Sequence features responsible for intron retention in human

BMC Genomics

Volumn 8, Issue , 2007, Pages

  Sakabe, Noboru Jo ^a,b   de Souza, Sandro José ^a  

^a HOSPITAL ALEMÃO OSWALDO CRUZ   (Brazil)

^b UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

ALTERNATIVE RNA SPLICING; ARTICLE; CONTROLLED STUDY; DNA SEQUENCE; ENHANCER REGION; EXON; GENE EXPRESSION; GENETIC CONSERVATION; HUMAN; INTRON; MOUSE; NONHUMAN; SILENCER ELEMENT; SPECIES DIFFERENCE; ANIMAL; GENETICS; NUCLEOTIDE SEQUENCE; RNA SPLICING;

ALTERNATIVE SPLICING; ANIMALS; BASE SEQUENCE; DNA, COMPLEMENTARY; ENHANCER ELEMENTS (GENETICS); HUMANS; INTRONS; MICE; RNA SPLICE SITES;

EID: 33947653234     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-8-59     Document Type: Article

References (41)

1. Matlin AJ Clark F Smith CW Understanding alternative splicing: Towards a cellular code Nat Rev Mol Cell Biol 2005 6 386-398 10.1038/nrm1645 15956978
2. Nott A Meislin SH Moore MJ A quantitative analysis of intron effects on mammalian gene expression RNA 2003 9 607-617 1370426 12702819 10.1261/ rna.5250403
3. Lareau LF Green RE Bhatnagar RS Brenner SE The evolving roles of alternative splicing Curr Opin Struct Biol 2004 14 273-282 10.1016/ j.sbi.2004.05.002 15193306
4. Melhuish TA Wotton D The Tgif2 gene contains a retained intron within the coding sequence BMC Mol Biol 2006 7 2 1402312 16436215 10.1186/ 1471-2199-7-2
5. Galante PA Sakabe NJ Kirschbaum-Slager N de Souza SJ Detection and evaluation of intron retention events in the human transcriptome RNA 2004 10 757-765 1370565 15100430 10.1261/rna.5123504
6. Stamm S Zhu J Nakai K Stoilov P Stoss O Zhang MQ An alternative-exon database and its statistical analysis DNA Cell Biol 2000 19 739-756 10.1089/104454900750058107 11177572
7. Romano M Marcucci R Baralle FE Splicing of constitutive upstream introns is essential for the recognition of intra-exonic suboptimal splice sites in the thrombopoietin gene Nucleic Acids Res 2001 29 886-894 29620 11160920 10.1093/nar/29.4.886
8. Dirksen WP Sun Q Rottman FM Multiple splicing signals control alternative intron retention of bovine growth hormone pre-mRNA J Biol Chem 1995 270 5346-5352 10.1074/jbc.270.10.5346 7890647
9. Sterner DA Berget SM In vivo recognition of a vertebrate mini-exon as an exon-intron-exon unit Mol Cell Biol 1993 13 2677-2687 359639 7682652
10. 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 4562-4571 232310 9234714
11. Talerico M Berget SM Intron definition in splicing of small Drosophila introns Mol Cell Biol 1994 14 3434-3445 358708 8164690
12. Romfo CM Alvarez CJ van Heeckeren WJ Webb CJ Wise JA Evidence for splice site pairing via intron definition in Schizosaccharomyces pombe Mol Cell Biol 2000 20 7955-7970 86406 11027266 10.1128/MCB.20.21.7955-7970.2000
13. Berget SM Exon recognition in vertebrate splicing J Biol Chem 1995 270 2411-2414 7852296
14. Popielarz M Cavaloc Y Mattei MG Gattoni R Stevenin J The gene encoding human splicing factor 9G8. Structure, chromosomal localization, and expression of alternatively processed transcripts J Biol Chem 1995 270 17830-17835 10.1074/jbc.270.30.17830 7629084
15. Ledee DR Chen J Tonelli LH Takase H Gery I Zelenka PS Differential expression of splice variants of chemokine CCL27 mRNA in lens, cornea, and retina of the normal mouse eye Mol Vis 2004 10 663-667 15448618
16. Lejeune F Cavaloc Y Stevenin J Alternative splicing of intron 3 of the serine/arginine-rich protein 9G8 gene. Identification of flanking exonic splicing enhancers and involvement of 9G8 as a trans-acting factor J Biol Chem 2001 276 7850-7858 10.1074/jbc.M009510200 11096110
17. Mount SM Burks C Hertz G Stormo GD White O Fields C Splicing signals in Drosophila: Intron size, information content, and consensus sequences Nucleic Acids Res 1992 20 4255-4262 334133 1508718 10.1093/nar/20.16.4255
18. Shapiro MB Senapathy P RNA splice junctions of different classes of eukaryotes: Sequence statistics and functional implications in gene expression Nucleic Acids Res 1987 15 7155-7174 306199 3658675 10.1093/ nar/15.17.7155
19. Sugnet CW Kent WJ Ares MJ Haussler D Transcriptome and genome conservation of alternative splicing events in humans and mice Pac Symp Biocomput 2004 66-77 14992493
20. 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 1777-1787 1370866 16251388 10.1261/rna.2660805
21. Ohler U Shorom N Burge CB Recognition of unknown conserved alternatively spliced exons PLoS Comput Biol 2005 1 113-122 1185642 16110330 10.1371/ journal.pcbi.0010015
22. Eisenberg E Levanon EY Human housekeeping genes are compact Trends Genet 2003 19 362-365 10.1016/S0168-9525(03)00140-9 12850439
23. Hong X Scofield DG Lynch M Intron Size, Abundance, and Distribution within Untranslated Regions of Genes Mol Biol Evol 2006 23 2392-2404 10.1093/molbev/msl111 16980575
24. Kornblihtt AR de la MM Fededa JP Munoz MJ Nogues G Multiple links between transcription and splicing RNA 2004 10 1489-1498 1370635 15383674 10.1261/rna.7100104
25. Wu Y Zhang Y Zhang J Distribution of exonic splicing enhancer elements in human genes Genomics 2005 86 329-336 10.1016/j.ygeno.2005.05.011 16005179
26. Wang Z Xiao X Nostrand EV Burge CB General and specific functions of exonic splicing silencers in splicing control Mol Cell 2006 23 61-70 10.1016/j.molcel.2006.05.018 16797197
27. Ibrahim C Schaal TD Hertel KJ Reed R Maniatis T Serine/arginine-rich protein-dependent suppression of exon skipping by exonic splicing enhancers Proc Natl Acad Sci U S A 2005 102 5002-5007 555999 15753297 10.1073/pnas.0500543102
28. Sterner DA Carlo T Berget SM Architectural limits on split genes Proc Natl Acad Sci U S A 1996 93 15081-15085 26359 8986767 10.1073/ pnas.93.26.15081
29. Takahara K Schwarze U Imamura Y Hoffman GG Toriello H Smith LT Byers PH Greenspan DS Order of intron removal influences multiple splice outcomes, including a two-exon skip, in a COL5A1 acceptor-site mutation that results in abnormal pro-alpha1(V) N-propeptides and Ehlers-Danlos syndrome type I Am J Hum Genet 2002 71 451-465 379186 12145749 10.1086/ 342099
30. Karolchik D Baertsch R Diekhans R Furey TS Hinrichs A Lu YT Roskin KM Schwartz M Sugnet CW Thomas DJ The UCSC Genome Browser Database Nucleic Acids Res 2003 31 51-54 165576 12519945 10.1093/nar/gkg129
31. Automatic annotation of alternative splicing on cDNA Clusters 2006 http://www.compbio.ludwig.org.br/asc
32. Florea L Hartzell G Zhang Z Rubin GM Miller W A computer program for aligning a cDNA sequence with a genomic DNA sequence Genome Res 1998 8 967-974 310774 9750195
33. Schneider TD Stormo GD Yarus MA Gold L Delila system tools Nucleic Acids Res 1984 12 129-140 320990 6694897 10.1093/nar/12.1Part1.129
34. Crooks GE Hon G Chandonia JM Brenner SE WebLogo: A sequence logo generator Genome Res 2004 14 1188-1190 419797 15173120 10.1101/gr.849004
35. Velculescu VE Zhang L Vogelstein B Kinzler KW Serial analysis of gene expression Science 1995 270 484-487 10.1126/science.270.5235.484 7570003
36. Boon K Osorio EC Greenhut SF Schaefer CF Shoemaker J Polyak K Morin PJ Buetow KH Strausberg RL de Souza SJ Riggins GJ An anatomy of normal and malignant gene expression Proc Natl Acad Sci U S A 2002 99 11287-11292 123249 12119410 10.1073/pnas.152324199
37. Cartegni L Wang J Zhu Z Zhang MQ Krainer AR ESEfinder: A web resource to identify exonic splicing enhancers Nucleic Acids Res 2003 31 3568-3571 169022 12824367 10.1093/nar/gkg616
38. Fairbrother WG Yeh RF Sharp PA Burge CB Predictive identification of exonic splicing enhancers in human genes Science 2002 297 1007-1013 10.1126/science.1073774 12114529
39. Louie E Ott J Majewski J Nucleotide frequency variation across human genes Genome Res 2003 13 2594-2601 403801 14613976 10.1101/gr.1317703
40. Altschul SF Madden TL Schaffer AA Zhang J Zhang Z Miller W Lipman DJ Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic Acids Res 1997 25 3389-3402 146917 9254694 10.1093/nar/ 25.17.3389
41. Rice P Longden I Bleasby A EMBOSS: The European Molecular Biology Open Software Suite Trends Genet 2000 16 276-277 10.1016/ S0168-9525(00)02024-2 10827456