The translatome,a profile of the translational status of genetic information within cells,provides a new perspective on gene expression.Although many plant genomes have been sequenced,comprehensive translatomic annota...The translatome,a profile of the translational status of genetic information within cells,provides a new perspective on gene expression.Although many plant genomes have been sequenced,comprehensive translatomic annotations are not available for plants due to a lack of efficient translatome profiling techniques.Here,we developed a new technique termed 30 ribosome-profiling sequencing(30Ribo-seq)for reliable,robust translatomic profiling.30Ribo-seq combines polysome profiling and 30 selection with a barcoding and pooling strategy.Systematic translatome profiling of different tissues of Arabidopsis,rice,and maize using conventional ribosome profiling(Ribo-seq)and 30Ribo-seq revealed many novel translational genomic loci,thereby complementing functional genome annotation in plants.Using the low-cost,efficient 30Ribo-seq technique and genome-wide association mapping of translatome expression(eGWAS),we performed a population-level dissection of the translatomes of 159 diverse maize inbred lines and identified 1,777 translational expression quantitative trait loci(eQTLs).Notably,local eQTLs are significantly enriched in the 30 untranslated regions of genes.Detailed eQTL analysis suggested that sequence variation around the polyadenylation(polyA)signal motif plays a key role in translatomic variation.Our study provides a comprehensive translatome annotation of plant functional genomes and introduces 30Ribo-seq,which paves the way for deep translatomic analysis at the population level.展开更多
In an era characterized by rapidly changing and less-predictable weather conditions fueled by the climate crisis,understanding the mechanisms underlying local adaptation in plants is of paramount importance for the co...In an era characterized by rapidly changing and less-predictable weather conditions fueled by the climate crisis,understanding the mechanisms underlying local adaptation in plants is of paramount importance for the conservation of species.As the frequency and intensity of extreme precipitation events increase,so are the flooding events resulting from soil water saturation.The subsequent onset of hypoxic stress is one of the leading causes of crop damage and yield loss.By combining genomics and remote sensing data,it is now possible to probe natural plant populations that have evolved in different rainfall regimes and look for molecular adaptation to hypoxia.Here,using an environmental genome-wide association study(eGWAS)of 934 non-redundant georeferenced Arabidopsis ecotypes,we have identified functional variants of the gene MED25 BINDING RING-H2 PROTEIN 1(MBR1).This gene encodes a ubiquitin-protein ligase that regulates MEDIATOR25(MED25),part of a multiprotein complex that interacts with transcription factors that act as key drivers of the hypoxic response in Arabidopsis,namely the RELATED TO AP2 proteins RAP2.2 and RAP2.12.Through experimental validation,we show that natural variants of MBR1 have different effects on the stability of MED25 and,in turn,on hypoxia tolerance.This study also highlights the pivotal role of the MBR1/MED25 module in establishing a comprehensive hypoxic response.Our findings show that molecular candidates for plant environmental adaptation can be effectively mined from large datasets.This thus supports the need for integration of forward and reverse genetics with robust molecular physiology validation of outcomes.展开更多
基金supported by the National Natural Science Foundation of China(31771798,92035302,31922068)the National Key Research and Development Program of China(2016YFD0100800)+1 种基金the Hubei Provincial Natural Science Foundation of China(2019CFA014)the Competition Fund of the National Key Laboratory of Crop Genetic Improvement,and Huazhong Agricultural University Scientific&Technological Selfinnovation Foundation(2015RC016).
文摘The translatome,a profile of the translational status of genetic information within cells,provides a new perspective on gene expression.Although many plant genomes have been sequenced,comprehensive translatomic annotations are not available for plants due to a lack of efficient translatome profiling techniques.Here,we developed a new technique termed 30 ribosome-profiling sequencing(30Ribo-seq)for reliable,robust translatomic profiling.30Ribo-seq combines polysome profiling and 30 selection with a barcoding and pooling strategy.Systematic translatome profiling of different tissues of Arabidopsis,rice,and maize using conventional ribosome profiling(Ribo-seq)and 30Ribo-seq revealed many novel translational genomic loci,thereby complementing functional genome annotation in plants.Using the low-cost,efficient 30Ribo-seq technique and genome-wide association mapping of translatome expression(eGWAS),we performed a population-level dissection of the translatomes of 159 diverse maize inbred lines and identified 1,777 translational expression quantitative trait loci(eQTLs).Notably,local eQTLs are significantly enriched in the 30 untranslated regions of genes.Detailed eQTL analysis suggested that sequence variation around the polyadenylation(polyA)signal motif plays a key role in translatomic variation.Our study provides a comprehensive translatome annotation of plant functional genomes and introduces 30Ribo-seq,which paves the way for deep translatomic analysis at the population level.
基金Scuola Superiore Sant'Anna and by MUR-PRIN2022(PRIN 2022-2022YHWH9RNext Generation EU)to P.P.and E.L.Agritech National Research Center and received funding from the European Union Next-Generation EU(PIANO NAZIONALE DI RIPRESA E RESILIENZA(PNRR)–MISSIONE 4 COMPONENTE 2,INVESTIMENTO 1.4–D.D.103217/06/2022,CN00000022).
文摘In an era characterized by rapidly changing and less-predictable weather conditions fueled by the climate crisis,understanding the mechanisms underlying local adaptation in plants is of paramount importance for the conservation of species.As the frequency and intensity of extreme precipitation events increase,so are the flooding events resulting from soil water saturation.The subsequent onset of hypoxic stress is one of the leading causes of crop damage and yield loss.By combining genomics and remote sensing data,it is now possible to probe natural plant populations that have evolved in different rainfall regimes and look for molecular adaptation to hypoxia.Here,using an environmental genome-wide association study(eGWAS)of 934 non-redundant georeferenced Arabidopsis ecotypes,we have identified functional variants of the gene MED25 BINDING RING-H2 PROTEIN 1(MBR1).This gene encodes a ubiquitin-protein ligase that regulates MEDIATOR25(MED25),part of a multiprotein complex that interacts with transcription factors that act as key drivers of the hypoxic response in Arabidopsis,namely the RELATED TO AP2 proteins RAP2.2 and RAP2.12.Through experimental validation,we show that natural variants of MBR1 have different effects on the stability of MED25 and,in turn,on hypoxia tolerance.This study also highlights the pivotal role of the MBR1/MED25 module in establishing a comprehensive hypoxic response.Our findings show that molecular candidates for plant environmental adaptation can be effectively mined from large datasets.This thus supports the need for integration of forward and reverse genetics with robust molecular physiology validation of outcomes.
