Computational analysis of splicing errors and mutations in human transcripts

BMC Genomics
Yerbol Z Kurmangaliyev, Mikhail S Gelfand

Abstract

Most retained introns found in human cDNAs generated by high-throughput sequencing projects seem to result from underspliced transcripts, and thus they capture intermediate steps of pre-mRNA splicing. On the other hand, mutations in splice sites cause exon skipping of the respective exon or activation of pre-existing cryptic sites. Both types of events reflect properties of the splicing mechanism. The retained introns were significantly shorter than constitutive ones, and skipped exons are shorter than exons with cryptic sites. Both donor and acceptor splice sites of retained introns were weaker than splice sites of constitutive introns. The authentic acceptor sites affected by mutations were significantly weaker in exons with activated cryptic sites than in skipped exons. The distance from a mutated splice site to the nearest equivalent site is significantly shorter in cases of activated cryptic sites compared to exon skipping events. The prevalence of retained introns within genes monotonically increased in the 5'-to-3' direction (more retained introns close to the 3'-end), consistent with the model of co-transcriptional splicing. The density of exonic splicing enhancers was higher, and the density of exonic splicing silencer...Continue Reading

References

Sep 1, 1991·Trends in Genetics : TIG·D C Rio
Nov 11, 1988·Nucleic Acids Research·J D Hawkins
Jan 19, 2000·Nucleic Acids Research·M S GelfandA A Mironov
Jul 13, 2002·Science·William G FairbrotherChristopher B Burge
Dec 6, 2002·Nature·Y OkazakiUNKNOWN RIKEN Genome Exploration Research Group Phase I & II Team
Dec 28, 2002·Proceedings of the National Academy of Sciences of the United States of America·Benjamin P LewisSteven E Brenner
Jun 26, 2003·Nucleic Acids Research·Luca CartegniAdrian R Krainer
Jul 11, 2003·Gene·Rujuan Dai, Clare Bergson
Oct 25, 2003·Nucleic Acids Research·Xavier RocaAdrian R Krainer
Nov 20, 2003·Brain Research. Molecular Brain Research·Solomon S ShaftelM Kerry O'Banion
Jan 28, 2004·Comptes rendus biologies·Noboru Jo SakabeSandro José de Souza
Apr 22, 2004·RNA·Pedro Alexandre Favoretto GalanteSandro José de Souza
May 18, 2004·Genes & Development·Xiang H-F Zhang, Lawrence A Chasin
Sep 24, 2004·RNA·Alberto R KornblihttGuadalupe Nogues
Oct 29, 2004·Nature Reviews. Genetics·Gil Ast
Dec 21, 2004·Cell·Zefeng WangChristopher B Burge
Jan 15, 2005·Clinical Chemistry·Iacovos P MichaelEleftherios P Diamandis
Feb 15, 2005·Proceedings of the National Academy of Sciences of the United States of America·Gene W YeoChristopher B Burge
Aug 2, 2005·Molecular and Cellular Biology·Xiang H-F ZhangLawrence A Chasin
Sep 6, 2005·Nucleic Acids Research·Jana KrálovicováIgor Vorechovský
Oct 6, 2005·Nucleic Acids Research·Michael HillerRolf Backofen
Jan 27, 2006·BMC Molecular Biology·Tiffany A Melhuish, David Wotton
Apr 25, 2006·Proceedings of the National Academy of Sciences of the United States of America·Bing-Bing Wang, Volker Brendel
Jun 27, 2006·Molecular Cell·Zefeng WangChristopher B Burge
Sep 15, 2006·Nature·Ying LiMarie-Louise Hammarskjöld
Sep 19, 2006·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Hadas Ner-Gaon, Robert Fluhr
Dec 13, 2006·Nucleic Acids Research·Eddo KimGil Ast
Feb 28, 2007·BMC Genomics·Noboru Jo Sakabe, Sandro José de Souza
Mar 16, 2007·American Journal of Human Genetics·Victor A McKusick

❮ Previous
Next ❯

Citations

Nov 18, 2010·Journal of Molecular Evolution·Anna A VakhrushevaGeorgii A Bazykin
May 4, 2013·Human Molecular Genetics·Yerbol Z KurmangaliyevMikhail S Gelfand
Apr 20, 2006·BMC Genomics·Ekaterina O ErmakovaMikhail S Gelfand
Apr 28, 2010·PLoS Computational Biology·Jayne Y Hehir-KwaJoris A Veltman
Jul 27, 2010·PloS One·David A de Lima Morais, Paul M Harrison
Feb 20, 2009·Growth Factors·Daniela KochAlbert M Ricken
Apr 19, 2015·BMC Genomics·Yerbol Z KurmangaliyevSergey V Nuzhdin
Dec 31, 2010·Die Naturwissenschaften·Erin Leigh BeckerCharles R Fisher
Nov 17, 2009·Science in China. Series C, Life Sciences·Zorica SvircevMirko Draganić
Aug 30, 2018·BMC Genomics·Shamsuddin A BhuiyanPaul Pavlidis

❮ Previous
Next ❯

Methods Mentioned

BETA
SELEX

Software Mentioned

PESX
ESE
RESCUE
ESEfinder
UCSC genome browser

Related Concepts

Related Feeds

Alternative splicing

Alternative splicing a regulated gene expression process that allows a single genetic sequence to code for multiple proteins. Here is that latest research.