title: Genome-wide assessment of differential translations with ribosome profiling data.
abstract: The closely regulated process of mRNA translation is crucial for precise control of protein abundance and quality. Ribosome profiling, a combination of ribosome foot-printing and RNA deep sequencing, has been used in a large variety of studies to quantify genome-wide mRNA translation. Here, we developed Xtail, an analysis pipeline tailored for ribosome profiling data that comprehensively and accurately identifies differentially translated genes in pairwise comparisons. Applied on simulated and real datasets, Xtail exhibits high sensitivity with minimal false-positive rates, outperforming existing methods in the accuracy of quantifying differential translations. With published ribosome profiling datasets, Xtail does not only reveal differentially translated genes that make biological sense, but also uncovers new events of differential translation in human cancer cells on mTOR signalling perturbation and in human primary macrophages on interferon gamma (IFN-γ) treatment. This demonstrates the value of Xtail in providing novel insights into the molecular mechanisms that involve translational dysregulations.
authors.affiliation: MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China.|Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China.|Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.|School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Zhengtao
authors.initials: Z
authors.lastname: Xiao
authors.affiliation: MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China.|Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.|School of Life Sciences, Tsinghua University, Beijing 100084, China.|Joint Graduate Program of Peking-Tsinghua-National Institute of Biological Science, Tsinghua University, Beijing 100084, China.
authors.forename: Qin
authors.initials: Q
authors.lastname: Zou
authors.affiliation: MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China.|Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China.|Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.|School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Liu
authors.affiliation: MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China.|Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China.|Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.|School of Life Sciences, Tsinghua University, Beijing 100084, China.
authors.forename: Xuerui
authors.initials: X
authors.lastname: Yang
mesh_terms: D000818:Animals; D002460:Cell Line; D045744:Cell Line, Tumor; D066264:Datasets as Topic; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007371:Interferon-gamma / Q000494:pharmacology; D008264:Macrophages / Q000166:cytology / Q000187:drug effects / Q000276:immunology; D051379:Mice; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D012270:Ribosomes / Q000235:genetics* / Q000378:metabolism; D012984:Software; D058570:TOR Serine-Threonine Kinases / Q000235:genetics / Q000378:metabolism
chemical_list: D012333:RNA, Messenger; D007371:Interferon-gamma; C546842:MTOR protein, human; D058570:TOR Serine-Threonine Kinases