Gene expression reprogramming by thousands of RNA sequences

A team from WCAIR has determined how trypanosomes post-transcriptionally reprogramme gene expression.

Researchers  from the Centre have used multiplexing, demultiplexing and decoding approaches to demonstrate how parasitic trypanosomes use pervasive sequences in their messenger RNAs to tune gene expression. Cells express thousands of proteins at wide-ranging abundance levels. In parasitic trypanosomes, which cause a range of neglected tropical diseases and veterinary diseases, there is a major emphasis on post-transcriptional controls. This is because these cells, unusually transcribe almost ‘everything everywhere all at once’. Indeed, more than one third of the trypanosome genome appears to be available to drive post-transcriptional controls.

In the current paper published in Nature Communications, David Horn, Professor of Parasite Molecular biology said “It has been known for decades that gene expression control is almost exclusively post-transcriptional in trypanosomes, but the sequences involved have remained largely mysterious”.

Anna Trenaman, first author on the paper, said “We’ve been developing and exploiting high-throughput forward genetic approaches in the lab for a number of years, and this inspired us to develop a new genetic approach known as a massive parallel reporter assay. We made a reporter library, used deep sequencing to profile the outputs and then, with Michele’s help, assigned regulatory scores to thousands of genomic fragments”.

Michele Tinti, joint first author on the paper, said “This study required a major reannotation of the Trypanosoma brucei non-coding genome and the application of a machine-learning approach that I’ve been developing for some time. I think the outputs synergise very nicely to illustrate the power of combining genetic screens in the lab with informatics approaches”.

David concluded “We can now effectively predict global gene expression levels in trypanosomes using cis-regulatory sequences alone, but outstanding questions remain. The results suggest a model whereby A-rich sequences increase translation, while U-rich sequences mask A-rich sequences to achieve developmental controls. We will test these hypotheses further in trypanosomes, look for further regulatory sequences and similar codes present in related parasites, and also seek to identify proteins responsible for interpreting these codes”.

The work was supported by Wellcome, and was greatly facilitated by support from the Tayside Centre for Genomic Analysis at the University of Dundee.