Essential Splice Site Research Articles

S39 Whole Exome Sequencing in Chronic Thromboembolic Pulmonary Hypertension Reveals Biologically Plausible Novel Genetic Variation

Chronic thromboembolic pulmonary hypertension (CTEPH) is a disease with no known heritability, the cumulative incidence of which has been placed at between 0.5 and 9.1% following acute pulmonary embolism [1,2]....

Defining the human reference protein-coding gene set

The number of coding genes in the human genome is still under debate [1]. Here, we present a proposal to define the human reference gene set that takes into account the inter-individual differences in gene numbers arising from gene inactivation events, such as premature termination or aberrant splicing due to nonsense SNPs or SNPs at essential splice sites respectively. We have analyzed SNPs (specifically nonsense SNPs and SNPs affecting essential splice sites) from 23 personal genomes and exomes. We see a wide range in numbers of SNPs in each of the categories surveyed. A large fraction of these SNPs are singletons. Using a data set of high-confidence SNPs obtained by intersecting SNPs from dbSNP and the personal genomes, we identify a common set of 279 genes predicted to be pseudogenic (non-functional) in some individuals and functional in others. We focused on two key questions arising from these considerations: (i) Which criteria should be used for inclusion and exclusion of genes from the reference set? (ii) What sequence should be used as the reference for genes that are non-functional in some humans? For the first question, we propose to include all genes that are functional even in one individual to produce a maximally-inclusive set of genes. For the second, we propose the use of the ancestral allele as the reference allele. This will provide a uniform basis for gene annotation and ensure that the reference gene set and sequence will be relatively stable as more individual genomes are sequenced. In the few cases where an ancestral state assignment is unavailable or ambiguous, we propose that genes be annotated as the functional allele.

Group I permuted intron-exon (PIE) sequences self-splice to produce circular exons.

Circularly permuted group I intron precursor RNAs, containing end-to-end fused exons which interrupt half-intron sequences, were generated and tested for self-splicing activity. An autocatalytic RNA can form when the primary order of essential intron sequence elements, splice sites, and exons are permuted in this manner. Covalent attachment of guanosine to the 5' half-intron product, and accurate exon ligation indicated that the mechanism and specificity of splicing were not altered. However, because the exons were fused and the order of the splice sites reversed, splicing released the fused-exon as a circle. With this arrangement of splice sites, circular exon production was a prediction of the group I splicing mechanism. Circular RNAs have properties that would make them attractive for certain studies of RNA structure and function. Reversal of splice site sequences in a context that allows splicing, such as those generated by circularly permuted group I introns, could be used to generate short defined sequences of circular RNA in vitro and perhaps in vivo.