rna biology

The regulation of genes transcribed by RNA polymerase II

Transcription of protein coding genes in kinetoplastid protozoa is unusual as arrays of genes aretranscribed polycistronically and individual mRNAs processed from the precursor RNA by transsplicing of a capped mini-exon onto the 5' end and cutting and polyadenylation at the 3' end. Thetranscription of most genes is constitutive and therefore mRNA levels are determined posttranscriptionally.

How are the levels of individual mRNAs set?

In the absence of selective transcriptional control, how are the levels of individual mRNAs set? In collaboration with Steve Kelly, we have shown that codon choice dictates the levels of constitutively expressed mRNAs. We developed and tested a novel codon usage metric, the gene expression codonad aptation index (geCAI) that maximised the relationship between codon choice and the measured abundance for a transcriptome. geCAI predictions of mRNA levels were tested using differently coded GFP transgenes and were successful over a 25-fold range, similar to the variation in endogenous mRNAs. Translation was necessary for the accelerated mRNA turnover resulting from codon choice. Thus, in trypanosomes, the information determining the levels of most mRNAs resides in the open reading frame and translation is required to access this information.

Figure: Fifty-fold range of GFP expression

Developmental regulation of mRNA stability

The differentiation of mammalian bloodstream trypanosomes to insect procyclic forms occurs over afew hours in response to defined external signals. During this process a small number of stable mRNAs become very unstable and remain unstable in mature and proliferating procyclic forms. We are concentrating on two of these genes: GPI-PLC, which encodes the glycosyphosphatidylinositol specific phospholipase C, and ISG65 which encodes invariant surface glycoprotein 65.

What is the mechanism for the developmental regulation of the mRNA levels? The approach we areusing is to make mutants that have lost developmental regulation and then to charaterise themolecular effect of the mutation.

Figure: XRNA (XRN1); XRND (RAT1); DNA

Selected publications