Table of Contents Author Guidelines Submit a Manuscript
BioMed Research International
Volume 2014, Article ID 736798, 7 pages
http://dx.doi.org/10.1155/2014/736798
Research Article

Computational Evidence of NAGNAG Alternative Splicing in Human Large Intergenic Noncoding RNA

1Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, Shandong 271018, China
2Biomedical Informatics Research Center, Marshfield Clinic Research Foundation, Marshfield, WI 54449, USA
3Affiliated Hospital of Shandong University of Traditional Chinese Medicine, No. 42 Wenhua West Road, Jinan, Shandong 250011, China

Received 4 February 2014; Revised 8 May 2014; Accepted 21 May 2014; Published 5 June 2014

Academic Editor: Shiwei Duan

Copyright © 2014 Xiaoyong Sun et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. R. K. Bradley, J. Merkin, N. J. Lambert, and C. B. Burge, “Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution,” PLoS Biology, vol. 10, no. 1, Article ID e1001229, 2012. View at Publisher · View at Google Scholar · View at Scopus
  2. L. Li and G. A. Howe, “Alternative splicing of prosystemin pre-mRNA produces two isoforms that are active as signals in the wound response pathway,” Plant Molecular Biology, vol. 46, no. 4, pp. 409–419, 2001. View at Publisher · View at Google Scholar · View at Scopus
  3. M. Hiller, K. Huse, K. Szafranski et al., “Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity,” Nature Genetics, vol. 36, no. 12, pp. 1255–1257, 2004. View at Google Scholar · View at Scopus
  4. C. W. Sugnet, W. J. Kent, M. Ares Jr., and D. Haussler, “Transcriptome and genome conservation of alternative splicing events in humans and mice,” Pacific Symposium on Biocomputing, pp. 66–77, 2004. View at Google Scholar · View at Scopus
  5. K. W. Tsai and W. C. Lin, “Quantitative analysis of wobble splicing indicates that it is not tissue specific,” Genomics, vol. 88, no. 6, pp. 855–864, 2006. View at Publisher · View at Google Scholar · View at Scopus
  6. T. Chern, E. van Nimwegen, C. Kai et al., “A simple physical model predicts small exon length variations,” PLoS Genetics, vol. 2, no. 4, article e45, 2006. View at Publisher · View at Google Scholar · View at Scopus
  7. K. Iida, M. Shionyu, and Y. Suso, “Alternative splicing at NAGNAG acceptor sites shares common properties in land plants and mammals,” Molecular Biology and Evolution, vol. 25, no. 4, pp. 709–718, 2008. View at Publisher · View at Google Scholar · View at Scopus
  8. R. Sinha, S. Nikolajewa, K. Szafranski et al., “Accurate prediction of NAGNAG alternative splicing,” Nucleic Acids Research, vol. 37, no. 11, pp. 3569–3579, 2009. View at Publisher · View at Google Scholar · View at Scopus
  9. R. Sinha, A. D. Zimmer, K. Bolte et al., “Identification and characterization of NAGNAG alternative splicing in the moss Physcomitrella patens,” BMC Plant Biology, vol. 10, article 76, 2010. View at Publisher · View at Google Scholar · View at Scopus
  10. G. Condorelli, R. Bueno, and R. J. Smith, “Two alternatively spliced forms of the human insulin-like growth factor I receptor have distinct biological activities and internalization kinetics,” The Journal of Biological Chemistry, vol. 269, no. 11, pp. 8510–8516, 1994. View at Google Scholar · View at Scopus
  11. K. Tadokoro, M. Yamazaki-Inoue, M. Tachibana et al., “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,” Journal of Human Genetics, vol. 50, no. 8, pp. 382–394, 2005. View at Publisher · View at Google Scholar · View at Scopus
  12. K. J. Vogan, D. A. Underhill, and P. Gros, “An alternative splicing event in the Pax-3 paired domain identifies the linker region as a key determinant of paired domain DNA-binding activity,” Molecular and Cellular Biology, vol. 16, no. 12, pp. 6677–6686, 1996. View at Google Scholar · View at Scopus
  13. Z. J. Lorković, R. Lehner, C. Forstner, and A. Barta, “Evolutionary conservation of minor U12-type spliceosome between plants and humans,” RNA, vol. 11, no. 7, pp. 1095–1107, 2005. View at Publisher · View at Google Scholar · View at Scopus
  14. M. Hiller, K. Szafranski, K. Huse, R. Backofen, and M. Platzer, “Selection against tandem splice sites affecting structured protein regions,” BMC Evolutionary Biology, vol. 8, no. 1, article 89, 2008. View at Publisher · View at Google Scholar · View at Scopus
  15. A. Maugeri, M. A. van Driel, D. J. R. van de Pol et al., “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,” The American Journal of Human Genetics, vol. 64, no. 4, pp. 1024–1035, 1999. View at Publisher · View at Google Scholar · View at Scopus
  16. L. Hui, X. Zhang, X. Wu et al., “Identification of alternatively spliced mRNA variants related to cancers by genome-wide ESTs alignment,” Oncogene, vol. 23, no. 17, pp. 3013–3023, 2004. View at Publisher · View at Google Scholar · View at Scopus
  17. P. Kapranov, A. T. Willingham, and T. R. Gingeras, “Genome-wide transcription and the implications for genomic organization,” Nature Reviews Genetics, vol. 8, no. 6, pp. 413–423, 2007. View at Publisher · View at Google Scholar · View at Scopus
  18. Y. Shi, G. Sha, and X. Sun, “Genome-wide study of NAGNAG alternative splicing in Arabidopsis,” Planta, vol. 239, no. 1, pp. 127–138, 2014. View at Publisher · View at Google Scholar
  19. C. Lee and Q. Wang, “Bioinformatics analysis of alternative splicing,” Briefings in Bioinformatics, vol. 6, no. 1, pp. 23–33, 2005. View at Publisher · View at Google Scholar · View at Scopus
  20. M. Cabili, C. Trapnell, L. Goff et al., “Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses,” Genes and Development, vol. 25, no. 18, pp. 1915–1927, 2011. View at Publisher · View at Google Scholar · View at Scopus
  21. C. Trapnell, L. Pachter, and S. L. Salzberg, “TopHat: discovering splice junctions with RNA-Seq,” Bioinformatics, vol. 25, no. 9, pp. 1105–1111, 2009. View at Publisher · View at Google Scholar · View at Scopus
  22. H. Li, B. Handsaker, A. Wysoker et al., “The sequence alignment/map format and SAMtools,” Bioinformatics, vol. 25, no. 16, pp. 2078–2079, 2009. View at Publisher · View at Google Scholar · View at Scopus
  23. A. Ameur, A. Wetterbom, L. Feuk, and U. Gyllensten, “Global and unbiased detection of splice junctions from RNA-seq data,” Genome Biology, vol. 11, no. 3, article R34, 2010. View at Publisher · View at Google Scholar · View at Scopus
  24. J. W. Nam and D. P. Bartel, “Long noncoding RNAs in C. elegans,” Genome Research, vol. 22, no. 12, pp. 2529–2540, 2012. View at Publisher · View at Google Scholar · View at Scopus
  25. G. E. Crooks, G. Hon, J. M. Chandonia, and S. E. Brenner, “WebLogo: a sequence logo generator,” Genome Research, vol. 14, no. 6, pp. 1188–1190, 2004. View at Publisher · View at Google Scholar · View at Scopus
  26. E. L. Huttlin, M. P. Jedrychowski, J. E. Elias et al., “A tissue-specific atlas of mouse protein phosphorylation and expression,” Cell, vol. 143, no. 7, pp. 1174–1189, 2010. View at Publisher · View at Google Scholar · View at Scopus
  27. M. Akerman and Y. Mandel-Gutfreund, “Alternative splicing regulation at tandem 3′ splice sites,” Nucleic Acids Research, vol. 34, no. 1, pp. 23–31, 2006. View at Publisher · View at Google Scholar · View at Scopus
  28. T. R. Mercer, M. E. Dinger, and J. S. Mattick, “Long non-coding RNAs: insights into functions,” Nature Reviews Genetics, vol. 10, no. 3, pp. 155–159, 2009. View at Publisher · View at Google Scholar · View at Scopus
  29. K. L. Fox-Walsh, Y. Dou, B. J. Lam, S. Hung, P. F. Baldi, and K. J. Hertel, “The architecture of pre-mRNAs affects mechanisms of splice-site pairing,” Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 45, pp. 16176–16181, 2005. View at Publisher · View at Google Scholar · View at Scopus
  30. T. Derrien, R. Johnson, G. Bussotti et al., “The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression,” Genome Research, vol. 22, no. 9, pp. 1775–1789, 2012. View at Publisher · View at Google Scholar · View at Scopus