RT Journal
A1 Michel, Audrey M.
A1 Choudhury, Kingshuk Roy
A1 Firth, Andrew E.
A1 Ingolia, Nicholas T.
A1 Atkins, John F.
A1 Baranov, Pavel V.
T1 Observation of dually decoded regions of the human genome using ribosome profiling data
JF Genome Research 
JO Genome Research 
YR 2012 
FD November 01 
VO 22 
IS 11 
SP 2219 
OP 2229 
DO 10.1101/gr.133249.111 
UL http://genome.cshlp.org/content/22/11/2219.abstract 
AB The recently developed ribosome profiling technique (Ribo-Seq) allows mapping of the locations of translating ribosomes on mRNAs with subcodon precision. When ribosome protected fragments (RPFs) are aligned to mRNA, a characteristic triplet periodicity pattern is revealed. We utilized the triplet periodicity of RPFs to develop a computational method for detecting transitions between reading frames that occur during programmed ribosomal frameshifting or in dual coding regions where the same nucleotide sequence codes for multiple proteins in different reading frames. Application of this method to ribosome profiling data obtained for human cells allowed us to detect several human genes where the same genomic segment is translated in more than one reading frame (from different transcripts as well as from the same mRNA) and revealed the translation of hitherto unpredicted coding open reading frames.