Mystery of intron splicing

CREATED: 200810200719 ** Paramecium (ciliate)

• macro nucleus, somatic genome
• micro nucleus, germline
• programmed genome rearrangement
• model eukaryotic unicellular organism
• ~39642 annotated genes, 24052 (2 copies, from WGD), 11451 (1 copy)
• 51% of ancestral genes present in 2 copies
• DNA-DNA alignment (L Spearling)
• 3 successive WGD! but 2x2x2 = 2 ** Lifespan of gene duplicates
• evolution of gene function (neo/sub functionalization)
• dosage constraints (gene balance hypothesis, Papp et al 2003)
• EST data, highly expressed genes more frequently retained
• expression -> retention? Yes, but not as predicted by models of gene retention
• cost of expression model ** energetic cost: ATP, GTP ** mobilizing gene expression machinery
• highly expressed genes are more dosage sensitive ** Mystery of intron splicing
• weak signals for splice sites/branch points
• ~2.3 introns/gene, short ~25bp
• deficient in introns of length = 3n
• selective pressure to have stop codon within 3n introns? Yes ** splicing is error prone ** retention of stop codon to stop production of aberrant mRNA ** 3n -> has stop codon ** non-3n -> introduce frame shift! May produce stop codons later in exons etc ** NMD machinery to remove aberrant mRNA
• deficient in 3n stopless introns in intron rich eukaryote
• Jaillon et al. Nature 2008