Nested introns in an intron: Evidence of multi-step splicing in a large intron of the human dystrophin pre-mRNA

FEBS Letters

Volumn 587, Issue 6, 2013, Pages 555-561

  Suzuki, Hitoshi ^a   Kameyama, Toshiki ^b   Ohe, Kenji ^b   Tsukahara, Toshifumi ^a   Mayeda, Akila ^b  

^a JAPAN ADVANCED INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

^b FUJITA HEALTH UNIVERSITY   (Japan)

Author keywords

Dystrophin gene; Large intron; Nested intron; Nested splicing; RNase R; Splicing

Indexed keywords

DYSTROPHIN; EXORIBONUCLEASE; MESSENGER RNA PRECURSOR; RNA;

ARTICLE; GENE SEQUENCE; HUMAN; HUMAN CELL; INTRON; MUSCLE CELL; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SPLICING;

DYSTROPHIN; EXORIBONUCLEASES; HUMANS; INTRONS; MOLECULAR SEQUENCE DATA; PLASMIDS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA PRECURSORS; RNA SPLICE SITES; RNA SPLICING;

EID: 84875230031     PISSN: 00145793     EISSN: 18733468     Source Type: Journal    
DOI: 10.1016/j.febslet.2013.01.057     Document Type: Article

References (28)

1. M.K. Sakharkar, B.S. Perumal, K.R. Sakharkar, and P. Kangueane An analysis on gene architecture in human and mouse genomes In Silico Biol. 5 2005 347 365
2. L. Zhu, Y. Zhang, W. Zhang, S. Yang, J.Q. Chen, and D. Tian Patterns of exon-intron architecture variation of genes in eukaryotic genomes BMC Genomics 10 2009 47
3. N. Sasaki-Haraguchi, M.K. Shimada, I. Taniguchi, M. Ohno, and A. Mayeda Mechanistic insights into human pre-mRNA splicing of human ultra-short introns: potential unusual mechanism identifies G-rich introns Biochem. Biophys. Res. Commun. 423 2012 289 294
4. T. Kameyama, H. Suzuki, and A. Mayeda Re-splicing of mature mRNA in cancer cells promotes activation of distant weak alternative splice sites Nucleic Acids Res. 40 2012 7896 7906
5. A.J. Matlin, and M.J. Moore Spliceosome assembly and composition Adv. Exp. Med. Biol. 623 2007 14 35
6. C.L. Will, and R. Lührmann Spliceosome structure and function Cold Spring Harb. Perspect. Biol. 3 2011 a003707
7. M.J. Dye, N. Gromak, and N.J. Proudfoot Exon tethering in transcription by RNA polymerase II Mol. Cell 21 2006 849 859
8. N. Fong, M. Ohman, and D.L. Bentley Fast ribozyme cleavage releases transcripts from RNA polymerase II and aborts co-transcriptional pre-mRNA processing Nat. Struct. Mol. Biol. 16 2009 916 922
9. A.R. Hatton, V. Subramaniam, and A.J. Lopez Generation of alternative Ultrabithorax isoforms and stepwise removal of a large intron by resplicing at exon-exon junctions Mol. Cell 2 1998 787 796
10. J.M. Burnette, E. Miyamoto-Sato, M.A. Schaub, J. Conklin, and A.J. Lopez Subdivision of large introns in Drosophila by recursive splicing at nonexonic elements Genetics 170 2005 661 674
11. J. Singh, and R.A. Padgett Rates of in situ transcription and splicing in large human genes Nat. Struct. Mol. Biol. 16 2009 1128 1133
12. F. Muntoni, S. Torelli, and A. Ferlini Dystrophin and mutations: one gene, several proteins, multiple phenotypes Lancet Neurol. 2 2003 731 740
13. A. Aartsma-Rus, J.C. Van Deutekom, I.F. Fokkema, G.J. Van Ommen, and J.T. Den Dunnen Entries in the Leiden Duchenne muscular dystrophy mutation database: an overview of mutation types and paradoxical cases that confirm the reading-frame rule Muscle Nerve 34 2006 135 144
14. S. Ott, Y. Tamada, H. Bannai, K. Nakai, and S. Miyano Intrasplicing-analysis of long intron sequences Pac. Symp. Biocomput 2003 339 350
15. H. Suzuki, Y. Zuo, J. Wang, M.Q. Zhang, A. Malhotra, and A. Mayeda Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing Nucleic Acids Res. 34 2006 e63
16. A.R. Krainer, T. Maniatis, B. Ruskin, and M.R. Green Normal and mutant human β-globin pre-mRNAs are faithfully and efficiently spliced in vitro Cell 36 1984 993 1005
17. A. Mayeda, and A.R. Krainer In vitro splicing assays S. Stamm, C. Smith, R. Lührmann, Alternative pre-mRNA Splicing: Theory and Protocols 2012 Wiley-Blackwell Weinheim, Germany 320 329
18. A. Mayeda, and Y. Ohshima β-globin transcripts carrying a single intron with three adjacent nucleotides of 5′ exon are efficiently spliced in vitro irrespective of intron position or surrounding exon sequences Nucleic Acids Res. 18 1990 4671 4676
19. J. Chelly, D. Montarras, C. Pinset, Y. Berwald-Netter, J.C. Kaplan, and A. Kahn Quantitative estimation of minor mRNAs by cDNA-polymerase chain reaction. Application to dystrophin mRNA in cultured myogenic and brain cells Eur. J. Biochem. 187 1990 691 698
20. D.W. Copertino, and R.B. Hallick Group II and group III introns of twintrons: potential relationships with nuclear pre-mRNA introns Trends Biochem. Sci. 18 1993 467 471
21. P. Scamborova, A. Wong, and J.A. Steitz An intronic enhancer regulates splicing of the twintron of Drosophila melanogaster prospero pre-mRNA by two different spliceosomes Mol. Cell. Biol. 24 2004 1855 1869
22. S. Borah, A.C. Wong, and J.A. Steitz Drosophila hnRNP A1 homologs Hrp36/Hrp38 enhance U2-type versus U12-type splicing to regulate alternative splicing of the prospero twintron Proc. Natl. Acad. Sci. USA 106 2009 2577 2582
23. M.K. Parra, J.S. Tan, N. Mohandas, and J.G. Conboy Intrasplicing coordinates alternative first exons with alternative splicing in the protein 4.1R gene EMBO J. 27 2008 122 131
24. M.K. Parra, T.L. Gallagher, S.L. Amacher, N. Mohandas, and J.G. Conboy Deep intron elements mediate nested splicing events at consecutive AG dinucleotides to regulate alternative 3′ splice site choice in vertebrate 4.1 genes Mol. Cell. Biol. 32 2012 2044 2053
25. H. Le Hir, and B. Seraphin EJCs at the heart of translational control Cell 133 2008 213 216
26. J. Saulière, N. Haque, S. Harms, I. Barbosa, M. Blanchette, and H. Le Hir The exon junction complex differentially marks spliced junctions Nat. Struct. Mol. Biol. 17 2010 1269 1271
27. J. Saulière, V. Murigneux, Z. Wang, E. Marquenet, I. Barbosa, O. Le Tonqueze, Y. Audic, L. Paillard, H. Roest Crollius, and H. Le Hir CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex Nat. Struct. Mol. Biol. 19 2012 1124 1131
28. K. Gao, A. Masuda, T. Matsuura, and K. Ohno Human branch point consensus sequence is yUnAy Nucleic Acids Res. 36 2008 2257 2267