorkovic ZJ, Lehner R, Forstner C, Barta A (2005) Evolutionary conservation of minor U12-type spliceosome between plants and humans. RNA 11: 1095-1107.
21. Maugeri A, van Driel MA, van de Pol DJ, Klevering BJ, van Haren FJ, Tijmes N, Bergen AA, Rohrschneider K et al (1999) The 2588G->C mutation in the ABCR gene is a mild frequent founder mutation in the Western European population and allows the classification of ABCR mutations in patients with Stargardt disease. Am J Hum Genet 64: 1024-1035.
22. McGuire AM, Pearson MD, Neafsey DE, Galagan JE (2008) Cross-kingdom patterns of alternative splicing and splice recognition. Genome Biol 9: R50.
23. Morgan M, Pagès H (2012) Rsamtools: binary alignment (BAM), variant call (BCF), or tabix file import. R package version 1. 6. 3. http://bioconductor. org/packages/release/bioc/html/Rsamtools. html.
24. Pages H, Aboyoun P, Lawrence M (2012a) IRanges: infrastructure for manipulating intervals on sequences. R package version 1. 12. 6.
25. Pages H, Aboyoun P, Gentleman R, DebRoy S (2012) Biostrings: String objects representing biological sequences, and matching algorithms. R package version 2. 22. 0.
26. Schindler S, Szafranski K, Hiller M, Ali GS, Palusa SG, Backofen R, Platzer M, Reddy AS (2008) Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes. BMC Genomics 9: 159.
27. Sinha R, Nikolajewa S, Szafranski K, Hiller M, Jahn N, Huse K, Platzer M, Backofen R (2009) Accurate prediction of NAGNAG alternative splicing. Nucleic Acids Res 37: 3569-3579.
28. Sinha R, Zimmer AD, Bolte K, Lang D, Reski R, Platzer M, Rensing SA, Backofen R (2010) Identification and characterization of NAGNAG alternative splicing in the moss Physcomitrella patens. BMC Plant Biol 10: 76.
29. Smyth GK (2005) Limma: linear models for microarray data. In: Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W (eds) Bioinformatics and computational biology solutions using R and Bioconductor. Springer, New York, pp 397-420.
30. Sugnet CW, Kent WJ, Ares M Jr, Haussler D (2004) Transcriptome and genome conservation of alternative splicing events in humans and mice. Pacific Symp Biocomput 9: 66-77.
31. Tadokoro K, Yamazaki-Inoue M, Tachibana M, Fujishiro M, Nagao K, Toyoda M, Ozaki M, Ono M et al (2005) Frequent occurrence of protein isoforms with or without a single amino acid residue by subtle alternative splicing: the case of Gln in DRPLA affects subcellular localization of the products. J Hum Genet 50: 382-394.
32. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111.
33. Tsai KW, Lin WC (2006) Quantitative analysis of wobble splicing indicates that it is not tissue specific. Genomics 88: 855-864.
34. Vogan KJ, Underhill DA, Gros P (1996) An alternative splicing event in the Pax-3 paired domain identifies the linker region as a key determinant of paired domain DNA-binding activity. Mol Cell Biol 16: 6677-6686.
35. Walenz B, Florea L (2011) Sim4db and leaff: utilities for fast batch spliced alignment and sequence indexing. Bioinformatics 27: 1869-1870.
36. Zhou FX, Merianos HJ, Brunger AT, Engelman DM (2001) Polar residues drive association of polyleucine transmembrane helices. Proc Natl Acad Sci USA 98: 2250-2255.