A primary hallmark of pathological cardiac hypertrophy is excess protein synthesis due to enhanced translational activity.However,regulatory mechanisms at the translational level under cardiac stress remain poorly und...A primary hallmark of pathological cardiac hypertrophy is excess protein synthesis due to enhanced translational activity.However,regulatory mechanisms at the translational level under cardiac stress remain poorly understood.Here we examined the translational regulations in a mouse cardiac hypertrophy model induced by transaortic constriction(TAC)and explored the conservative networks versus the translatome pattern in human dilated cardiomyopathy(DCM).The results showed that the heart weight to body weight ratio was significantly elevated,and the ejection fraction and fractional shortening significantly decreased 8 weeks after TAC.Puromycin incorporation assay showed that TAC significantly increased protein synthesis rate in the left ventricle.RNAseq revealed 1,632 differentially expressed genes showing functional enrichment in pathways including extracellular matrix remodeling,metabolic processes,and signaling cascades associated with pathological cardiomyocyte growth.When combined with ribosome profiling analysis,we revealed that translation efficiency(TE)of 1,495 genes was enhanced,while the TE of 933 genes was inhibited following TAC.In DCM patients,1,354 genes were upregulated versus 1,213 genes were downregulated at the translation level.Although the majority of the genes were not shared between mouse and human,we identified 93 genes,including Nos3,Kcnj8,Adcy4,Itpr1,Fasn,Scd1,etc.,with highly conserved translational regulations.These genes were remarkably associated with myocardial function,signal transduction,and energy metabolism,particularly related to cGMP-PKG signaling and fatty acid metabolism.Motif analysis revealed enriched regulatory elements in the 5′untranslated regions(5′UTRs)of transcripts with differential TE,which exhibited strong cross-species sequence conservation.Our study revealed novel regulatory mechanisms at the translational level in cardiac hypertrophy and identified conserved translation-sensitive targets with potential applications to treat cardiac hypertrophy and heart failure in the clinic.展开更多
Turnip mosaic virus(TuMV)constitutes one of the primary diseases affecting Brassica rapa,severely impacting its production and resulting in crop failures in various regions worldwide.Recent research has demonstrated t...Turnip mosaic virus(TuMV)constitutes one of the primary diseases affecting Brassica rapa,severely impacting its production and resulting in crop failures in various regions worldwide.Recent research has demonstrated the significance of plant translation initiation factors,specifically the eIF4E and eIF4G family genes,as essential recessive disease resistance genes.In our study,we conducted evolutionary and gene expression studies,leading us to identify e IF(iso)4E.c as a potential TuMV-resistant gene.Leveraging CRISPR/Cas9 technology,we obtained mutant B.rapa plants with edited eIF(iso)4E.c gene.We confirmed eIF(iso)4E.c confers resistance against TuMV through phenotypic observations and virus content evaluations.Furthermore,we employed ribosome profiling assays on eif(iso)4e.c mutant seedlings to unravel the translation landscape in response to TuMV.Interestingly,we observed a moderate correlation between the fold changes in gene expression at the transcriptional and translational levels(R^(2)=0.729).Comparative analysis of ribosome profiling and RNA-seq data revealed that plant-pathogen interaction,and MAPK signaling pathway-plant pathways were involved in eIF(iso)4E.c-mediated TuMV resistance.Further analysis revealed that sequence features,coding sequence length,and normalized minimal free energy,influenced the translation efficiency of genes.Our study highlights that the loss of e IF(iso)4E.c can result in a highly intricate translation mechanism,acting synergistically with transcription to confer resistance against TuMV.展开更多
Heterosis,the phenomenon in which hybrids outperform their parents,has been utilized in maize(Zea mays L.)for over 100 years.To provide a more complete understanding of heterosis,we collected a comprehensive transcrip...Heterosis,the phenomenon in which hybrids outperform their parents,has been utilized in maize(Zea mays L.)for over 100 years.To provide a more complete understanding of heterosis,we collected a comprehensive transcriptome and translatome dataset on seedling leaves for B73,Mo17,and their F1 hybrid,which provided a dynamic landscape of transcriptomic and translatomic variation in maize.Although additivity accounted for a large proportion of variation at two omics-levels,an elevated nonadditive effect was observed in the translatome,especially in the translated subgenome maize1 genes,and the genes that switched from additivity in the transcriptome to nonadditivity in the translatome were significantly enriched in the subgenome maize1.Many genes with allele-specific expression and translation show dramatic regulatory switches between the transcriptome and translatome,and partial genes with allele-specific translation underlying regulatory mechanism also exhibited subgenome bias.Interestingly,we found the translated isoforms show different expression patterns compared with transcriptome and more genes changed their dominant isoforms during the genetic flow from parents to the hybrid at the translatome level.The translated genes with switched dominant isoforms significantly biased to the subgenome maize2 while genes with conserved dominant isoforms significantly enriched in subgenome maize1.Together,the dynamic changed patterns in translatome across hybrid and parental lines show translational fractionation of the maize subgenomes,which may be associated with heterosis in maize and provides a potential theoretical basis for breeding.展开更多
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
A great number of non-coding RNAs(ncRNAs) account for the majority of the genome. The translation of these ncRNAs has been noted but seriously underestimated due to both technological and theoretical limitations. Base...A great number of non-coding RNAs(ncRNAs) account for the majority of the genome. The translation of these ncRNAs has been noted but seriously underestimated due to both technological and theoretical limitations. Based on the development of ribosome profiling(Ribo-seq), full length translating RNA analysis(RNC-seq) and mass spectrometry technology, more and more ncRNAs are being found to be translated in different organism, and some of them can produce functional peptides. While recently, not only individual new functional proteins, but also a new proteome have been experimentally discovered to be encoded by endogenous lncRNAs and circRNAs. These new proteins are of biological significance, suggesting the connection of the translation of ncRNAs to human physiology and diseases. Therefore, an in-depth and systematic understanding of the coding capabilities of ncRNAs is necessary for basic biology and medicine. In this review, we summarize the advances in the field of discovering this new proteome, i.e. "ncRNA-coded" proteins.展开更多
Translational regulation is a critical step in the process of gene expression and governs the synthesis of proteins from mRNAs.Many studies have revealed translational regulation in plants in response to various envir...Translational regulation is a critical step in the process of gene expression and governs the synthesis of proteins from mRNAs.Many studies have revealed translational regulation in plants in response to various environmental stimuli.However,there have been no studies documenting the comprehensive landscape of translational regulation and allele-specific translational efficiency in multiple plant tissues,especially those of rice,a main staple crop that feeds nearly half of the world’s population.Here we used RNA sequencing and ribosome profiling data to analyze the transcriptome and translatome of an elite hybrid rice,Shanyou 63(SY63),and its parental varieties Zhenshan 97 and Minghui 63.The results revealed that gene expression patterns varied more among tissues than among varieties at the transcriptional and translational levels.We identified 3392 upstream open reading frames(uORFs),and the uORF-containing genes were enriched in transcription factors.Only 668 of 13492 long non-coding RNAs could be translated into peptides.Finally,we discovered numerous genes with allele-specific translational efficiency in SY63 and demonstrated that some cis-regulatory elements may contribute to allelic divergence in translational efficiency.Overall,these findings may improve our understanding of translational regulation in rice and provide information for molecular breeding research.展开更多
基金supported by grants from National Natural Science Foundation of China(No.82370392)Shenzhen Medical Research Fund(No.B2302026)+4 种基金Science,Technology and Innovation Commission of Shenzhen Municipality(No.RCJC20210706091947009)National Key R&D Program of China(No.2022YFA1104500)CAMS Innovation Fund for Medical Sciences(No.2023-I2M-1-003 and 2022-I2M-2-001)Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences(No.2019PT320026)National High Level Hospital Clinical Research Funding(No.2022-GSP-GG-7)。
文摘A primary hallmark of pathological cardiac hypertrophy is excess protein synthesis due to enhanced translational activity.However,regulatory mechanisms at the translational level under cardiac stress remain poorly understood.Here we examined the translational regulations in a mouse cardiac hypertrophy model induced by transaortic constriction(TAC)and explored the conservative networks versus the translatome pattern in human dilated cardiomyopathy(DCM).The results showed that the heart weight to body weight ratio was significantly elevated,and the ejection fraction and fractional shortening significantly decreased 8 weeks after TAC.Puromycin incorporation assay showed that TAC significantly increased protein synthesis rate in the left ventricle.RNAseq revealed 1,632 differentially expressed genes showing functional enrichment in pathways including extracellular matrix remodeling,metabolic processes,and signaling cascades associated with pathological cardiomyocyte growth.When combined with ribosome profiling analysis,we revealed that translation efficiency(TE)of 1,495 genes was enhanced,while the TE of 933 genes was inhibited following TAC.In DCM patients,1,354 genes were upregulated versus 1,213 genes were downregulated at the translation level.Although the majority of the genes were not shared between mouse and human,we identified 93 genes,including Nos3,Kcnj8,Adcy4,Itpr1,Fasn,Scd1,etc.,with highly conserved translational regulations.These genes were remarkably associated with myocardial function,signal transduction,and energy metabolism,particularly related to cGMP-PKG signaling and fatty acid metabolism.Motif analysis revealed enriched regulatory elements in the 5′untranslated regions(5′UTRs)of transcripts with differential TE,which exhibited strong cross-species sequence conservation.Our study revealed novel regulatory mechanisms at the translational level in cardiac hypertrophy and identified conserved translation-sensitive targets with potential applications to treat cardiac hypertrophy and heart failure in the clinic.
基金supported by grants from the Scientist Training Program of BAAFS (Grant No.JKZX202406)the Innovation and Capacity-Building Project of BAAFS (Grant No.KJCX20230221)+2 种基金Collaborative innovation program of the Beijing Vegetable Research Center (Grant No.XTCX202302)the National Natural Science Foundation of China (Grant No.32072567)the China Agriculture Research System of MOF and MARA (Grant No.CARS-A03)。
文摘Turnip mosaic virus(TuMV)constitutes one of the primary diseases affecting Brassica rapa,severely impacting its production and resulting in crop failures in various regions worldwide.Recent research has demonstrated the significance of plant translation initiation factors,specifically the eIF4E and eIF4G family genes,as essential recessive disease resistance genes.In our study,we conducted evolutionary and gene expression studies,leading us to identify e IF(iso)4E.c as a potential TuMV-resistant gene.Leveraging CRISPR/Cas9 technology,we obtained mutant B.rapa plants with edited eIF(iso)4E.c gene.We confirmed eIF(iso)4E.c confers resistance against TuMV through phenotypic observations and virus content evaluations.Furthermore,we employed ribosome profiling assays on eif(iso)4e.c mutant seedlings to unravel the translation landscape in response to TuMV.Interestingly,we observed a moderate correlation between the fold changes in gene expression at the transcriptional and translational levels(R^(2)=0.729).Comparative analysis of ribosome profiling and RNA-seq data revealed that plant-pathogen interaction,and MAPK signaling pathway-plant pathways were involved in eIF(iso)4E.c-mediated TuMV resistance.Further analysis revealed that sequence features,coding sequence length,and normalized minimal free energy,influenced the translation efficiency of genes.Our study highlights that the loss of e IF(iso)4E.c can result in a highly intricate translation mechanism,acting synergistically with transcription to confer resistance against TuMV.
基金supported by the National Natural Science Foundation of China(31771798)the National Key Research and Development Program of China(2016YFD0100800)+1 种基金the Competition Fund of the National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural University Scientific&Technological Self-Innovation Foundation(2015RC016)。
文摘Heterosis,the phenomenon in which hybrids outperform their parents,has been utilized in maize(Zea mays L.)for over 100 years.To provide a more complete understanding of heterosis,we collected a comprehensive transcriptome and translatome dataset on seedling leaves for B73,Mo17,and their F1 hybrid,which provided a dynamic landscape of transcriptomic and translatomic variation in maize.Although additivity accounted for a large proportion of variation at two omics-levels,an elevated nonadditive effect was observed in the translatome,especially in the translated subgenome maize1 genes,and the genes that switched from additivity in the transcriptome to nonadditivity in the translatome were significantly enriched in the subgenome maize1.Many genes with allele-specific expression and translation show dramatic regulatory switches between the transcriptome and translatome,and partial genes with allele-specific translation underlying regulatory mechanism also exhibited subgenome bias.Interestingly,we found the translated isoforms show different expression patterns compared with transcriptome and more genes changed their dominant isoforms during the genetic flow from parents to the hybrid at the translatome level.The translated genes with switched dominant isoforms significantly biased to the subgenome maize2 while genes with conserved dominant isoforms significantly enriched in subgenome maize1.Together,the dynamic changed patterns in translatome across hybrid and parental lines show translational fractionation of the maize subgenomes,which may be associated with heterosis in maize and provides a potential theoretical basis for breeding.
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supported by the National Key Research and Development Program (2017YFA0505100, 2017YFA0505001, 2018YFC0910202)the National Natural and Science Foundation of China (81372135 to TW+1 种基金81322028 and 31300649 to GZ31570828 and 31770888 to Q.Y.H.)。
文摘A great number of non-coding RNAs(ncRNAs) account for the majority of the genome. The translation of these ncRNAs has been noted but seriously underestimated due to both technological and theoretical limitations. Based on the development of ribosome profiling(Ribo-seq), full length translating RNA analysis(RNC-seq) and mass spectrometry technology, more and more ncRNAs are being found to be translated in different organism, and some of them can produce functional peptides. While recently, not only individual new functional proteins, but also a new proteome have been experimentally discovered to be encoded by endogenous lncRNAs and circRNAs. These new proteins are of biological significance, suggesting the connection of the translation of ncRNAs to human physiology and diseases. Therefore, an in-depth and systematic understanding of the coding capabilities of ncRNAs is necessary for basic biology and medicine. In this review, we summarize the advances in the field of discovering this new proteome, i.e. "ncRNA-coded" proteins.
基金supported by the National Natural Science Foundation of China(31871269 and 32270712)the Hubei Provincial Natural Science Foundation of China(2019CFA014)a starting research grant for High-level Talents from Guangxi University.
文摘Translational regulation is a critical step in the process of gene expression and governs the synthesis of proteins from mRNAs.Many studies have revealed translational regulation in plants in response to various environmental stimuli.However,there have been no studies documenting the comprehensive landscape of translational regulation and allele-specific translational efficiency in multiple plant tissues,especially those of rice,a main staple crop that feeds nearly half of the world’s population.Here we used RNA sequencing and ribosome profiling data to analyze the transcriptome and translatome of an elite hybrid rice,Shanyou 63(SY63),and its parental varieties Zhenshan 97 and Minghui 63.The results revealed that gene expression patterns varied more among tissues than among varieties at the transcriptional and translational levels.We identified 3392 upstream open reading frames(uORFs),and the uORF-containing genes were enriched in transcription factors.Only 668 of 13492 long non-coding RNAs could be translated into peptides.Finally,we discovered numerous genes with allele-specific translational efficiency in SY63 and demonstrated that some cis-regulatory elements may contribute to allelic divergence in translational efficiency.Overall,these findings may improve our understanding of translational regulation in rice and provide information for molecular breeding research.
