Wheat yellow dwarf disease(BYD),caused by different species of barley/cereal yellow dwarf viruses(B/CYDVs),is one of the most serious cereal diseases in China and the Czech Republic.Because genetic diversity of the vi...Wheat yellow dwarf disease(BYD),caused by different species of barley/cereal yellow dwarf viruses(B/CYDVs),is one of the most serious cereal diseases in China and the Czech Republic.Because genetic diversity of the virus directly influences disease epidemiology,the molecular diversity and population structure of 24 Chinese isolates and 16 the Czech Republic isolates of BYDV-PAV from different regions in two countries were analyzed by sequencing their coat protein(CP)and readthrough protein(RTP)domain(RTD)genes and comparing the sequences with six CP and 16 RTP sequences of BYDVPAV isolates from the NCBI database based on nucleotide identity position,phylogenetic analysis and nucleotide diversity.Nucleotide identities between the Chinese and the Czech Republic isolates for the CP were 76.6–99.4%,73.9–89.1%for RTD(ORF5),respectively.The Chinese and the other country isolates showed 74.7–99.2%nucleotide identity for RTP(ORF3+ORF5).Phylogenetic analysis of CP sequences showed that 20 Chinese isolates clustered in the same clade,but the other four Chinese isolates clustered in another clade with the isolates from the Czech Republic and other counties.The population of BYDV-PAV in China had greater nucleotide variability and was more divergent than that in the Czech Republic.Geographical and ecological factors but not hosts might contribute to the population differences in the two countries.展开更多
Suppressor tRNAs are engineered or naturally occurring transfer RNA molecules that have shown promise in gene therapy for diseases caused by nonsense mutations,which result in premature termination codons(PTCs)in codi...Suppressor tRNAs are engineered or naturally occurring transfer RNA molecules that have shown promise in gene therapy for diseases caused by nonsense mutations,which result in premature termination codons(PTCs)in coding sequence,leading to truncated,often nonfunctional proteins.Suppressor t RNAs can recognize and pair with these PTCs,allowing the ribosome to continue translation and produce a full-length protein.This review introduces the mechanism and development of suppressor t RNAs,compares suppressor tRNAs with other readthrough therapies,discusses their potential for clinical therapy,limitations,and obstacles.We also summarize the applications of suppressor tRNAs in both in vitro and in vivo,offering new insights into the research and treatment of nonsense mutation diseases.展开更多
Background:A key step in gene expression is the recognition of the stop codon to terminate translation at the correct position.However,it has been observed that ribosomes can misinterpret the stop codon and continue t...Background:A key step in gene expression is the recognition of the stop codon to terminate translation at the correct position.However,it has been observed that ribosomes can misinterpret the stop codon and continue the translation in the 3′UTR region.This phenomenon is called stop codon read-through(SCR).It has been suggested that these events would occur on a programmed basis,but the underlying mechanisms are still not well understood.Methods:Here,we present a strategy for the comprehensive identification of SCR events in the Drosophila melanogaster transcriptome by evaluating the ribosomal density profiles.The associated ribosomal leak rate was estimated for every event identified.A statistical characterization of the frequency of nucleotide use in the proximal region to the stop codon in the sequences associated to SCR events was performed.Results:The results show that the nucleotide usage pattern in transcripts with the UGA codon is different from the pattern for those transcripts ending in the UAA codon,suggesting the existence of at least two mechanisms that could alter the translational termination process.Furthermore,a linear regression models for each of the three stop codons was developed,and we show that the models using the nucleotides at informative positions outperforms those models that consider the entire sequence context to the stop codon.Conclusions:We report that distal nucleotides can affect the SCR rate in a stop-codon dependent manner.展开更多
Importance:Nagashima-type palmoplantar keratosis(NPPK)is a hereditary dermatosis mostly caused by a nonsense mutation in SERPINB7.Despite the increasing interest in readthrough gentamicin treatment of NPPK,clinical ev...Importance:Nagashima-type palmoplantar keratosis(NPPK)is a hereditary dermatosis mostly caused by a nonsense mutation in SERPINB7.Despite the increasing interest in readthrough gentamicin treatment of NPPK,clinical evidence for this treatment is limited.Objective:This study aimed to provide further evidence for the use of topical gentamicin in the treatment of NPPK in children with nonsense mutations.Methods:We designed a bilaterally controlled study of topical gentamicin ointment.Children diagnosed with NPPK carrying nonsense mutations were enrolled in this study.A 0.1%gentamicin ointment was applied to one hand and an emollient to the other for 3 months.A bilateral comparison of the visual analog scale scores for clinical manifestations and safety was performed.Results:Ten children with NPPK were included in this study.In comparison with the emollient side,the topical gentamicin side showed significant improvements in hyperkeratosis,erythema,maceration,and desquamation after 1 and 3 months of treatment(P<0.05).However,hyperhidrosis and odor did not improve significantly.No adverse events were observed during the systemic safety monitoring examinations.Interpretation:Topical gentamicin ointment showed good safety in the treatment of NPPK with nonsense mutations,indicating that it is a promising therapeutic choice in children with NPPK.展开更多
The super elongation complex(SEC)containing positive transcription elongation factor b plays a critical role in regulating transcription elongation.AFF1 and AFF4,two members of the AF4/FMR2 family,act as central scaff...The super elongation complex(SEC)containing positive transcription elongation factor b plays a critical role in regulating transcription elongation.AFF1 and AFF4,two members of the AF4/FMR2 family,act as central scaffold proteins of SEC and are associated with various human diseases.However,their precise roles in transcriptional control remain unclear.Here,we investigate differences in the genomic distribution patterns of AFF1 and AFF4 around transcription start sites(TSSs).AFF1 mainly binds upstream of the TSS,while AFF4 is enriched downstream of the TSS.Notably,disruption of AFF4 results in slow elongation and early termination in a subset of AFF4-bound active genes,whereas AFF1 deletion leads to fast elongation and transcriptional readthrough in the same subset of genes.Additionally,AFF1 knockdown increases AFF4 levels at chromatin,and vice versa.In summary,these findings demonstrate that AFF1 and AFF4 function antagonistically to regulate RNA polymerase Ⅱ transcription.展开更多
The 5’-terminal (RTn) and 3’-terminal (RTc) halves of the coat protein readthrough domain and the 19 ku cysteine-rich protein of Chinese wheat mosaic virus (CWMV) were amplified by RT-PCR, cloned and expressed in E....The 5’-terminal (RTn) and 3’-terminal (RTc) halves of the coat protein readthrough domain and the 19 ku cysteine-rich protein of Chinese wheat mosaic virus (CWMV) were amplified by RT-PCR, cloned and expressed in E. coll. Antisera and monoclonal antibodies against these proteins were prepared by immunising these purified proteins to mice. Detection of RTn, RTc and 19 ku proteins in CWMV infected wheat sap and leaf tissue indicated that the RTn and RTc proteins were distributed on the surface of virus particles whereas the 19 ku protein was in the cytoplasm of the infected wheat cells.展开更多
Background The clinical use of gentamicin always lies in its antimicrobial activity in the past as an aminoglycoside antibiotic.However,in the past decade,there were considerable interests in therapeutic approaches in...Background The clinical use of gentamicin always lies in its antimicrobial activity in the past as an aminoglycoside antibiotic.However,in the past decade,there were considerable interests in therapeutic approaches in treating hereditary diseases.Some of the genodermatosis is caused by nonsense mutations that create premature termination codons and lead to the production of truncated or non-functional proteins.Gentamicin could induce readthrough of nonsense mutations and enable the synthesis of full-length proteins.We focus on previous publications on topical application of gentamicin and review its utility in genetic skin diseases.Data sources We search the MEDLINE through PubMed,EMBASE databases,and the Clinical Trials Registry Platform from January 1960 to July 2020 using the key search terms"gentamicin,topical gentamicin,genodermatosis,genetic skin diseases".Results The application of gentamicin in genodermatosis yielded promising results,both in vivo and in vitro,including Nagashima-type palmoplantar keratosis,epidermolysis bullosa,Hailey-Hailey disease,hereditary hypotrichosis simplex of the scalp,etc.Conclusions Topical gentamicin is a potential treatment option for genodermatosis caused by nonsense mutation.展开更多
基金This research was supported by the Inter-Governmental S&T Cooperation Project of China(2016YFE0131000)the Research Program of the Ministry of Education,Youth and Sports of the Czech Republic(LTACH-17010).
文摘Wheat yellow dwarf disease(BYD),caused by different species of barley/cereal yellow dwarf viruses(B/CYDVs),is one of the most serious cereal diseases in China and the Czech Republic.Because genetic diversity of the virus directly influences disease epidemiology,the molecular diversity and population structure of 24 Chinese isolates and 16 the Czech Republic isolates of BYDV-PAV from different regions in two countries were analyzed by sequencing their coat protein(CP)and readthrough protein(RTP)domain(RTD)genes and comparing the sequences with six CP and 16 RTP sequences of BYDVPAV isolates from the NCBI database based on nucleotide identity position,phylogenetic analysis and nucleotide diversity.Nucleotide identities between the Chinese and the Czech Republic isolates for the CP were 76.6–99.4%,73.9–89.1%for RTD(ORF5),respectively.The Chinese and the other country isolates showed 74.7–99.2%nucleotide identity for RTP(ORF3+ORF5).Phylogenetic analysis of CP sequences showed that 20 Chinese isolates clustered in the same clade,but the other four Chinese isolates clustered in another clade with the isolates from the Czech Republic and other counties.The population of BYDV-PAV in China had greater nucleotide variability and was more divergent than that in the Czech Republic.Geographical and ecological factors but not hosts might contribute to the population differences in the two countries.
基金supported by the National Natural Science Foundation of China(82371861)Key R&D Program of Zhejiang(2024SSYS0020)+1 种基金Henan Province Key Research and Promotion Project(242102311023)the Starting Fund from Zhejiang University。
文摘Suppressor tRNAs are engineered or naturally occurring transfer RNA molecules that have shown promise in gene therapy for diseases caused by nonsense mutations,which result in premature termination codons(PTCs)in coding sequence,leading to truncated,often nonfunctional proteins.Suppressor t RNAs can recognize and pair with these PTCs,allowing the ribosome to continue translation and produce a full-length protein.This review introduces the mechanism and development of suppressor t RNAs,compares suppressor tRNAs with other readthrough therapies,discusses their potential for clinical therapy,limitations,and obstacles.We also summarize the applications of suppressor tRNAs in both in vitro and in vivo,offering new insights into the research and treatment of nonsense mutation diseases.
基金LIE is funded by CONICET Ph.D.Fellowship.AMA and LD are researchers of CONICET(Argentina).JRR is Full Professor at the UNLP(Argentina).This work was supported by CONICET,Argentina(PIP2017-00059).
文摘Background:A key step in gene expression is the recognition of the stop codon to terminate translation at the correct position.However,it has been observed that ribosomes can misinterpret the stop codon and continue the translation in the 3′UTR region.This phenomenon is called stop codon read-through(SCR).It has been suggested that these events would occur on a programmed basis,but the underlying mechanisms are still not well understood.Methods:Here,we present a strategy for the comprehensive identification of SCR events in the Drosophila melanogaster transcriptome by evaluating the ribosomal density profiles.The associated ribosomal leak rate was estimated for every event identified.A statistical characterization of the frequency of nucleotide use in the proximal region to the stop codon in the sequences associated to SCR events was performed.Results:The results show that the nucleotide usage pattern in transcripts with the UGA codon is different from the pattern for those transcripts ending in the UAA codon,suggesting the existence of at least two mechanisms that could alter the translational termination process.Furthermore,a linear regression models for each of the three stop codons was developed,and we show that the models using the nucleotides at informative positions outperforms those models that consider the entire sequence context to the stop codon.Conclusions:We report that distal nucleotides can affect the SCR rate in a stop-codon dependent manner.
基金Children’s Medicine Research Project of Beijing Children’s Hospital,Capital Medical University,Grant/Award Number:YZZD202002
文摘Importance:Nagashima-type palmoplantar keratosis(NPPK)is a hereditary dermatosis mostly caused by a nonsense mutation in SERPINB7.Despite the increasing interest in readthrough gentamicin treatment of NPPK,clinical evidence for this treatment is limited.Objective:This study aimed to provide further evidence for the use of topical gentamicin in the treatment of NPPK in children with nonsense mutations.Methods:We designed a bilaterally controlled study of topical gentamicin ointment.Children diagnosed with NPPK carrying nonsense mutations were enrolled in this study.A 0.1%gentamicin ointment was applied to one hand and an emollient to the other for 3 months.A bilateral comparison of the visual analog scale scores for clinical manifestations and safety was performed.Results:Ten children with NPPK were included in this study.In comparison with the emollient side,the topical gentamicin side showed significant improvements in hyperkeratosis,erythema,maceration,and desquamation after 1 and 3 months of treatment(P<0.05).However,hyperhidrosis and odor did not improve significantly.No adverse events were observed during the systemic safety monitoring examinations.Interpretation:Topical gentamicin ointment showed good safety in the treatment of NPPK with nonsense mutations,indicating that it is a promising therapeutic choice in children with NPPK.
基金supported by grants from the National Key R&D Program of China(2018YFA0800100 to C.L.,2018YFA0800103 to Z.L.)the National Natural Science Foundation of China(32030017 and 31970617 to C.L.,31970626 to Z.L.)Shenzhen Science and Technology Program(JCYJ20210324133602008 to C.L.,JCYJ20210324133601005 to Z.L.).
文摘The super elongation complex(SEC)containing positive transcription elongation factor b plays a critical role in regulating transcription elongation.AFF1 and AFF4,two members of the AF4/FMR2 family,act as central scaffold proteins of SEC and are associated with various human diseases.However,their precise roles in transcriptional control remain unclear.Here,we investigate differences in the genomic distribution patterns of AFF1 and AFF4 around transcription start sites(TSSs).AFF1 mainly binds upstream of the TSS,while AFF4 is enriched downstream of the TSS.Notably,disruption of AFF4 results in slow elongation and early termination in a subset of AFF4-bound active genes,whereas AFF1 deletion leads to fast elongation and transcriptional readthrough in the same subset of genes.Additionally,AFF1 knockdown increases AFF4 levels at chromatin,and vice versa.In summary,these findings demonstrate that AFF1 and AFF4 function antagonistically to regulate RNA polymerase Ⅱ transcription.
基金This work was supported by the Zhejiang Provincial Natural Science Foundation (Grant Nos. 399421 and RC9604)the National Natural Science Foundation of China (Grant No. 399704820)a special grant for the Key Laboratory of Zhejiang Province (Grant No. 0
文摘The 5’-terminal (RTn) and 3’-terminal (RTc) halves of the coat protein readthrough domain and the 19 ku cysteine-rich protein of Chinese wheat mosaic virus (CWMV) were amplified by RT-PCR, cloned and expressed in E. coll. Antisera and monoclonal antibodies against these proteins were prepared by immunising these purified proteins to mice. Detection of RTn, RTc and 19 ku proteins in CWMV infected wheat sap and leaf tissue indicated that the RTn and RTc proteins were distributed on the surface of virus particles whereas the 19 ku protein was in the cytoplasm of the infected wheat cells.
基金supported by Children's Medicine Research Project of Beijing Children's Hospital,Capital Medical University(YZZD202002).
文摘Background The clinical use of gentamicin always lies in its antimicrobial activity in the past as an aminoglycoside antibiotic.However,in the past decade,there were considerable interests in therapeutic approaches in treating hereditary diseases.Some of the genodermatosis is caused by nonsense mutations that create premature termination codons and lead to the production of truncated or non-functional proteins.Gentamicin could induce readthrough of nonsense mutations and enable the synthesis of full-length proteins.We focus on previous publications on topical application of gentamicin and review its utility in genetic skin diseases.Data sources We search the MEDLINE through PubMed,EMBASE databases,and the Clinical Trials Registry Platform from January 1960 to July 2020 using the key search terms"gentamicin,topical gentamicin,genodermatosis,genetic skin diseases".Results The application of gentamicin in genodermatosis yielded promising results,both in vivo and in vitro,including Nagashima-type palmoplantar keratosis,epidermolysis bullosa,Hailey-Hailey disease,hereditary hypotrichosis simplex of the scalp,etc.Conclusions Topical gentamicin is a potential treatment option for genodermatosis caused by nonsense mutation.
