The Elongator complex is conserved in a wide range of species and plays crucial roles in diverse cellular processes.We have previously shown that the Elongator protein PoElp3 was involved in the asexual development,pa...The Elongator complex is conserved in a wide range of species and plays crucial roles in diverse cellular processes.We have previously shown that the Elongator protein PoElp3 was involved in the asexual development,pathogenicity,and autophagy of the rice blast fungus.In this study,we further revealed that PoElp3 functions via tRNA-mediated protein integrity.Phenotypic analyses revealed that overexpression of two of the tRNAs,tK(UUU)and tQ(UUG)could rescue the defects inΔPoelp3 strain.TMT-based proteomic and transcriptional analyses demonstrated that 386 proteins were down-regulated inΔPoelp3 strain compared with wild type strain Guy11,in a transcription-independent manner.Codon usage assays revealed an enrichment of Glutamine CAA-biased mRNA in the 386 proteins compared with the 70-15 genome.In addition to those reported previously,we also found that PoErp9,a sphingolipid C9-methyltransferase,was down-regulated in theΔPoelp3strain.Through an ILV2-specific integration of PoERP9-GFP into the wild type andΔPoelp3 strain,we were able to show that PoErp9 was positively regulated by PoElp3 translationally but not transcriptionally.Functional analyses revealed that PoErp9 was involved in the fungal growth,conidial development,pathogenicity,and TORrelated autophagy homeostasis in Pyricularia oryzae.Taken together,our results suggested that PoElp3 acts through the tRNA-mediated translational efficiency to regulate asexual development,pathogenicity,sphingolipid metabolism,and autophagy in the rice blast fungus.展开更多
Selenium is a crucial trace element that contributes to physiological processes in the body as selenoproteins.Selenoproteins serve as an integral role in the body in controlling the redox state of cells and protecting...Selenium is a crucial trace element that contributes to physiological processes in the body as selenoproteins.Selenoproteins serve as an integral role in the body in controlling the redox state of cells and protecting against damage induced by oxidative stress.This study aimed to investigate the effects and possible mechanism of selenium on selenoproteins expression in EA.hy926 cells induced by oxidized low density lipoprotein(oxLDL).The impact of selenium on the viability of EA.hy926 cells was detected by the methylthiazolyldiphenyltetrazolium bromide(MTT)method,and intracellular reactive oxygen species(ROS)level and mitochondrial membrane potential were assessed by fluorescent probe DCFH-DA and JC-1,respectively.RNA-seq,quantitative real-time polymerase chain reaction(qPCR),and Western blot were used to investigate the selenoprotein expression.Selenoprotein mRNA translation efficiency was analyzed by ribosome profiling(Ribo-Seq)coupled with transcriptomics.Our data showed that selenium supplementation(0.5μmol/L)significantly decreased ROS production,increased mitochondrial inner membrane potential and increased the proliferative activity of EA.hy926 cells induced by oxLDL.Moreover,The protective effects of selenium against oxLDL-induced EA.hy926 cell injury were associated with the upregulation of the expressions of selenoproteins glutathione peroxidase 1(GPX1),glutathione peroxidase 4(GPX4),and thioredoxin reductase 1(TXNRD1).Furthermore,the expressions of selenoproteins GPX1 and GPX4 were hierarchically controlled,but the expressions of selenoproteins TXNRD1 were mainly regulated by oxLDL.Finally,Ribo-Seq coupled with transcriptomics results demonstrated that the expressions of selenoproteins GPX1,GPX4,and TXNRD1 were regulated at the translation process level.These findings suggested that selenium could have preventive effects in oxLDL induced EA.hy926 cell injury by regulating the selenoprotein expression,and the selenoproteins expressions at the translation level in vascular endothelial cells need further study.展开更多
Objective The most prevalent mRNA modification,N6-methyladenosine(m^(6)A)plays an important role in various RNA metabolism,including gene expression and translation.By recruiting different“reader”proteins and their ...Objective The most prevalent mRNA modification,N6-methyladenosine(m^(6)A)plays an important role in various RNA metabolism,including gene expression and translation.By recruiting different“reader”proteins and their cofactors,m^(6)A modification can affect messenger RNA(mRNA)degradation,splicing,nuclear export and translation.However,the selective mechanism by which m^(6)A sites regulate mRNA translation through m^(6)A reader YTHDF1 binding remains poorly understood,due to a lack of computational methods for identifying context-specific m^(6)A sites that regulate translation.To address this,we developed a novel computational framework named m^(6)ATEpre,the first tool designed to predict cell-specific m^(6)A sites that regulate translation efficiency.Methods m^(6)ATEpre integrates multi-omics data,introduces a novel feature representation strategy for m^(6)A site sequences,and employs an autoencoder to effectively capture embedded feature representations.Specifically,m^(6)ATEpre first integrated MeRIP-seq data and PAR-CLIP data through overlapping m^(6)A sites with YTHDF1 binding sites and identified YTHDF1-mediated m^(6)A sites.Then,m^(6)ATEpre detected the translation gene by analyzing the Ribo-seq data under YTHDF1 knockdown vs control condition.Genes whose translation is mediated by YTHDF1 in an m^(6)A-dependent manner were identified by a significant decrease in translation efficiency upon YTHDF1 knockdown.Next,we proposed a binary vector indicating the presence or absence of YTHDF1 binding motifs to characterize each m^(6)A site sequence.This represents a novel feature representation strategy for m^(6)A sites.m^(6)ATEpre utilized the autoencoder to extract the potentially important feature representations and constructed a multilayer perceptron neural networks model to predict potential m^(6)A sites that regulating translation efficiency.Results A comprehensive evaluation of m^(6)ATEpre was conducted through a series of experiments.We compared its performance against that of a similar prediction task model,as well as other classifiers.The results indicate that m^(6)ATEpre achieved the best prediction performance.In addition,we analyzed different feature representation strategies and performed ablation experiments to validate the rationality of the model design.The results demonstrate that our proposed feature representation strategy has a greater advantage in improving prediction performance.In the HeLa cell line,bioinformatic analysis of the metagene distribution and sequence minimum free energy of m^(6)A sites regulating translation efficiency(m^(6)A-reg-TE sites)revealed their specific properties in translation regulation.Functional enrichment analysis indicated that m^(6)A-reg-TE genes are associated with specific biological processes and KEGG pathways.By integrating the binding sites of YTHDF1 co-factors with m^(6)A-reg-TE sites,we revealed that YTHDF1-mediated and m^(6)A-dependent translation efficiency regulation requires the cooperation of multiple translation-regulatory RNA-binding proteins among its co-factors in the HeLa cell line.Furthermore,we extended our predictions to the dataset of the HEK293T cell line.Similarly,bioinformatic analysis of the metagene distribution and functional enrichment revealed the cell-specific characteristic of these predicted m^(6)A-reg-TE sites in HEK293T cells.Likewise,integrated analysis of multiple YTHDF1 co-factors and m^(6)A-reg-TE sites predicted in the HEK293T cell line reveals their m^(6)A-dependent cooperation in regulating translation efficiency.Conclusion m^(6)ATEpre is a timely tool that will advance our understanding of the mechanisms of m^(6)A regulation in translation efficiency.The source code and datasets used in this work can be downloaded from https://www.scidb.cn/s/bAZZFr.展开更多
Dear Editor,In vitro transcribed(IVT)mRNA is an emerging class of drug for both therapeu-tics and vaccines(Hao et al..2024;Sahin et al.,2014).Enhancing its translation efficiency remains a core challenge for mRNA-base...Dear Editor,In vitro transcribed(IVT)mRNA is an emerging class of drug for both therapeu-tics and vaccines(Hao et al..2024;Sahin et al.,2014).Enhancing its translation efficiency remains a core challenge for mRNA-based applications(Karikó,2019).展开更多
Circular RNAs (circ RNAs) are covalently closed,singlestranded non-coding RNAs generated through pre-m RNA back-splicing [1,2],exhibiting broad biological functions across cells and organisms [3,4].Recent advances in ...Circular RNAs (circ RNAs) are covalently closed,singlestranded non-coding RNAs generated through pre-m RNA back-splicing [1,2],exhibiting broad biological functions across cells and organisms [3,4].Recent advances in developing circular RNA (circ RNA)-based therapeutics and vaccines underscore their clinical utility [1,5–10].Nevertheless,circ RNA-based therapeutics face critical technical hurdles,including optimization of efficient circularization sequences,translation enhancement,and improved in vivo delivery [10].展开更多
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
RNA modifications have revealed essential regulatory roles in messenger RNA(mRNA)metabolism to affect cellular gene regulation,and have also received widespread applications in RNA therapeutics such as mRNA vaccine an...RNA modifications have revealed essential regulatory roles in messenger RNA(mRNA)metabolism to affect cellular gene regulation,and have also received widespread applications in RNA therapeutics such as mRNA vaccine and protein replacement.Most efforts focus on mRNA internal base and ribose modifications,however,chemical modification within mRNA poly(A)tail remains unexplored.In this work,we synthesized luciferase and GFP(Green Fluorescent Protein)mRNAs with a fully chemically modified poly(A)tail,in which adenosine is replaced by either base-modified N^(6)-methyladenosine(m^(6)A)/N^(6)-ethyladenosine(Et^(6)A)or ribose-modified 2’-O-methyladenosine(Am),and investigated the effect of these tail modifications on mRNA stability and translation efficiency upon transfection into cells using fluorescent and chemiluminescent reporter assays.The results showed that all these modifications impaired translation without affecting mRNA stability.Further study demonstrated that modified poly(A)tail weakens its binding to PABPC1(Polyadenylate-Binding Protein 1),which reduces the formation of mRNA head-to-tail loop and thus decreases the translation efficiency.Our finding reveals the translation-regulatory role of the adenosine modifications within poly(A)tail,offering a new way for manipulating mRNA translation inside cells.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
Understanding how corals adapt to changes in seawater carbonate chemistry is crucial for developing effective coral con-servation strategies.Research to date has mostly focused on short-term experiments,overlooking lo...Understanding how corals adapt to changes in seawater carbonate chemistry is crucial for developing effective coral con-servation strategies.Research to date has mostly focused on short-term experiments,overlooking long-term evolutionary effects.Here,we investigated the link between short-term stress responses and long-term genetic adaptations in the coral species Porites pukoensis through experiments under varying CO_(2) and alkalinity conditions.Our results showed that alkalin-ity enrichment significantly increased coral calcification rates by 35%-45%compared to high CO_(2) treatment,highlighting the potential of alkalinity enrichment to mitigate acidification impacts.Corals modulated relative expression levels of basic and acidic proteins in response to changes in seawater carbonate chemistry in the stress experiments.Genomic data revealed that this mechanism has been evolutionarily fixed in various organisms adapting to seawater carbonate chemistry.Addition-ally,both experimental and genomic results showed that extracellular matrix proteins,like collagen with von Willebrand factor type A domain,were modified in response to distinct carbonate environments.Molecular dynamics simulations and in-vitro experiments demonstrated that the structural stability of these proteins contributes to coral resilience under acidified conditions.This study established an integrated framework combining stress experiments,multi-omics analyses,molecular simulations,and in-vitro validation to identify key proteins involved in coral adaptation to acidification.展开更多
Background:In recent years,avian influenza viruses(AIVs)have seriously threatened human health.Questions such as:why do AIVs infect humans?,how quickly can an AIV become pandemic?,and which virus is the most dangerous...Background:In recent years,avian influenza viruses(AIVs)have seriously threatened human health.Questions such as:why do AIVs infect humans?,how quickly can an AIV become pandemic?,and which virus is the most dangerous?cannot be sufficiently answered using current bioinformatic studies.Method:Secondary structures and energies of representative 5′-untranslated region(UTR)of the HA gene were calculated.Then their secondary structures and energies were re-calculated after one or two nucleotide substitutions were introduced into the HA 5′-UTR.Phylogenetic trees on the basis of hemagglutinin(HA)and polymerase basic protein 2(PB2)amino acid sequences and HA 5′-UTR nucleotide sequences were constructed.The connection between the energy and translation efficiency of 5′-UTR was confirmed by in vitro coupled transcription/translation assay.Results:The simplicity of the secondary structure of the 5′-UTR of the HA gene determines the overall virus replication rate and transmission potential.Point mutation assays show that the 5′-UTR sequences of the HA gene in the influenza subtypes H2N2,H3N2,and H7N9 have greater variation potentials than other virus subtypes.Conclusion:Some high-virulent strains of avian influenza might emerge in the next two to three years.The H2N2 subtype,once disappeared in humans,may stage a comeback.The current outbreak of H7N9 may become pandemic and cause even more deaths,if one or two bases are substituted in the 5′-UTR sequence of the HA gene.展开更多
Although the function of tRNAs in the translational process is well established,it remains controversial whether tRNA abundance is tightly associated with translational efficiency(TE)in mammals.Moreover,how critically...Although the function of tRNAs in the translational process is well established,it remains controversial whether tRNA abundance is tightly associated with translational efficiency(TE)in mammals.Moreover,how critically the expression of tRNAs contributes to the establishment of tissue-specific proteomes in mammals has not been well addressed.Here,we measured both tRNA expression using demethylase-tRNA sequencing(DM-tRNA-seq)and TE of mRNAs using ribosome-tagging sequencing(RiboTag-seq)in the brain,heart,and testis of mice.Remarkable variation in the expression of tRNA isodecoders was observed among different tissues.When the statistical effect of isodecoder-grouping on reducing variations is considered through permutating the anticodons,we observed an expected reduction in the variation of anticodon expression across all samples,an unexpected smaller variation of anticodon usage bias,and an unexpected larger variation of tRNA isotype expression at amino acid level.Regardless of whether or not they share the same anticodons,the isodecoders encoding the same amino acids are co-expressed across different tissues.Based on the expression of tRNAs and the TE of mRNAs,we find that the tRNA adaptation index(tAI)and TE are significantly correlated in the same tissues but not between tissues;and tRNA expression and the amino acid composition of translating peptides are positively correlated in the same tissues but not between tissues.We therefore hypothesize that the tissue-specific expression of tRNAs might be due to post-transcriptional mechanisms.This study provides a resource for tRNA and translation studies,as well as novel insights into the dynamics of tRNAs and their roles in translational regulation.展开更多
基金supported by National Natural Science Foundation of China(32172365 and 32272513)the Central Guidance on Local Science and Technology Development Fund of Fujian Province,China(2022L3088)the Innovative Research Funding of Fujian Agriculture and Forestry University,China(CXZX2020153D)。
文摘The Elongator complex is conserved in a wide range of species and plays crucial roles in diverse cellular processes.We have previously shown that the Elongator protein PoElp3 was involved in the asexual development,pathogenicity,and autophagy of the rice blast fungus.In this study,we further revealed that PoElp3 functions via tRNA-mediated protein integrity.Phenotypic analyses revealed that overexpression of two of the tRNAs,tK(UUU)and tQ(UUG)could rescue the defects inΔPoelp3 strain.TMT-based proteomic and transcriptional analyses demonstrated that 386 proteins were down-regulated inΔPoelp3 strain compared with wild type strain Guy11,in a transcription-independent manner.Codon usage assays revealed an enrichment of Glutamine CAA-biased mRNA in the 386 proteins compared with the 70-15 genome.In addition to those reported previously,we also found that PoErp9,a sphingolipid C9-methyltransferase,was down-regulated in theΔPoelp3strain.Through an ILV2-specific integration of PoERP9-GFP into the wild type andΔPoelp3 strain,we were able to show that PoErp9 was positively regulated by PoElp3 translationally but not transcriptionally.Functional analyses revealed that PoErp9 was involved in the fungal growth,conidial development,pathogenicity,and TORrelated autophagy homeostasis in Pyricularia oryzae.Taken together,our results suggested that PoElp3 acts through the tRNA-mediated translational efficiency to regulate asexual development,pathogenicity,sphingolipid metabolism,and autophagy in the rice blast fungus.
基金supported by grants from the National Natural Science Foundation of China(NSFC,81960588)the Ningxia Natural Science Foundation(2020AAC03146)support from the Ningxia Medical University。
文摘Selenium is a crucial trace element that contributes to physiological processes in the body as selenoproteins.Selenoproteins serve as an integral role in the body in controlling the redox state of cells and protecting against damage induced by oxidative stress.This study aimed to investigate the effects and possible mechanism of selenium on selenoproteins expression in EA.hy926 cells induced by oxidized low density lipoprotein(oxLDL).The impact of selenium on the viability of EA.hy926 cells was detected by the methylthiazolyldiphenyltetrazolium bromide(MTT)method,and intracellular reactive oxygen species(ROS)level and mitochondrial membrane potential were assessed by fluorescent probe DCFH-DA and JC-1,respectively.RNA-seq,quantitative real-time polymerase chain reaction(qPCR),and Western blot were used to investigate the selenoprotein expression.Selenoprotein mRNA translation efficiency was analyzed by ribosome profiling(Ribo-Seq)coupled with transcriptomics.Our data showed that selenium supplementation(0.5μmol/L)significantly decreased ROS production,increased mitochondrial inner membrane potential and increased the proliferative activity of EA.hy926 cells induced by oxLDL.Moreover,The protective effects of selenium against oxLDL-induced EA.hy926 cell injury were associated with the upregulation of the expressions of selenoproteins glutathione peroxidase 1(GPX1),glutathione peroxidase 4(GPX4),and thioredoxin reductase 1(TXNRD1).Furthermore,the expressions of selenoproteins GPX1 and GPX4 were hierarchically controlled,but the expressions of selenoproteins TXNRD1 were mainly regulated by oxLDL.Finally,Ribo-Seq coupled with transcriptomics results demonstrated that the expressions of selenoproteins GPX1,GPX4,and TXNRD1 were regulated at the translation process level.These findings suggested that selenium could have preventive effects in oxLDL induced EA.hy926 cell injury by regulating the selenoprotein expression,and the selenoproteins expressions at the translation level in vascular endothelial cells need further study.
文摘Objective The most prevalent mRNA modification,N6-methyladenosine(m^(6)A)plays an important role in various RNA metabolism,including gene expression and translation.By recruiting different“reader”proteins and their cofactors,m^(6)A modification can affect messenger RNA(mRNA)degradation,splicing,nuclear export and translation.However,the selective mechanism by which m^(6)A sites regulate mRNA translation through m^(6)A reader YTHDF1 binding remains poorly understood,due to a lack of computational methods for identifying context-specific m^(6)A sites that regulate translation.To address this,we developed a novel computational framework named m^(6)ATEpre,the first tool designed to predict cell-specific m^(6)A sites that regulate translation efficiency.Methods m^(6)ATEpre integrates multi-omics data,introduces a novel feature representation strategy for m^(6)A site sequences,and employs an autoencoder to effectively capture embedded feature representations.Specifically,m^(6)ATEpre first integrated MeRIP-seq data and PAR-CLIP data through overlapping m^(6)A sites with YTHDF1 binding sites and identified YTHDF1-mediated m^(6)A sites.Then,m^(6)ATEpre detected the translation gene by analyzing the Ribo-seq data under YTHDF1 knockdown vs control condition.Genes whose translation is mediated by YTHDF1 in an m^(6)A-dependent manner were identified by a significant decrease in translation efficiency upon YTHDF1 knockdown.Next,we proposed a binary vector indicating the presence or absence of YTHDF1 binding motifs to characterize each m^(6)A site sequence.This represents a novel feature representation strategy for m^(6)A sites.m^(6)ATEpre utilized the autoencoder to extract the potentially important feature representations and constructed a multilayer perceptron neural networks model to predict potential m^(6)A sites that regulating translation efficiency.Results A comprehensive evaluation of m^(6)ATEpre was conducted through a series of experiments.We compared its performance against that of a similar prediction task model,as well as other classifiers.The results indicate that m^(6)ATEpre achieved the best prediction performance.In addition,we analyzed different feature representation strategies and performed ablation experiments to validate the rationality of the model design.The results demonstrate that our proposed feature representation strategy has a greater advantage in improving prediction performance.In the HeLa cell line,bioinformatic analysis of the metagene distribution and sequence minimum free energy of m^(6)A sites regulating translation efficiency(m^(6)A-reg-TE sites)revealed their specific properties in translation regulation.Functional enrichment analysis indicated that m^(6)A-reg-TE genes are associated with specific biological processes and KEGG pathways.By integrating the binding sites of YTHDF1 co-factors with m^(6)A-reg-TE sites,we revealed that YTHDF1-mediated and m^(6)A-dependent translation efficiency regulation requires the cooperation of multiple translation-regulatory RNA-binding proteins among its co-factors in the HeLa cell line.Furthermore,we extended our predictions to the dataset of the HEK293T cell line.Similarly,bioinformatic analysis of the metagene distribution and functional enrichment revealed the cell-specific characteristic of these predicted m^(6)A-reg-TE sites in HEK293T cells.Likewise,integrated analysis of multiple YTHDF1 co-factors and m^(6)A-reg-TE sites predicted in the HEK293T cell line reveals their m^(6)A-dependent cooperation in regulating translation efficiency.Conclusion m^(6)ATEpre is a timely tool that will advance our understanding of the mechanisms of m^(6)A regulation in translation efficiency.The source code and datasets used in this work can be downloaded from https://www.scidb.cn/s/bAZZFr.
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(XDA24020203)the National Key Research and Development Program of China(2018YFA0107001,2024YFA1802403)+3 种基金the National Natural Science Foundation of China(31970588,32470860,32201060,32371357,32170606)Natural Science Foundation of Heilongjiang province(YQ2023C023)the Fundamental Research Funds for the Central Universities(2572023CT09,2572025JT05)CAS Project for Young Scientists in Basic Research(YSBR-012).
文摘Dear Editor,In vitro transcribed(IVT)mRNA is an emerging class of drug for both therapeu-tics and vaccines(Hao et al..2024;Sahin et al.,2014).Enhancing its translation efficiency remains a core challenge for mRNA-based applications(Karikó,2019).
基金supported by the National Key Research and Development Program of China (2022YFC3401402)the National Natural Science Foundation of China (T2188102,82272406,22574161)+3 种基金the Zhejiang Provincial Natural Science Foundation of China (QKHM25C0805,LDQ23B050001)the support from the Hangzhou Institute of Medicine (HIM)(2024ZZBS02)the Chinese Academy of Sciencesthe Joint Research Program of Eye Research Center (ERC202408)。
文摘Circular RNAs (circ RNAs) are covalently closed,singlestranded non-coding RNAs generated through pre-m RNA back-splicing [1,2],exhibiting broad biological functions across cells and organisms [3,4].Recent advances in developing circular RNA (circ RNA)-based therapeutics and vaccines underscore their clinical utility [1,5–10].Nevertheless,circ RNA-based therapeutics face critical technical hurdles,including optimization of efficient circularization sequences,translation enhancement,and improved in vivo delivery [10].
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supports from the Zhejiang Provincial Natural Science Foundation of China(LZ23B020004 to J.L.)the National Natural Science Foundation of China(22477109 and 91853110 to J.L.)+1 种基金the National Key R&D Program of China(2022YFA1103702 to J.L.)the Fundamental Research Funds for the Central Universities,and MOE Key Laboratory of Macromolecular Synthesis and Functionalization,Zhejiang University.
文摘RNA modifications have revealed essential regulatory roles in messenger RNA(mRNA)metabolism to affect cellular gene regulation,and have also received widespread applications in RNA therapeutics such as mRNA vaccine and protein replacement.Most efforts focus on mRNA internal base and ribose modifications,however,chemical modification within mRNA poly(A)tail remains unexplored.In this work,we synthesized luciferase and GFP(Green Fluorescent Protein)mRNAs with a fully chemically modified poly(A)tail,in which adenosine is replaced by either base-modified N^(6)-methyladenosine(m^(6)A)/N^(6)-ethyladenosine(Et^(6)A)or ribose-modified 2’-O-methyladenosine(Am),and investigated the effect of these tail modifications on mRNA stability and translation efficiency upon transfection into cells using fluorescent and chemiluminescent reporter assays.The results showed that all these modifications impaired translation without affecting mRNA stability.Further study demonstrated that modified poly(A)tail weakens its binding to PABPC1(Polyadenylate-Binding Protein 1),which reduces the formation of mRNA head-to-tail loop and thus decreases the translation efficiency.Our finding reveals the translation-regulatory role of the adenosine modifications within poly(A)tail,offering a new way for manipulating mRNA translation inside cells.
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.
基金Funding Hainan Province Key R&D Program Project(ZDYF-2023SHFZ131)National Key R&D Program Project(2021YFF0502800,20223-6),and NSFC(42494882,U23A2036)+3 种基金The Key Special Project for Introduced Talents Team(GML2019ZD0404)NRSTS Natural Resources Science and Technology Strategy Research Project(2023-ZL-66)Lin was in part supported by the Gordon and Betty Moore Foundation grant#4980.01Feng was supported by Tai Young Scholar Fund.
文摘Understanding how corals adapt to changes in seawater carbonate chemistry is crucial for developing effective coral con-servation strategies.Research to date has mostly focused on short-term experiments,overlooking long-term evolutionary effects.Here,we investigated the link between short-term stress responses and long-term genetic adaptations in the coral species Porites pukoensis through experiments under varying CO_(2) and alkalinity conditions.Our results showed that alkalin-ity enrichment significantly increased coral calcification rates by 35%-45%compared to high CO_(2) treatment,highlighting the potential of alkalinity enrichment to mitigate acidification impacts.Corals modulated relative expression levels of basic and acidic proteins in response to changes in seawater carbonate chemistry in the stress experiments.Genomic data revealed that this mechanism has been evolutionarily fixed in various organisms adapting to seawater carbonate chemistry.Addition-ally,both experimental and genomic results showed that extracellular matrix proteins,like collagen with von Willebrand factor type A domain,were modified in response to distinct carbonate environments.Molecular dynamics simulations and in-vitro experiments demonstrated that the structural stability of these proteins contributes to coral resilience under acidified conditions.This study established an integrated framework combining stress experiments,multi-omics analyses,molecular simulations,and in-vitro validation to identify key proteins involved in coral adaptation to acidification.
基金We thank LetPub for its linguistic assistance during the preparation of this paper.This work was supported by the National Natural Science Foundation of China(Grant no.31300207)the Preeminent Youth Fund of Sichuan Province(Grant no.2015JQO045)the Support Program of Sichuan Agricultural University(Grant no.03570305).
文摘Background:In recent years,avian influenza viruses(AIVs)have seriously threatened human health.Questions such as:why do AIVs infect humans?,how quickly can an AIV become pandemic?,and which virus is the most dangerous?cannot be sufficiently answered using current bioinformatic studies.Method:Secondary structures and energies of representative 5′-untranslated region(UTR)of the HA gene were calculated.Then their secondary structures and energies were re-calculated after one or two nucleotide substitutions were introduced into the HA 5′-UTR.Phylogenetic trees on the basis of hemagglutinin(HA)and polymerase basic protein 2(PB2)amino acid sequences and HA 5′-UTR nucleotide sequences were constructed.The connection between the energy and translation efficiency of 5′-UTR was confirmed by in vitro coupled transcription/translation assay.Results:The simplicity of the secondary structure of the 5′-UTR of the HA gene determines the overall virus replication rate and transmission potential.Point mutation assays show that the 5′-UTR sequences of the HA gene in the influenza subtypes H2N2,H3N2,and H7N9 have greater variation potentials than other virus subtypes.Conclusion:Some high-virulent strains of avian influenza might emerge in the next two to three years.The H2N2 subtype,once disappeared in humans,may stage a comeback.The current outbreak of H7N9 may become pandemic and cause even more deaths,if one or two bases are substituted in the 5′-UTR sequence of the HA gene.
基金supported by the National Key R&D Program of China(Grant No.2018YFA0107200 to Jinkai Wang)the National Natural Science Foundation of China(Grant Nos.31970594 and 31771446 to Jinkai Wang,Grant Nos.81922052 and 81974435 to Shuibin Lin+3 种基金Grant No.31971335 to Dan Ohtan Wang)the Natural Science Foundation of Guangdong,China(Grant No.2019B151502011 to Shuibin LinGrant No.2021A1515110650 to Yan Gao)the China Postdoctoral Science Foundation(Grant No.2021M703755 to Yan Gao).
文摘Although the function of tRNAs in the translational process is well established,it remains controversial whether tRNA abundance is tightly associated with translational efficiency(TE)in mammals.Moreover,how critically the expression of tRNAs contributes to the establishment of tissue-specific proteomes in mammals has not been well addressed.Here,we measured both tRNA expression using demethylase-tRNA sequencing(DM-tRNA-seq)and TE of mRNAs using ribosome-tagging sequencing(RiboTag-seq)in the brain,heart,and testis of mice.Remarkable variation in the expression of tRNA isodecoders was observed among different tissues.When the statistical effect of isodecoder-grouping on reducing variations is considered through permutating the anticodons,we observed an expected reduction in the variation of anticodon expression across all samples,an unexpected smaller variation of anticodon usage bias,and an unexpected larger variation of tRNA isotype expression at amino acid level.Regardless of whether or not they share the same anticodons,the isodecoders encoding the same amino acids are co-expressed across different tissues.Based on the expression of tRNAs and the TE of mRNAs,we find that the tRNA adaptation index(tAI)and TE are significantly correlated in the same tissues but not between tissues;and tRNA expression and the amino acid composition of translating peptides are positively correlated in the same tissues but not between tissues.We therefore hypothesize that the tissue-specific expression of tRNAs might be due to post-transcriptional mechanisms.This study provides a resource for tRNA and translation studies,as well as novel insights into the dynamics of tRNAs and their roles in translational regulation.
