Small open reading frames(sORFs) are distributed over a wide variety of transcripts. sORFs encoding functional peptides have been identified in various configurations within apparently long noncoding RNAs. Many transl...Small open reading frames(sORFs) are distributed over a wide variety of transcripts. sORFs encoding functional peptides have been identified in various configurations within apparently long noncoding RNAs. Many translated sORFs have been identified across mRNAs, including 5’-upstream, coding domain, and 3’-downstream. sORFs have also been found in circular RNAs, pri-miRNAs, and ribosomal RNAs. Here, we present an overview of the wide distribution of the sORFs in transcripts and their functional roles in organisms.展开更多
本研究针对火鸡疱疹病毒(Herpesvirus of turkey,HVT)FC-126毒株sorf1基因序列,设计特异性的扩增引物和探针,建立了检测HVT的TaqMan荧光定量PCR方法,并对其特异性、敏感性和重复性进行检测。结果表明,建立的荧光定量PCR方法灵敏度高,最...本研究针对火鸡疱疹病毒(Herpesvirus of turkey,HVT)FC-126毒株sorf1基因序列,设计特异性的扩增引物和探针,建立了检测HVT的TaqMan荧光定量PCR方法,并对其特异性、敏感性和重复性进行检测。结果表明,建立的荧光定量PCR方法灵敏度高,最低可检测到1×10~2 copies/μL,比普通PCR灵敏10倍;对鸭瘟病毒、传染性喉气管炎病毒、鹅细小病毒、4型禽腺病毒和8型禽腺病毒均无特异性扩增,具有较好的特异性;组间和组内变异系数均小于1%,表明该方法重复性好。用建立的荧光定量PCR方法对82份HVT样品进行检测,结果43份为阳性,普通PCR只检测出30份阳性样品。结果表明本研究建立的HVT TaqMan荧光定量PCR检测方法特异性好,灵敏度高,重要性好,为监测HVT的病毒含量提供了一种有效的手段。展开更多
With the development of modern sequencing techniques and bioinformatics, genomes that were once thought to be noncoding have been found to encode abundant functional micropeptides(miPs), a kind of small polypeptides. ...With the development of modern sequencing techniques and bioinformatics, genomes that were once thought to be noncoding have been found to encode abundant functional micropeptides(miPs), a kind of small polypeptides. Although miPs are difficult to analyze and identify, a number of studies have begun to focus on them. More and more miPs have been revealed as essential for energy metabolism homeostasis, immune regulation, and tumor growth and development. Many reports have shown that miPs are especially essential for regulating glucose and lipid metabolism and regulating mitochondrial function.MiPs are also involved in the progression of related diseases. This paper reviews the sources and identification of miPs, as well as the functional significance of miPs for metabolism-related diseases, with the aim of revealing their potential clinical applications.展开更多
One of the main goals of the Human Genome Project is to identify all protein-coding genes.There are~20,5o0 protein-coding genes annotated in the human reference databases.However,in the last few years,proteogenomics s...One of the main goals of the Human Genome Project is to identify all protein-coding genes.There are~20,5o0 protein-coding genes annotated in the human reference databases.However,in the last few years,proteogenomics studies have predicted thousands of novel protein-coding regions,including low-molecular-weight proteins encoded by small open reading frames(sORFs)in untranslated regions of messenger RNAs and non-coding RNAs.Most of these predictions are based on bioinformatics analyses and ribosome footprint data.The validity of some of these sORF-encoded proteins(SEPs)has been established through functional characterization.With the growing number of predicted novel proteins,a strategy to identify reliable candidates that warrant further studies is needed.In this study,we developed an integrated proteoge-nomics workflow to identify a reliable set of novel protein-coding regions in the human genome based on their recurrent observations across multiple samples.Publicly available ribosome profiling and global proteomic datasets were used to establish protein-coding evidence.We pre-dicted protein translation from 4008 sORFs based on recurrent ribosome occupancy signals across samples.In addition,we identified 825 SEPs based on proteomic data.Some of the novel protein-coding regions identified were located in genome-wide association study(GWAS)loci associated with various traits and disease phenotypes.Peptides from SEPs are also presented by major histocompatibility complex class I(MHC-I),similar to canonical proteins.Novel protein-coding regions reported in this study expand the current catalog of protein-coding genes and warrant experimental studies to elucidate their cellular functions and potential roles in human diseases.展开更多
小开放阅读框(small open reading frame,sORF)广泛存在于不同生物基因组中,由于其序列短,以及编码的产物小蛋白(small protein,或称微蛋白;microprotein或迷你蛋白miniprotein)检测困难等原因,小开放阅读框长期未得到充分注释和研究。...小开放阅读框(small open reading frame,sORF)广泛存在于不同生物基因组中,由于其序列短,以及编码的产物小蛋白(small protein,或称微蛋白;microprotein或迷你蛋白miniprotein)检测困难等原因,小开放阅读框长期未得到充分注释和研究。近年来,随着高通量测序、翻译组和质谱分析等技术的不断发展,在不同生物中发现大量新的小开放阅读框,其编码的小蛋白及介导的翻译调控已应用于药物开发及植物抗病机理等研究。但是,目前对微生物的小开放阅读框相关研究和应用还相对有限。本文综述了小开放阅读框编码产物小蛋白的发现和鉴定,以及上游开放阅读框(upstream open reading frame,uORF)对mRNA翻译调控等最新研究进展,重点介绍了微生物基因组中小开放阅读框的鉴定和功能研究进展,为深入认识微生物中小开放阅读框的功能和作用机制,以及植物和动物等高等其他生物的小蛋白和翻译调控相关研究提供参考。展开更多
基金supported by the Project Program of State Key Laboratory of Natural Medicines(No. SKLNMBZ201403)the National Science and Technology Major Projects of New Drugs (Nos.2012ZX09103301-004 and 2014ZX09508007) in ChinaThis project was also funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD)
文摘Small open reading frames(sORFs) are distributed over a wide variety of transcripts. sORFs encoding functional peptides have been identified in various configurations within apparently long noncoding RNAs. Many translated sORFs have been identified across mRNAs, including 5’-upstream, coding domain, and 3’-downstream. sORFs have also been found in circular RNAs, pri-miRNAs, and ribosomal RNAs. Here, we present an overview of the wide distribution of the sORFs in transcripts and their functional roles in organisms.
文摘本研究针对火鸡疱疹病毒(Herpesvirus of turkey,HVT)FC-126毒株sorf1基因序列,设计特异性的扩增引物和探针,建立了检测HVT的TaqMan荧光定量PCR方法,并对其特异性、敏感性和重复性进行检测。结果表明,建立的荧光定量PCR方法灵敏度高,最低可检测到1×10~2 copies/μL,比普通PCR灵敏10倍;对鸭瘟病毒、传染性喉气管炎病毒、鹅细小病毒、4型禽腺病毒和8型禽腺病毒均无特异性扩增,具有较好的特异性;组间和组内变异系数均小于1%,表明该方法重复性好。用建立的荧光定量PCR方法对82份HVT样品进行检测,结果43份为阳性,普通PCR只检测出30份阳性样品。结果表明本研究建立的HVT TaqMan荧光定量PCR检测方法特异性好,灵敏度高,重要性好,为监测HVT的病毒含量提供了一种有效的手段。
基金supported by the National Natural Science Foundation of China(No.81870237)。
文摘With the development of modern sequencing techniques and bioinformatics, genomes that were once thought to be noncoding have been found to encode abundant functional micropeptides(miPs), a kind of small polypeptides. Although miPs are difficult to analyze and identify, a number of studies have begun to focus on them. More and more miPs have been revealed as essential for energy metabolism homeostasis, immune regulation, and tumor growth and development. Many reports have shown that miPs are especially essential for regulating glucose and lipid metabolism and regulating mitochondrial function.MiPs are also involved in the progression of related diseases. This paper reviews the sources and identification of miPs, as well as the functional significance of miPs for metabolism-related diseases, with the aim of revealing their potential clinical applications.
文摘One of the main goals of the Human Genome Project is to identify all protein-coding genes.There are~20,5o0 protein-coding genes annotated in the human reference databases.However,in the last few years,proteogenomics studies have predicted thousands of novel protein-coding regions,including low-molecular-weight proteins encoded by small open reading frames(sORFs)in untranslated regions of messenger RNAs and non-coding RNAs.Most of these predictions are based on bioinformatics analyses and ribosome footprint data.The validity of some of these sORF-encoded proteins(SEPs)has been established through functional characterization.With the growing number of predicted novel proteins,a strategy to identify reliable candidates that warrant further studies is needed.In this study,we developed an integrated proteoge-nomics workflow to identify a reliable set of novel protein-coding regions in the human genome based on their recurrent observations across multiple samples.Publicly available ribosome profiling and global proteomic datasets were used to establish protein-coding evidence.We pre-dicted protein translation from 4008 sORFs based on recurrent ribosome occupancy signals across samples.In addition,we identified 825 SEPs based on proteomic data.Some of the novel protein-coding regions identified were located in genome-wide association study(GWAS)loci associated with various traits and disease phenotypes.Peptides from SEPs are also presented by major histocompatibility complex class I(MHC-I),similar to canonical proteins.Novel protein-coding regions reported in this study expand the current catalog of protein-coding genes and warrant experimental studies to elucidate their cellular functions and potential roles in human diseases.
文摘小开放阅读框(small open reading frame,sORF)广泛存在于不同生物基因组中,由于其序列短,以及编码的产物小蛋白(small protein,或称微蛋白;microprotein或迷你蛋白miniprotein)检测困难等原因,小开放阅读框长期未得到充分注释和研究。近年来,随着高通量测序、翻译组和质谱分析等技术的不断发展,在不同生物中发现大量新的小开放阅读框,其编码的小蛋白及介导的翻译调控已应用于药物开发及植物抗病机理等研究。但是,目前对微生物的小开放阅读框相关研究和应用还相对有限。本文综述了小开放阅读框编码产物小蛋白的发现和鉴定,以及上游开放阅读框(upstream open reading frame,uORF)对mRNA翻译调控等最新研究进展,重点介绍了微生物基因组中小开放阅读框的鉴定和功能研究进展,为深入认识微生物中小开放阅读框的功能和作用机制,以及植物和动物等高等其他生物的小蛋白和翻译调控相关研究提供参考。
