Deep sequencing reveals the universal alternative RNA regulations in human tissues

Why it is so complicated?
* Alternative splicing
* Alternative cleavage
* Alternative polyadenylation
* Alternative promoter usage
in part by tissue-specific RNA-binding factors, … ,
and there is also a role of small RNAs …
Is that why we are human?

Nature. 2008 Nov 2;456(7221):470-476.
Alternative isoform regulation in human tissue transcriptomes.

Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB.

[1] Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [2] Harvard-MIT Division of Health Sciences and Technology, Cambridge, Massachusetts 02139, USA [3] These authors contributed equally to this work.

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, approximately 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.

PMID: 18978772

F1000 review:

Ken Irvine with Yongqiang Feng
Rutgers University, State University of New Jersey, United States of America
Developmental Biology

In this study, 15 human tissue and cell line transcriptomes were analyzed by deep sequencing. The authors present the surprising finding that most (92-94%) human genes are alternatively spliced, which varies between tissues and individuals.
With its higher throughput and relatively low cost-to-read ratio, new sequencing technology is opening new horizons to biologists. It is now possible to compare the details of transcriptomes between tissues and individuals not only at the expression level, as measured by microarrays, but also at the sequence level. As an excellent example, 15 human tissue and cell line transcriptomes were analyzed in this paper by deep sequencing. The authors demonstrated the strategies and methods to analyze the splicing events from sequenced data. They found that most (92-94%) of human genes are alternatively spliced, which varies between tissues. Their observations raise interesting questions. What is the mechanism of tissue-specific alternative splicing? What are the functions of these alternatively spliced genes in different tissues? The paper also showed that there are, to a lesser degree, alternative splicing variations between individuals. If these differences are statistically significant, they might contribute to the phenotypic distinctiveness of each individual.