Alternative isoform regulation in human tissue transcriptomes

Through alternative processing of pre-messenger RNAs, individual mammalian genes often produce multiple mRNA and protein isoforms that may have related, distinct or even opposing functions. Here we report an in-depth analysis of 15 diverse human tissue and cell line transcriptomes on the basis of deep sequencing of complementary DNA fragments, yielding a digital inventory of gene and mRNA isoform expression. Analyses in which sequence reads are mapped to exon–exon junctions indicated that 92–94% of human genes undergo alternative splicing, ∼86% with a minor isoform frequency of 15% or more. Differences in isoform-specific read densities indicated that most alternative splicing and alternative cleavage and polyadenylation events vary between tissues, whereas variation between individuals was approximately twofold to threefold less common. Extreme or ‘switch-like’ regulation of splicing between tissues was associated with increased sequence conservation in regulatory regions and with generation of full-length open reading frames. Patterns of alternative splicing and alternative cleavage and polyadenylation were strongly correlated across tissues, suggesting coordinated regulation of these processes, and sequence conservation of a subset of known regulatory motifs in both alternative introns and 3′ untranslated regions suggested common involvement of specific factors in tissue-level regulation of both splicing and polyadenylation. When the human genome was decoded, the lower than expected number of genes prompted renewed interest in alternative splicing — a mechanism by which more than one protein is made from a single gene. Licatalosi et al. have developed an unbiased, genome-wide method to characterize RNA–protein binding interactions in living tissue, and demonstrate its potential by applying it to the mammalian brain. They characterize the binding sites of the neuronal alternative splicing regulator, Nova, and make the unexpected discovery that it may have an additional function in regulating alternative polyadenylation. In a separate study, Wang et al. used deep sequencing of mRNAs to study alternative splicing in various human tissues and cancers. By mapping sequence reads to splice junctions, they show that alternative splicing is essentially universal in human multi-exon genes. They also show that alternative splicing is mechanistically linked to mRNA polyadenylation. This paper reports on an intensive bioinformatic analysis of human alternative splicing in various tissues and cancers. The analysis offers insight into tissue specificity, coordinated regulation and sequence conservation of alternative splicing. Evidence is also obtained that alternative splicing is mechanistically linked to a modification of mRNAs known as polyadenylation.