Recent advances of studies on alternative intron retention

Trends in Evolutionary Biology

Volumn 5, Issue 1, 2013, Pages 1-6

  Zhan, Lei Lei ^a  

^a ZHEJIANG UNIVERSITY   (China)

Author keywords

Alternative splicing; Intron retention; Mechanism; Origin and evolution

Indexed keywords

EID: 84875188952     PISSN: 20362641     EISSN: 2036265X     Source Type: Journal    
DOI: 10.4081/eb.2013.e1     Document Type: Review

References (48)

1. Black DL. Mechanisms of alternative premessenger RNA splicing. Annu Rev Biochem 2003;72:291-336.
2. Wang ET, Sandberg R, Luo S, et al. Alternative isoform regulation in human tissue transcriptomes. Nature 2008;456: 470-6.
3. Wahl MC, Will CL, Luhrmann R. The spliceosome: design principles of a dynamic RNP machine. Cell 2009;136:701-18.
4. Matlin AJ, Clark F, Smith CW. Understanding alternative splicing: towards a cellular code. Nat Rev Mol Cell Biol 2005;6:386-98.
5. Schmucker D, Clemens JC, Shu H, et al. Drosophila Dscam is an axon guidance receptor exhibiting extraordinary molecular diversity. Cell 2000;101:671-84.
6. Ast G. How did alternative splicing evolve? Nat Rev Genet 2004;5:773-82.
7. Calvanese V, Mallya M, Campbell RD, Aguado B. Regulation of expression of two LY-6 family genes by intron retention and transcription induced chimerism. BMC Mol Biol 2008;9:81.
8. Berget SM. Exon recognition in vertebrate splicing. J Biol Chem 1995;270:2411-4.
9. Romfo CM, Alvarez CJ, van Heeckeren WJ, et al. Evidence for splice site pairing via intron definition in Schizosaccharomyces pombe. Mol Cell Biol 2000;20:7955-70.
10. Sterner DA, Berget SM. In vivo recognition of a vertebrate mini-exon as an exonintron-exon unit. Mol Cell Biol 1993; 13:2677-87.
11. Sakabe NJ, de Souza SJ. Sequence features responsible for intron retention in human. BMC Genomics 2007;8:59.
12. Talerico M, Berget SM. Intron definition in splicing of small Drosophila introns. Mol Cell Biol 1994;14:3434-45.
13. Yatzkan E, Yarden O. The B regulatory subunit of protein phosphatase 2A is required for completion of macroconidiation and other developmental processes in Neurospora crassa. Mol Microbiol 1999; 31:197-209.
14. Davis CA, Grate L, Spingola M, Ares M Jr. Test of intron predictions reveals novel splice sites, alternatively spliced mRNAs and new introns in meiotically regulated genes of yeast. Nucleic Acids Res 2000; 28:1700-6.
15. Okazaki K, Niwa O. mRNAs encoding zinc finger protein isoforms are expressed by alternative splicing of an in-frame intron in fission yeast. DNA Res 2000;7:27-30.
16. Vilardell J, Chartrand P, Singer RH, Warner JR. The odyssey of a regulated transcript. RNA 2000;6:1773-80.
17. Ebbole DJ, Jin Y, Thon M, et al. Gene discovery and gene expression in the rice blast fungus, Magnaporthe grisea: analysis of expressed sequence tags. Mol Plant Microbe Interact 2004;17:1337-47.
18. Escalante R, Moreno N, Sastre L. Dictyostelium discoideum developmentally regulated genes whose expression is dependent on MADS box transcription factor SrfA. Eukaryot Cell 2003; 2:1327-35.
19. Muhia DK. Multiple splice variants encode a novel adenylyl cyclase of possible plastid origin expressed in the sexual stage of the malaria parasite Plasmodium falciparum. J Biol Chem 2003; 278:22014-22.
20. Kim E, Goren A, Ast G. Alternative splicing: current perspectives. Bioessays 2008;30: 38-47.
21. Keren H, Lev-Maor G, Ast G. Alternative splicing and evolution: diversification, exon definition and function. Nat Rev Genet 2010;11:345-55.
22. Guo YL. Gene family evolution in green plants with emphasis on the origination and evolution of Arabidopsis thaliana genes. Plant J 2012 Dec 6. [Epub ahead of print]
23. Kopelman NM, Lancet D, Yanai I. Alternative splicing and gene duplication are inversely correlated evolutionary mechanisms. Nat Genet 2005; 37:588-9.
24. Iida K, Seki M, Sakurai T, et al. Genomewide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences. Nucleic Acids Res 2004;32:5096-103.
25. Ner-Gaon H, Halachmi R, Savaldi-Goldstein S, et al. Intron retention is a major phenomenon in alternative splicing in Arabidopsis. Plant J 2004;39:877-85.
26. Kim E, Magen A, Ast G. Different levels of alternative splicing among eukaryotes. Nucleic Acids Res 2007; 35:125-31.
27. McCullough AJ, Berget SM. G triplets located throughout a class of small vertebrate introns enforce intron borders and regulate splice site selection. Mol Cell Biol 1997;17:4562-71.
28. Gontijo AM, Miguela V, Whiting MF, et al. Intron retention in the Drosophila melanogaster Rieske Iron Sulphur Protein gene generated a new protein. Nat Commun 2011;2:323.
29. Irimia M, Rukov JL, Penny D, et al. Origin of introns by 'intronization' of exonic sequences. Trends Genet 2008;24:378-81.
30. Iwamoto M, Maekawa M, Saito A, et al. Evolutionary relationship of plant catalase genes inferred from intron-exon structures: isozyme divergence after the separation of monocots and dicots. Theor Appl Genet 1998;97:9-19.
31. Iwamoto M, Nagashima H, Nagamine T, et al. p-SINE1-like intron of the CatA catalase homologs and phylogenetic relationships among AA-genome Oryza and related species. Theor Appl Genet 1999;98:853-61.
32. Roy SW, Gilbert W. The evolution of spliceosomal introns: pattern, puzzles and progress. Nat Rev Genet 2006;7:211-21.
33. Stamm S, Zhu J, Nakai K, et al. An alternative-exon database and its statistical analysis. DNA Cell Biol 2000;19:739-56.
34. Zheng CL, Fu XD, Gribskov M. Characteristics and regulatory elements defining constitutive splicing and different modes of alternative splicing in human and mouse. RNA 2005;11:1777-87.
35. Romano M, Marcucci R, Baralle FE. Splicing of constitutive upstream introns is essential for the recognition of intraexonic suboptimal splice sites in the thrombopoietin gene. Nucleic Acids Res 2001;29:886-94.
36. Dirksen WP, Sun Q, Rottman FM. Multiple splicing signals control alternative intron retention of bovine growth hormone premRNA. J Biol Chem 1995;270:5346-52.
37. Marinescu V, Loomis PA, Ehmann S, et al. Regulation of retention of FosB intron 4 by PTB. PLoS ONE 2007;2:e828.
38. Yap K, Lim ZQ, Khandelia P, et al. Coordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention. Genes Dev 2012;26:1209-23.
39. Zhou HL, Hinman MN, Barron VA, et al. Hu proteins regulate alternative splicing by inducing localized histone hyperacetylation in an RNA-dependent manner. Proc Natl Acad Sci USA 2011;108:627-35.
40. Galante PA, Sakabe NJ, Kirschbaum-Slager N, de Souza SJ. Detection and evaluation of intron retention events in the human transcriptome. RNA 2004;10:757-65.
41. Li Y, Bor YC, Misawa Y, et al. An intron with a constitutive transport element is retained in a Tap messenger RNA. Nature 2006;443:234-7.
42. Ding W, Lin L, Xiao Z, et al. Multiple sequence elements determine the intron retention in histamine H3 receptors in rats and mice. Int J Biochem Cell Biol 2009;41:2281-86.
43. Bell TJ, Miyashiro KY, Sul JY, et al. Intron retention facilitates splice variant diversity in calcium-activated big potassium channel populations. Proc Natl Acad Sci USA 2010;107:21152-7.
44. Garcia-Blanco MA, Baraniak AP, Lasda EL. Alternative splicing in disease and therapy. Nat Biotechnol 2004;22:535-46.
45. Nelson ME, Thurmes PJ, Hoyer JD, Steensma DP. A novel 5′ ATRX mutation with splicing consequences in acquired alpha thalassemia-myelodysplastic syndrome. Haematologica 2005;90:1463-70.
46. Cartault F, Nava C, Malbrunot AC, et al. A new XPC gene splicing mutation has lead to the highest worldwide prevalence of xeroderma pigmentosum in black Mahori patients. DNA Repair 2011;10:577-85.
47. Saredi S, Ardissone A, Ruggieri A, et al. Novel POMGNT1 point mutations and intragenic rearrangements associated with muscle-eye-brain disease. J Neurol Sci 2012;318:45-50.
48. Forrest ST, Barringhaus KG, Perlegas D, et al. Intron retention generates a novel Id3 isoform that inhibits vascular lesion formation. J Biol Chem 2004;279:32897-903.