title: Super-resolution ribosome profiling reveals unannotated translation events inArabidopsis.
abstract: Deep sequencing of ribosome footprints (ribosome profiling) maps and quantifies mRNA translation. Because ribosomes decode mRNA every 3 nt, the periodic property of ribosome footprints could be used to identify novel translated ORFs. However, due to the limited resolution of existing methods, the 3-nt periodicity is observed mostly in a global analysis, but not in individual transcripts. Here, we report a protocol applied toArabidopsisthat maps over 90% of the footprints to the main reading frame and thus offers super-resolution profiles for individual transcripts to precisely define translated regions. The resulting data not only support many annotated and predicted noncanonical translation events but also uncover small ORFs in annotated noncoding RNAs and pseudogenes. A substantial number of these unannotated ORFs are evolutionarily conserved, and some produce stable proteins. Thus, our study provides a valuable resource for plant genomics and an efficient optimization strategy for ribosome profiling in other organisms.
authors: Department of Biology, Duke University, Durham, NC 27708.
authors: Polly Yingshan
authors: PY
authors: Hsu
authors: Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany.|Department of Biology, Humboldt Universität zu Berlin, 10099 Berlin, Germany.
authors: Lorenzo
authors: L
authors: Calviello
authors: Bioinformatics Research Center and Department of Statistics, North Carolina State University, Raleigh, NC 27695.
authors: Hsin-Yen Larry
authors: HL
authors: Wu
authors: Department of Biology, Duke University, Durham, NC 27708.|University Herbarium, University of California, Berkeley, CA 94720.|Department of Integrative Biology, University of California, Berkeley, CA 94720.
authors: Fay-Wei
authors: FW
authors: Li
authors: University Herbarium, University of California, Berkeley, CA 94720.|Department of Integrative Biology, University of California, Berkeley, CA 94720.
authors: Carl J
authors: CJ
authors: Rothfels
authors: Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany.|Department of Biology, Humboldt Universität zu Berlin, 10099 Berlin, Germany.
authors: Uwe
authors: U
authors: Ohler
authors: Department of Biology, Duke University, Durham, NC 27708; philip.benfey@duke.edu.|Howard Hughes Medical Institute, Duke University, Durham, NC 27708.
authors: Philip N
authors: PN
authors: Benfey
keywords: Ribo-seq; ncRNA; ribosome footprint; sORF; translation