Modeling the ribosomal small subunit dynamic in Saccharomyces cerevisiae based on TCP-seq data.

ABSTRACT: Translation Complex Profile Sequencing (TCP-seq), a protocol that was developed and implemented on Saccharomyces cerevisiae, provides the footprints of the small subunit (SSU) of the ribosome (with additional factors) across the entire transcriptome of the analyzed organism. In this study, based on the TCP-seq data, we developed for the first-time a predictive model of the SSU density and analyzed the effect of transcript features on the dynamics of the SSU scan in the 5'UTR. Among others, our model is based on novel tools for detecting complex statistical relations tailored to TCP-seq. We quantitatively estimated the effect of several important features, including the context of the upstream AUG, the upstream ORF length and the mRNA folding strength. Specifically, we suggest that around 5

SUBMITTER: Neumann T 

PROVIDER: S-EPMC8860609 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature