title: Insights into the mechanisms of eukaryotic translation gained with ribosome profiling.
abstract: The development of Ribosome Profiling (RiboSeq) has revolutionized functional genomics. RiboSeq is based on capturing and sequencing of the mRNA fragments enclosed within the translating ribosome and it thereby provides a 'snapshot' of ribosome positions at the transcriptome wide level. Although the method is predominantly used for analysis of differential gene expression and discovery of novel translated ORFs, the RiboSeq data can also be a rich source of information about molecular mechanisms of polypeptide synthesis and translational control. This review will focus on how recent findings made with RiboSeq have revealed important details of the molecular mechanisms of translation in eukaryotes. These include mRNA translation sensitivity to drugs affecting translation initiation and elongation, the roles of upstream ORFs in response to stress, the dynamics of elongation and termination as well as details of intrinsic ribosome behavior on the mRNA after translation termination. As the RiboSeq method is still at a relatively early stage we will also discuss the implications of RiboSeq artifacts on data interpretation.
authors.affiliation: Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia cycloheximide@yandex.ru.
authors.forename: Dmitry E
authors.initials: DE
authors.lastname: Andreev
authors.affiliation: School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.
authors.forename: Patrick B F
authors.initials: PB
authors.lastname: O'Connor
authors.affiliation: School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland.
authors.forename: Gary
authors.initials: G
authors.lastname: Loughran
authors.affiliation: Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia.
authors.forename: Sergey E
authors.identifier: 0000-0002-1774-8475
authors.initials: SE
authors.lastname: Dmitriev
authors.affiliation: School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland p.baranov@ucc.ie.
authors.forename: Pavel V
authors.initials: PV
authors.lastname: Baranov
authors.affiliation: Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia shatsky@genebee.msu.su.
authors.forename: Ivan N
authors.initials: IN
authors.lastname: Shatsky
mesh_terms: D000818:Animals; D018387:Codon, Initiator; D005786:Gene Expression Regulation; D006801:Humans; D046912:Multiprotein Complexes; D016366:Open Reading Frames; D010441:Peptide Chain Elongation, Translational; D010442:Peptide Chain Initiation, Translational; D010443:Peptide Chain Termination, Translational; D011485:Protein Binding; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D054657:Ribosome Subunits / Q000378:metabolism; D012270:Ribosomes / Q000378:metabolism*
chemical_list: D018387:Codon, Initiator; D046912:Multiprotein Complexes; D012333:RNA, Messenger