title: Computational analysis of full-length cDNAs reveals frequent coupling between transcriptional and splicing programs.
abstract: High-throughput sequencing studies revealed that the majority of human and mouse multi-exon genes have multiple splice forms. High-density oligonucleotide array-based measurements have further established that many exons are expressed in a tissue-specific manner. The mechanisms underlying the tissue-dependent expression of most alternative exons remain, however, to be understood. In this study, we focus on one possible mechanism, namely the coupling of (tissue specific) transcription regulation with alternative splicing. We analyzed the FANTOM3 and H-Invitational datasets of full-length mouse and human cDNAs, respectively, and found that in transcription units with multiple start sites, the inclusion of at least 15% and possibly up to 30% of the 'cassette' exons correlates with the use of specific transcription start sites (TSS). The vast majority of TSS-associated exons are conserved between human and mouse, yet the conservation is weaker when compared with TSS-independent exons. Additionally, the currently available data only support a weak correlation between the probabilities of TSS association of orthologous exons. Our analysis thus suggests frequent coupling of transcriptional and splicing programs, and provides a large dataset of exons on which the molecular basis of this coupling can be further studied.
authors.affiliation: Division of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50-70, Basel CH-4056, Switzerland.
authors.forename: Tzu-Ming
authors.initials: TM
authors.lastname: Chern
authors.forename: Nicodeme
authors.initials: N
authors.lastname: Paul
authors.forename: Erik
authors.initials: E
authors.lastname: van Nimwegen
authors.forename: Mihaela
authors.initials: M
authors.lastname: Zavolan
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D018076:DNA, Complementary / Q000235:genetics*; D005091:Exons / Q000235:genetics; D005786:Gene Expression Regulation; D006801:Humans; D051379:Mice; D012333:RNA, Messenger / Q000235:genetics; D015398:Signal Transduction; D014158:Transcription, Genetic
chemical_list: D018076:DNA, Complementary; D012333:RNA, Messenger