We focused on two crucial steps in eukaryotic gene expression: transcription (the polymerization of mRNA from a DNA template) and splicing (the removal of non-coding “intron” regions from the mRNA). We applied these to the best available data from “next-generation sequencing” measurements in budding yeast. Budding yeast (Saccharomyces cerevisiae) is a popular “model organism”, because it is easy to manipulate and key features of its biology are shared with other funig, plants, and humans, including the gene expression machinery. We used data science tools, including model-based data analysis, to show that for most yeast genes splicing happens very quickly after transcription, but for some it does not. We found that splicing is particularly fast for most mRNAs coding for parts of the ribosome, the molecular machine that makes proteins from a mRNA template. This work was published in:
Wallace EWJ, Beggs JD. 2017. Extremely fast and incredibly close: cotranscriptional splicing in budding yeast. RNA 23: 601–610.
https://doi.org/10.1261/rna.060830.117(odnośnik otworzy się w nowym oknie)The accompanying image, taken from the paper, compares the different splicing measurements (SMIT, nascent RNA-seq, 4tU-seq) and other relevant features of yeast mRNAs (intron length, mRNA abundance). It highlights the different features and splicing patterns of ribosomal vs non-ribosomal RNAs.
We also developed computational models and software to understand a later stage of gene expression, the production of protein from mRNA by ribosomes.
Carja O, Xing T, Wallace EWJ, Plotkin JB, Shah P. 2017. riboviz: analysis and visualization of ribosome profiling datasets. BMC Bioinformatics 18: 461.
https://doi.org/10.1186/s12859-017-1873-8(odnośnik otworzy się w nowym oknie)
