title: Quantitative profiling of initiating ribosomes in vivo.
abstract: Cells have evolved exquisite mechanisms to fine-tune the rate of protein synthesis in response to stress. Systemic mapping of start-codon positions and precise measurement of the corresponding initiation rate would transform our understanding of translational control. Here we present quantitative translation initiation sequencing (QTI-seq), with which the initiating ribosomes can be profiled in real time at single-nucleotide resolution. Resultant initiation maps not only delineated variations of start-codon selection but also highlighted a dynamic range of initiation rates in response to nutrient starvation. The integrated data set provided unique insights into principles of alternative translation and mechanisms controlling different aspects of translation initiation. With RiboTag mice, QTI-seq permitted tissue-specific profiling of initiating ribosomes in vivo. Liver cell-specific ribosome profiling uncovered a robust translational reprogramming of the proteasome system in fasted mice. Our findings illuminated the prevalence and dynamic nature of translational regulation pivotal to physiological adaptation in vivo.
authors.affiliation: Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA.
authors.forename: Xiangwei
authors.initials: X
authors.lastname: Gao
authors.affiliation: Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA.
authors.forename: Ji
authors.initials: J
authors.lastname: Wan
authors.affiliation: Graduate Field of Genetics, Genomics &Development, Cornell University, Ithaca, New York, USA.
authors.forename: Botao
authors.initials: B
authors.lastname: Liu
authors.affiliation: Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, USA.
authors.forename: Ming
authors.identifier: 0000000174816705
authors.initials: M
authors.lastname: Ma
authors.affiliation: 1] Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, USA. [2] Molecular Therapeutics and Natural Products Library Initiative, The Scripps Research Institute, Jupiter, Florida, USA.
authors.forename: Ben
authors.initials: B
authors.lastname: Shen
authors.affiliation: 1] Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA. [2] Graduate Field of Genetics, Genomics &Development, Cornell University, Ithaca, New York, USA.
authors.forename: Shu-Bing
authors.initials: SB
authors.lastname: Qian
mesh_terms: D000818:Animals; D018929:Cell Culture Techniques; D003470:Culture Media; D057809:HEK293 Cells; D006801:Humans; D008099:Liver / Q000378:metabolism; D008822:Mice, Transgenic; D010442:Peptide Chain Initiation, Translational / Q000235:genetics; D046988:Proteasome Endopeptidase Complex / Q000235:genetics / Q000378:metabolism; D014176:Protein Biosynthesis / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D012270:Ribosomes / Q000378:metabolism*; D013312:Stress, Physiological / Q000235:genetics
chemical_list: D003470:Culture Media; D012333:RNA, Messenger; D046988:Proteasome Endopeptidase Complex