Datasets

Title	Buffer composition affects ribosome footprint precision in Arabidopsis root and shoot
Organism
Number of Samples	8
Release Date	2016/05/10 00:00
Sequencing Types
Protocol Details

GWIPS-viz	Trips-Viz
Visit GWIPS-viz

Title
Authors	Hsu PY,Calviello L,Wu HL,Li FW,Rothfels CJ,Ohler U,Benfey PN
Journal	Proceedings of the National Academy of Sciences of the United States of America
Publication Date	2016 Nov 8
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 to Arabidopsis that 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.
PMC	PMC5111709
PMID	27791167
DOI

Hsu et al. 2016 (PRJNA321201)