Unconstrained mining of transcript data reveals increased alternative splicing complexity in the human transcriptome

Unconstrained mining of transcript data reveals increased alternative splicing complexity in the human transcriptome
I. G. Mollet1,*, Claudia Ben-Dov2, Daniel Felício-Silva1, A. R. Grosso1, Pedro Eleutério1, Ruben Alves1, Ray Staller3, Tito Santos Silva4 and Maria Carmo-Fonseca1

1Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal, 2CRG-Centre de Regulació Genómica, Barcelona, Spain, 3Independent Senior Consultant on Statistics & Mathematics, Amsterdam, the Netherlands and 4Faculdade de Engenharia, Universidade Católica Portuguesa, Lisbon, Portugal

*To whom correspondence should be addressed. Tel: ; Fax: +46(0)40-391222; Email: ines.mollet@med.lu.se; inesmollet@yahoo.com

Received November 17, 2009. Revised February 22, 2010. Accepted March 9, 2010.

Mining massive amounts of transcript data for alternative splicing information is paramount to help understand how the maturation of RNA regulates gene expression. We developed an algorithm to cluster transcript data to annotated genes to detect unannotated splice variants. A higher number of alternatively spliced genes and isoforms were found compared to other alternative splicing databases. Comparison of human and mouse data revealed a marked increase, in human, of splice variants incorporating novel exons and retained introns. Previously unannotated exons were validated by tiling array expression data and shown to correspond preferentially to novel first exons. Retained introns were validated by tiling array and deep sequencing data. The majority of retained introns were shorter than 500 nt and had weak polypyrimidine tracts. A subset of retained introns matching small RNAs and displaying a high GC content suggests a possible coordination between splicing regulation and production of noncoding RNAs. Conservation of unannotated exons and retained introns was higher in horse, dog and cow than in rodents, and 64% of exon sequences were only found in primates. This analysis highlights previously bypassed alternative splice variants, which may be crucial to deciphering more complex pathways of gene regulation in human.