GWIPS-viz as a tool for exploring ribosome profiling evidence supporting the synthesis of alternative proteoforms.
The boundaries of protein coding sequences are more difficult to define at the 5' end than at the 3' end due to potential multiple translation initiation sites (TISs). Even in the presence of phylogenetic data, the use of sequence information only may not be sufficient for the accurate identification of TISs. Traditional proteomics approaches may also fail because the N-termini of newly synthesized proteins are often processed. Thus ribosome profiling (ribo-seq), producing a snapshot of the ribosome distribution across the entire transcriptome, is an attractive experimental technique for the purpose of TIS location exploration. The GWIPS-viz (Genome Wide Information on Protein Synthesis visualized) browser (http://gwips.ucc.ie) provides free access to the genomic alignments of ribo-seq data and corresponding mRNA-seq data along with relevant annotation tracks. In this brief, we illustrate how GWIPS-viz can be used to explore the ribosome occupancy at the 5' ends of protein coding genes to assess the activity of AUG and non-AUG TISs responsible for the synthesis of proteoforms with alternative or heterogeneous N-termini. The presence of ribo-seq tracks for various organisms allows for cross-species comparison of orthologous genes and the availability of datasets from multiple laboratories permits the assessment of the technical reproducibility of the ribosome densities.
School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.
Audrey M
AM
Michel
School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.
Anna M
AM
Ahern
School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.
Claire A
CA
Donohue
School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.
Pavel V
PV
Baranov
D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D016678:Genome; D023281:Genomics / Q000379:methods; D006801:Humans; D051379:Mice; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D014176:Protein Biosynthesis; D011506:Proteins / Q000737:chemistry / Q000235:genetics*; D040901:Proteomics / Q000379:methods*; D012333:RNA, Messenger / Q000235:genetics*; D012270:Ribosomes / Q000235:genetics*; D016415:Sequence Alignment; D012984:Software
D011506:Proteins; D012333:RNA, Messenger
Bioinformatics; Non-AUG initiation; Ribosome profiling; Translatomics; ribo-seq; uORF