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

SUBMITTER: Chern TM 

PROVIDER: S-EPMC2650624 | biostudies-literature | 2008 Apr

REPOSITORIES: biostudies-literature