Survey of transcription initiation in the streamlined genomes of Paramecium

In the genus Paramecium, the macronuclear genome is remarkably compact and optimized for gene expression. As a means to explore eukaryotic transcription in the context of a streamlined genome and shed light on the role of sequence architecture on gene expression and loss, we analyzed the distribution and diversity of candidate transcription initiation sites (TISs) in Paramecium sexaurelia, Paramecium tetraurelia and their outgroup, Paramecium caudatum. Our analysis suggests that for Paramecium, most genes have very short 5 prime UTRs (40 bp or less) and their transcription initiation regions (TIRs) have a median dispersion (akin to width) of 8-10 bp. The TIRs for the three species have high AT content. TIR dispersion is not to gene expression. However, mean TIS position relative to the translation start site per gene does in gene expression for the three species, and is often conserved between them. While mean TIS position and gene expression are linked, gene expression itself is the main driver of paralog retention in the aurelias. As compared to other eukaryotes, Paramecium has a uniquely well-defined and short main TIS region, and sequence motifs that likely diverge from the consensus in multicellular eukaryotes.