title: Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution.
abstract: Understanding translational control in gene expression relies on precise and comprehensive determination of translation initiation sites (TIS) across the entire transcriptome. The recently developed ribosome-profiling technique enables global translation analysis, providing a wealth of information about both the position and the density of ribosomes on mRNAs. Here we present an approach, global translation initiation sequencing, applying in parallel the ribosome E-site translation inhibitors lactimidomycin and cycloheximide to achieve simultaneous detection of both initiation and elongation events on a genome-wide scale. This approach provides a view of alternative translation initiation in mammalian cells with single-nucleotide resolution. Systemic analysis of TIS positions supports the ribosome linear-scanning mechanism in TIS selection. The alternative TIS positions and the associated ORFs identified by global translation initiation sequencing are conserved between human and mouse cells, implying physiological significance of alternative translation. Our study establishes a practical platform for uncovering the hidden coding potential of the transcriptome and offers a greater understanding of the complexity of translation initiation.
authors.affiliation: Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA.
authors.forename: Sooncheol
authors.initials: S
authors.lastname: Lee
authors.forename: Botao
authors.initials: B
authors.lastname: Liu
authors.forename: Soohyun
authors.initials: S
authors.lastname: Lee
authors.forename: Sheng-Xiong
authors.initials: SX
authors.lastname: Huang
authors.forename: Ben
authors.initials: B
authors.lastname: Shen
authors.forename: Shu-Bing
authors.initials: SB
authors.lastname: Qian
mesh_terms: D000818:Animals; D018387:Codon, Initiator / Q000235:genetics; D003513:Cycloheximide / Q000494:pharmacology; D017931:DNA Primers / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics; D057809:HEK293 Cells; D006801:Humans; D015151:Immunoblotting; D018942:Macrolides / Q000494:pharmacology; D051379:Mice; D010442:Peptide Chain Initiation, Translational / Q000187:drug effects / Q000235:genetics*; D010881:Piperidones / Q000494:pharmacology; D010957:Plasmids / Q000235:genetics; D012333:RNA, Messenger / Q000378:metabolism*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012270:Ribosomes / Q000378:metabolism*; D017422:Sequence Analysis, DNA / Q000379:methods; D059467:Transcriptome / Q000235:genetics*
chemical_list: D018387:Codon, Initiator; D017931:DNA Primers; D018076:DNA, Complementary; D018942:Macrolides; D010881:Piperidones; D012333:RNA, Messenger; C077633:lactimidomycin; D003513:Cycloheximide