The implications of alternative splicing in the ENCODE protein complement

Abstract

Alternative premessenger RNA splicing enables genes to generate more than one gene product. Splicing events that occur within protein coding regions have the potential to alter the biological function of the expressed protein and even to create new protein functions. Alternative splicing has been suggested as one explanation for the discrepancy between the number of human genes and functional complexity. Here, we carry out a detailed study of the alternatively spliced gene products annotated in the ENCODE pilot project. We find that alternative splicing in human genes is more frequent than has commonly been suggested, and we demonstrate that many of the potential alternative gene products will have markedly different structure and function from their constitutively spliced counterparts. For the vast majority of these alternative isoforms, little evidence exists to suggest they have a role as functional proteins, and it seems unlikely that the spectrum of conventional enzymatic or structural functions can be substantially extended through alternative splicing.function ͉ human ͉ isoforms ͉ splice ͉ structure A lternative mRNA splicing, the generation of a diverse range of mature RNAs, has considerable potential to expand the cellular protein repertoire (1-3), and recent studies have estimated that 40-80% of multiexon human genes can produce differently spliced mRNAs (4, 5). The importance of alternative splicing in processes such as development (6) has long been recognized, and proteins coded by alternatively spliced transcripts have been implicated in a number of cellular pathways (7-9). The extent of alternative splicing in eukaryotic genomes has lead to suggestions that alternative splicing is key to understanding how human complexity can be encoded by so few genes (10).The pilot project of the Encyclopedia of DNA Elements (ENCODE) (11), which aims to identify all the functional elements in the human genome, has undertaken a comprehensive analysis of 44 selected regions that make up 1% of the human genome. One valuable element of the project has been the detailing of a reference set of manually annotated splice variants by the GENCODE consortium (12). The annotation by the GENCODE consortium is an extension of the manually curated annotation by the Havana team at The Sanger Institute.Although a full understanding of the functional implications of alternative splicing is still a long way off, the GENCODE set has provided us with the material to make an in-depth assessment of a systematically collected reference set of splice variants. ResultsAlternative Splicing Frequency. The GENCODE set is made up of 2,608 annotated transcripts for 487 distinct loci. A total of 1,097 transcripts from 434 loci are predicted to be protein coding. There are on average 2.53 protein coding variants per locus; 182 loci have only one variant, whereas one locus, RP1-309K20.2 (CPNE1) has 17 coding variants.A total of 57.8% of the loci are annotated with alternatively spliced transcripts, although there are differences between target re...

Identification of Androgen Receptor Splice Variant Transcripts in Breast Cancer Cell Lines and Human Tissues

“…Importantly, if expression of these ARVs is demonstrated at the protein level, in particular in response to AR targeted therapies as has been reported in prostate cancer [35], expression of ARVs may have relevance for women with breast cancer currently being treated with similar AR-targeted therapies as in the clinical trials cited above. One of the significant discoveries to arise from the EN-CODE project [36] is that the large majority of human genes exhibit some degree of alternative splicing; up to 25 splice variants commonly arise from a single gene in addition to the wild type transcript. The splice variants are generally expressed in a pattern whereby 2-3 variant transcripts are dominant, followed by a wide array of variant transcripts that are expressed at very low copy numbers.…”

“…It has been proposed that alternative splice variants of genes are rapidly degraded under physiological conditions but may be highly expressed under pathological conditions or other conditions of environmental stress if they are able to provide a selective advantage over their wild type counterparts [36]. This appears to be the case for truncated ARVs in prostate cancer.…”

Differential splicing across immune system lineages

“…However, a proportion of AS events may have little or no functional significance with regard to the encoded protein (3,30): 45% fall outside of the protein-coding region, and some modify only a few amino acids in structurally tolerant domains, such as leader peptides or Gln-rich domains.…”

“…AS can result in different protein isoforms or generate mRNAs of identical coding sequence but varying in their stability, localization, susceptibility to translational control, or microRNA regulation. AS is frequent and ubiquitous, affecting 55-95% of multiexon genes in mammals in different estimates (3)(4)(5)(6). It is involved in a wide range of biological phenomena, ranging from sex determination to apoptosis or tumor formation.…”

The impact of microRNAs and alternative splicing in pharmacogenomics

“…The rate of alternative splicing of mRNAs has been the focus of different studies and it seems that more than 60% of the human genes produce at least one alternative mRNA. 25 The functional implication of alternative splicing in normal and pathological states has been studied by several groups, 26,27 but there are still many questions to be answered. Future studies will be focused on the functional relevance of splice variants in the context of whole genome studies, instead of a single gene to understand how they will affect cellular networks and pathways.…”