Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting

• DOI: 10.1101/gr.139568.112
• Publication Date: 2012-08-12T00:43:43Z
• Authors: Claudia Fritsch; Alexander Herrmann; Michael Nothnagel; Karol Szafranski; Klaus Huse; Frank Schumann; Stefan Schreiber; Matthias Platzer; Michael Krawczak; Jochen Hampe; Mario Brosch
• Keywords: Footprinting; Ribosomal protein; Eukaryotic translation; Proteome

So far, the annotation of translation initiation sites (TISs) has been based mostly upon bioinformatics rather than experimental evidence. We adapted ribosomal footprinting to puromycin-treated cells generate a transcriptome-wide map TISs in human monocytic cell line. A neural network was trained on footprints observed at previously annotated AUG codons (TICs), and used for ab initio prediction 5062 transcripts with sufficient sequence coverage. Functional interpretation suggested 2994 novel upstream open reading frames (uORFs) 5′ UTR, 1406 uORFs overlapping coding sequence, 546 N-terminal protein extensions. The TIS detection method validated basis published alternative uORFs. Among primates, TICs newly were significantly more conserved control codons, both AUGs near-cognate codons. candidate derived as part study will shed further light way which proteome diversity is influenced by regulation.