Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs

Abstract

We report the first genome-wide identification and characterization of alternative splicing in human gene transcripts based on analysis of the full-length cDNAs. Applying both manual and computational analyses for 56 419 completely sequenced and precisely annotated full-length cDNAs selected for the H-Invitational human transcriptome annotation meetings, we identified 6877 alternative splicing genes with 18 297 different alternative splicing variants. A total of 37 670 exons were involved in these alternative splicing events. The encoded protein sequences were affected in 6005 of the 6877 genes. Notably, alternative splicing affected protein motifs in 3015 genes, subcellular localizations in 2982 genes and transmembrane domains in 1348 genes. We also identified interesting patterns of alternative splicing, in which two distinct genes seemed to be bridged, nested or having overlapping protein coding sequences (CDSs) of different reading frames (multiple CDS). In these cases, completely unrelated proteins are encoded by a single locus. Genome-wide annotations of alternative splicing, relying on full-length cDNAs, should lay firm groundwork for exploring in detail the diversification of protein function, which is mediated by the fast expanding universe of alternative splicing variants.

A General Definition and Nomenclature for Alternative Splicing Events

“…Also, since cases of overlapping transcripts from hitherto distinctly annotated genes are increasingly reported [59,60], genes can no longer be regarded as isolated units of transcription. Transcription Induced Chimeras [60][61][62], i.e., genes that are fused by a transcript sharing at least one splice site with either one of them, are to be respected when investigating the phenomenon of AS. Therefore, AStalavista includes its own clustering schema in order to ensure an exhaustive detection of AS events, by pooling in a single transcriptional locus all transcripts that overlap on the same strand of the genome sequence.…”

Promoting transcriptome diversity

“…Through these studies it is anticipated that a better understanding of the rules governing the structure of use of promoters in non-protein-encoding genes will emerge. Toward that end, full-length cDNA sequencing, especially from human and mouse, has provided data sets that give insight not only into alternative splice forms, but also the utilization of alternative promoters (Okazaki et al 2002;Strausberg et al 2002;Imanishi et al 2004;Ota et al 2004;Carninci et al 2005;Takeda et al 2006). Especially valuable for these studies have been cDNA libraries generated with technologies that select for the presence of the 5Ј-CAP.…”

Bidirectional Gene Pairs in the Human Genome

“…For example, some genes are clustered in an exquisitely specific manner on the human genome (Adachi and Lieber, 2002;Lercher et al, 2002) in addition to the already known functionally related duplicated gene clusters such as the globin and Hox gene clusters. Furthermore, quite a few overlapping genes such as cis sense-antisense pairs and nested genes are observed in mammalian genomes (Okazaki et al, 2002;Takeda et al, 2006). This kind of genome organization recently found in the human genome is of interest because it may be associated with transcriptional regulation and the functional relationships of different genes in the genome.…”