RT Journal Article
SR Electronic
T1 Ribosomal stalling landscapes revealed by high-throughput inverse toeprinting of mRNA libraries
JF Life Science Alliance
JO Life Sci. Alliance
FD Life Science Alliance LLC
SP e201800148
DO 10.26508/lsa.201800148
VO 1
IS 5
A1 Britta Seip
A1 Guénaël Sacheau
A1 Denis Dupuy
A1 C Axel Innis
YR 2018
UL https://www.life-science-alliance.org/content/1/5/e201800148.abstract
AB Although it is known that the amino acid sequence of a nascent polypeptide can impact its rate of translation, dedicated tools to systematically investigate this process are lacking. Here, we present high-throughput inverse toeprinting, a method to identify peptide-encoding transcripts that induce ribosomal stalling in vitro. Unlike ribosome profiling, inverse toeprinting protects the entire coding region upstream of a stalled ribosome, making it possible to work with random or focused transcript libraries that efficiently sample the sequence space. We used inverse toeprinting to characterize the stalling landscapes of free and drug-bound Escherichia coli ribosomes, obtaining a comprehensive list of arrest motifs that were validated in vivo, along with a quantitative measure of their pause strength. Thanks to the modest sequencing depth and small amounts of material required, inverse toeprinting provides a highly scalable and versatile tool to study sequence-dependent translational processes.