title: Comparative survey of the relative impact of mRNA features on local ribosome profiling read density.
abstract: Ribosome profiling (Ribo-seq), a promising technology for exploring ribosome decoding rates, is characterized by the presence of infrequent high peaks in ribosome footprint density and by long alignment gaps. Here, to reduce the impact of data heterogeneity we introduce a simple normalization method, Ribo-seq Unit Step Transformation (RUST). RUST is robust and outperforms other normalization techniques in the presence of heterogeneous noise. We illustrate how RUST can be used for identifying mRNA sequence features that affect ribosome footprint densities globally. We show that a few parameters extracted with RUST are sufficient for predicting experimental densities with high accuracy. Importantly the application of RUST to 30 publicly available Ribo-seq data sets revealed a substantial variation in sequence determinants of ribosome footprint frequencies, questioning the reliability of Ribo-seq as an accurate representation of local ribosome densities without prior quality control. This emphasizes our incomplete understanding of how protocol parameters affect ribosome footprint densities.
authors.affiliation: School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.
authors.forename: Patrick B F
authors.initials: PB
authors.lastname: O'Connor
authors.affiliation: School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.|Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia.
authors.forename: Dmitry E
authors.initials: DE
authors.lastname: Andreev
authors.affiliation: School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.
authors.forename: Pavel V
authors.initials: PV
authors.lastname: Baranov
mesh_terms: D000818:Animals; D003062:Codon; D003198:Computer Simulation; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D051379:Mice; D015233:Models, Statistical; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000378:metabolism*; D015203:Reproducibility of Results; D012270:Ribosomes / Q000737:chemistry* / Q000648:ultrastructure; D015003:Yeasts / Q000378:metabolism
chemical_list: D003062:Codon; D012333:RNA, Messenger