Unconstrained mining of transcript data reveals increased alternative splicing complexity in the human transcriptome.

Mining massive amounts of transcript data for alternative splicing information is paramount to help understand how the maturation of RNA regulates gene expression. We developed an algorithm to cluster transcript data to annotated genes to detect unannotated splice variants. A higher number of alternatively spliced genes and isoforms were found compared to other alternative splicing databases. Comparison of human and mouse data revealed a marked increase, in human, of splice variants incorporating novel exons and retained introns. Previously unannotated exons were validated by tiling array expression data and shown to correspond preferentially to novel first exons. Retained introns were validated by tiling array and deep sequencing data. The majority of retained introns were shorter than 500 nt and had weak polypyrimidine tracts. A subset of retained introns matching small RNAs and displaying a high GC content suggests a possible coordination between splicing regulation and production of noncoding RNAs. Conservation of unannotated exons and retained introns was higher in horse, dog and cow than in rodents, and 64% of exon sequences were only found in primates. This analysis highlights previously bypassed alternative splice variants, which may be crucial to deciphering more complex pathways of gene regulation in human.

Mytilus galloprovincialis CYP1A-like mRNAs reveal closer proximity of mytilid CYP1A to the eumetazoan CYP2 family.

Due to the role of Cytochrome P450, Family 1, Subfamily A (CYP1A) in the detoxification of many polycyclic aromatic hydrocarbons (PAHs), there has been an effort to characterise the gene and the products from its expression in organisms that are relevant for biomonitoring and toxicity testing procedures. Nonetheless, the existence of functional homologues in aquatic invertebrates is not entirely consensual, especially in bivalve molluscs, which pose as one of the most important models for aquatic toxicologists, especially mytilids. After isolation and sequencing of CYP1A-like mRNA from the Mediterranean mussel, Mytilus galloprovincialis, phylogenetics incorporating homologues from molluscs and other eumetazoans, vertebrates included, yielded notorious similarity to sequences belonging to the CYP2 Family. Altogether, the findings further indicate that CYP1A-like CYPs may be absent in bivalves, in lieu of Families CYP2, 3 and 4, suggesting caution when interpreting data from common biomarkers of exposure to aromatic hydrocarbons that have been developed for CYP1A activity and expression in higher deuterostomes.