RT Journal
A1 Fritsch, Claudia
A1 Herrmann, Alexander
A1 Nothnagel, Michael
A1 Szafranski, Karol
A1 Huse, Klaus
A1 Schumann, Frank
A1 Schreiber, Stefan
A1 Platzer, Matthias
A1 Krawczak, Michael
A1 Hampe, Jochen
A1 Brosch, Mario
T1 Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting
JF Genome Research 
JO Genome Research 
YR 2012 
FD November 01 
VO 22 
IS 11 
SP 2208 
OP 2218 
DO 10.1101/gr.139568.112 
UL http://genome.cshlp.org/content/22/11/2208.abstract 
AB 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 to generate a transcriptome-wide map of TISs in a human monocytic cell line. A neural network was trained on the ribosomal footprints observed at previously annotated AUG translation initiation codons (TICs), and used for the ab initio prediction of TISs in 5062 transcripts with sufficient sequence coverage. Functional interpretation suggested 2994 novel upstream open reading frames (uORFs) in the 5′ UTR, 1406 uORFs overlapping with the coding sequence, and 546 N-terminal protein extensions. The TIS detection method was validated on the basis of previously published alternative TISs and uORFs. Among primates, TICs in newly annotated TISs were significantly more conserved than control codons, both for AUGs and near-cognate codons. The transcriptome-wide map of novel candidate TISs derived as part of the study will shed further light on the way in which human proteome diversity is influenced by alternative translation initiation and regulation.