水稻小RNA的基因组分布和分子进化研究
摘要
多数真核生物都包含多种以小RNA(small RNA)为核心的基因沉默途径,其在转录或转录后水平上对基因、重复序列和病毒等进行负调控。随着实验和计算生物学技术的发展,在植物中发现了越来越多的小RNA。目前已知有2种主要的小RNA,分别是微RNA(microRNA,miRNA),小干扰RNA(small interferingRNA,siRNA),各自都具有不同的生物合成模式和基因组座位。小RNA的产生位点,尤其是产生24-nt小干扰RNA的位点,和基因组中的重复序列高度相关。在植物小RNA途径中,已发现有许多蛋白组分的参与,比如RNA依赖性RNA聚合酶(RNA-dependent RNA polymerase,RDR),类Dicer酶(Dicer-like enzyme,DCL),基因沉默抑制子(Supressor of Gene Silencing,SGS)和Argonaute(AGO)等。所有小RNA介导的基因沉默途径都需要AGO家族成员的参与。新的测序技术使得对小RNA群体有效深入的测序成为可能,在植物中已有多项小RNA测序计划开展,帮助人们发现新的小RNA种类和基因,并对小RNA的表达进行分析。虽然对小RNA的多样性,产生机制和功能的研究很多,但是对其进化过程的了解还不多。基因组倍增是进化的重要驱动力,产生了大量基因家族和新基因。多种生物,比如酵母、脊椎动物、拟南芥和禾本科均经历了古老的基因组倍增事件。最近的研究发现,倍增或复制事件在拟南芥若干miRNA家族(比如miR169和miR395)的分化和进化过程中扮演了重要角色。
本研究利用分子生物学和计算生物学方法,主要研究了禾本科重要的模式植物,水稻的两个典型小RNA家族(TAS3和miR156)的进化过程及其小RNA在水稻基因组上的分布与表达分化。
反式作用siRNA(trans-acting siRNA,tasiRNA)是长为21nt的植物特异性内源性siRNA,与目标位点非完全互补结合后,诱导对靶基因的剪切反应。每个tasiRNA基因座位(TAS基因)转录后被转变成dsRNA,然后以21nt为步长,进行相位(phase)式切割,生成tasiRNA,这个过程需要SGS3/RDR6/DCL4途径的参与。在tasiRNA的形成过程中,需要miRNA的参与来锚定切割的目标序列区域。已经鉴别了植物上来自4个TAS基因家族(TAS1-TAS4)的10多个TAS3基因,包括拟南芥中的TAS1-TAS4和水稻中的TAS3基因。来自TAS3家族的tasiRNA,tasiARF对编码生长素应答因子(Auxin Response Factors,ARFs),包括ARF2,ARF3和ARF4的mRNA有下调作用,并且在营养枝发育和叶极性的时序性调控中也发挥作用。TAS3家族和其他已经识别的TAS基因座位至少在两方面有所不同:(1)在双子叶(拟南芥),单子叶(水稻),甚至在裸子植物中(苔藓)中,TAS3都需要两个miR390结合位点;(2)miR390在植物界中相当保守。TAS3在水稻和拟南芥上的高度保守性,为通过计算识别的方法在其他植物上发现候选的TAS3基因提供了可能。这些基因序列可用来分析TAS3家族在禾本科以及其他植物中的进化。本研究通过数据库挖掘和PCR扩增识别了56个候选TAS3基因。系统发育分析表明,在禾本科中,TAS3基因的扩张至少经历了3次基因组/基因倍增事件,并且许多TAS3基因已经在进化中丢失。我们的结果呈现了在基因组倍增事件背景下,禾本科中TAS3家族基因在进化中频繁生灭的历史。同时,序列分析表明在tasiARF和3'miR390互补位点之间的区域上,TAS3基因序列的相位排布结构具有高度的保守性,也就是说,这个区域长度的变化遵守以21nt为单位的规则。我们还在水稻和拟南芥的miR390靶标LRR激酶基因中找到了类似TAS3的序列。在这些结果的基础上,我们对TAS3基因的起源和产生机制进行了探讨。
miRNA是长约21-24 nt的小RNA分子,最初作为pri-miRNA(primarymiRNA)的一部分由RNA聚合酶Ⅱ转录,pri-miRNA经加工后形成具茎环结构的miRNA前体(pre-miRNA),然后由DCL进一步加工为成熟miRNA。miRNA通过介导对目标基因的降解或翻译抑制而产生转录后水平上的基因沉默功能。在水稻中,通过克隆或计算识别,也已发现了几百个miRNA。对拟南芥中含多成员的miRNA家族的进化研究发现,倍增或复制事件在这些miRNA家族的分化和进化过程中扮演了重要角色。miR156家族是植物中最早被鉴定的miRNA家族之一。这个家族在水稻中有12个成员,在45个不同的植物中均发现了miR156,且其在植物界中高度保守。研究表明,miR156的靶基因为SPL,是一种包含SBP盒的植物特异性转录因子。在位于水稻6条染色体上的12个miR156家族成员中,miR156b和miR156e基因(以下称为MIR156b/c)是位于1号染色体上的串联基因。一个全长cDNA(AK110797)同时编码这两个miRNA。miR156b的过表达导致水稻和玉米中的多分蘖和丛生性状。序列分析表明,MIR156b/c基因座位在禾本科作物中具有高度保守性,但是在双子叶植物中并不保守。同时,基因组倍增事件在miR156家族的进化过程中有重要影响。本研究对30个栽培稻和15个野生稻的MIR156b/c座位进行了测序。遗传多样性研究表明,栽培稻中MIR156b/c基因座位只保留了野生稻(Oryza rufipogon)约9%的核苷酸多样性。Tajima's JD检验以及Fu and Li's D~*和F~*检验的结果拒绝了中性假设(P＜0.05),表明MIR156b/c基因座位在O.rufipogon中受到了显著的自然选择。在栽培稻中检测到强的正向选择信号,表明栽培稻也经历了显著的自然或驯化选择过程。
为了获得水稻小RNA在基因组水平上的分布等特征,我们对前期所测定的680多万条水稻种子发育过程中产生的小RNA序列在水稻基因组上的分布和表达等进行了分析。结果表明,小RNA主要产生于重复序列和基因间隔区,且基因组不同区域上小RNA的产生量有非常大的差异,提示小RNA的产生有基因组区域上的特异性。水稻基因组倍增块之间小RNA分布的差异分析表明,基因组倍增事件在小RNA的进化过程中扮演重要的角色。
It has been known that most eukaryotes contain a diversified set of small RNA-guided pathways that negatively regulate or control genes,repeated sequences, and viruses at the transcriptional and posttranscriptional levels.Owing to the development of better experimental and computational approaches,an ever increasing number of small RNAs are uncovered in different plant genomes.There are two major classes of small RNAs that are found in the plant kingdom,namely small interfering RNAs(siRNAs),microRNAs(miRNAs),each derived from distinct modes of biogenesis and genomic loci.Small RNA-generating loci,especially those producing predominantly 24-nt siRNAs,were found to be highly correlated with repetitive elements across the genome.It was found that there are many different components, such as RNA-dependent RNA polymerase(RDR),Dicer-like enzyme(DCL), Supressor of Gene Silencing(SGS)and Argonaute(AGO),are involved in diverse small RNA pathway in plant.All forms of silencing by small RNAs require an effector protein of the AGO family.Recent advances in technology permit practical deep sequencing of small RNA populations.Several studies applying high-throughput sequencing methods have helped on both qualitative discovery of new small RNAs or small RNA classes,as well as quantitative profiling of small RNA populations. Although our understanding of the diversity,biogenesis and function of these regulatory RNAs is growing rapidly,their evolutionary process is not well understood. Genome duplication is one of the primary accelerators of evolution.It provide a source of genetic material for mutation,drift,and selection to act upon,making new evolutionary opportunities possible.Ancient genome duplication events have been identified in diverse organisms,such as yeast,vertebrates,Arabidopsis and Poaceae (Gramineae,grass family).Recent investigations found that duplication events played an important role in the main mechanisms involved in the diversification and evolution of several Arabidopsis miRNA families,such as the miR159 and miR395 families.
Here,we adopt the approach combining experimental and computational methods, to infer the evolution of two typical small RNA family,TAS3 and miR156 in grass family.Using the small RNA data generated from our high-throughput sequencing of small RNA populations of developing rice grain,we analyzed the distribution and expression divergence of small RNA-generating loci in rice genome.
trans-acting siRNAs(tasiRNAs)are a plant-specific class of 21-nt endogenous siRNA.It function in a similar manner to miRNAs,cleave target mRNAs via interaction with a target site with non-perfect complementarity.Each tasiRNA locus (known as a TAS gene)produces a non-coding transcript,a portion of which is converted into dsRNA,this in turn is successively cleaved into mostly 21-nt tasiRNAs phased in a 21-nt register.The production of tasiRNAs requires SGS3/RDR6/DCL4 pathway,miRNA function is required to set the phasing register for tasiRNA production.Over ten TAS genes have been characterized to date,from one locus in rice(TAS3)to four loci in Arabidopsis(TAS1-4).Biological functions have been assigned to a TAS3 family tasiRNA,tasiARF,tasiARF downregulates mRNAs encoding Auxin Response Factors(ARFs),including ARF2,ARF3 and ARF4,and is involved in the proper timing of vegetative shoot development and establishment of leaf polarity.The TAS3 family is distinguished from other TAS loci by the dual miR390 complementary sites flanking the tasiRNA region.TAS3 loci have been reported in rice and other seed plants based on their conserved tasiARFs and dual miR390 complementary sites.Computational procedures have also been successfully used to identify small RNAs based on evolutionary conservation.In this study,56 putative TAS3 genes were identified by database mining and PCR amplification. Phylogenetic analysis indicated that at least three genome/gene duplication events have been involved in the expansion of TAS3 genes and that many TAS3 genes have been lost during evolution in the grass family.Sequence analysis reveals that a high conservation of 21-nt changes in length between tasiARF and the 3' miR390 binding site and the presence of TAS3-like loci in a miR390-targeted protein-coding gene (LRR kinase)in rice and Arabidopsis.We discussed the origin and potential mechanisms for the biogenesis of TAS3 genes in the light of these findings。
miRNAs are～21-24 nt long.They derive from hairpin structured miRNA precursors(pre-miRNAs)that are processed by DCL1 from primary miRNAs (pri-miRNAs)transcribed by RNA polymeraseⅡ.miRNAs post-transcriptionally down-regulate gene expression by cleavage or translational repression of target mRNAs.In rice,hundreds of miRNAs have been identified by cloning or computational prediction.It was found that duplication was also one of the main mechanisms involved in the evolution of several miRNA families in Arabidopsis.The miR156 family was one of the first characterized miRNA families in plants,and has 12 members in rice.It is highly conserved in the plant kingdom and has been identified in 45 different plant species,miR156 has been demonstrated to target SPL genes,which are plant specific transcription factors containing an SBP box.Of 12 miR156 family members located on six chromosomes in rice genome,miR156b and miR156c gene(MIR156b/c hereafter)are tandem genes on chromosome 1.A full-length cDNA(AK110797)encodes both miRNAs.Over-expression of miR156b resulted in multiple-tillers and bushy phenotype in maize and flee.MIR156b/c locus was highly conserved among cereals,but not in dicots.Genome duplication events played an important role in the evolution of the miR156 family.We performed sequencing on the miR156b/c loci from 45 diverse Oryza accessions,with 15 accessions of O.rufipogon and 30 domesticated lines of O.sativa(15 indica and 15 japonica cultivars).Genetic diversity investigation at the locus indicated that only～9%of nucleotide diversity observed in wild rice(O.rufigogon)was maintained in the cultivated rice and the neutral model was rejected(P＜0.05)based on Tajima's D and Fu and Li's D~* and F~* tests.These results indicated that the MIR156b/c locus experienced strong natural selection in O.rufipogon,and natural and/or domestication selection in the cultivated rice.
To study the distribution and expression divergence of small RNA-generating loci in rice genome,we analyzed the small RNA data generated from our high-throughput sequencing of small RNA populations in developing rice grain.Our results showed that small RNA-generating loci from the repeat associated and intergenic region are most abundant and highly active.Scrolling-window analysis along each chromosome showed that some regions spawn relatively high numbers of small RNA.The significant distribution difference of small RNA populations between duplicated segmental pairs in rice genome was found.It suggested that duplication events played an important role in diversification and evolution of small RNA.
本研究利用分子生物学和计算生物学方法,主要研究了禾本科重要的模式植物,水稻的两个典型小RNA家族(TAS3和miR156)的进化过程及其小RNA在水稻基因组上的分布与表达分化。
反式作用siRNA(trans-acting siRNA,tasiRNA)是长为21nt的植物特异性内源性siRNA,与目标位点非完全互补结合后,诱导对靶基因的剪切反应。每个tasiRNA基因座位(TAS基因)转录后被转变成dsRNA,然后以21nt为步长,进行相位(phase)式切割,生成tasiRNA,这个过程需要SGS3/RDR6/DCL4途径的参与。在tasiRNA的形成过程中,需要miRNA的参与来锚定切割的目标序列区域。已经鉴别了植物上来自4个TAS基因家族(TAS1-TAS4)的10多个TAS3基因,包括拟南芥中的TAS1-TAS4和水稻中的TAS3基因。来自TAS3家族的tasiRNA,tasiARF对编码生长素应答因子(Auxin Response Factors,ARFs),包括ARF2,ARF3和ARF4的mRNA有下调作用,并且在营养枝发育和叶极性的时序性调控中也发挥作用。TAS3家族和其他已经识别的TAS基因座位至少在两方面有所不同:(1)在双子叶(拟南芥),单子叶(水稻),甚至在裸子植物中(苔藓)中,TAS3都需要两个miR390结合位点;(2)miR390在植物界中相当保守。TAS3在水稻和拟南芥上的高度保守性,为通过计算识别的方法在其他植物上发现候选的TAS3基因提供了可能。这些基因序列可用来分析TAS3家族在禾本科以及其他植物中的进化。本研究通过数据库挖掘和PCR扩增识别了56个候选TAS3基因。系统发育分析表明,在禾本科中,TAS3基因的扩张至少经历了3次基因组/基因倍增事件,并且许多TAS3基因已经在进化中丢失。我们的结果呈现了在基因组倍增事件背景下,禾本科中TAS3家族基因在进化中频繁生灭的历史。同时,序列分析表明在tasiARF和3'miR390互补位点之间的区域上,TAS3基因序列的相位排布结构具有高度的保守性,也就是说,这个区域长度的变化遵守以21nt为单位的规则。我们还在水稻和拟南芥的miR390靶标LRR激酶基因中找到了类似TAS3的序列。在这些结果的基础上,我们对TAS3基因的起源和产生机制进行了探讨。
miRNA是长约21-24 nt的小RNA分子,最初作为pri-miRNA(primarymiRNA)的一部分由RNA聚合酶Ⅱ转录,pri-miRNA经加工后形成具茎环结构的miRNA前体(pre-miRNA),然后由DCL进一步加工为成熟miRNA。miRNA通过介导对目标基因的降解或翻译抑制而产生转录后水平上的基因沉默功能。在水稻中,通过克隆或计算识别,也已发现了几百个miRNA。对拟南芥中含多成员的miRNA家族的进化研究发现,倍增或复制事件在这些miRNA家族的分化和进化过程中扮演了重要角色。miR156家族是植物中最早被鉴定的miRNA家族之一。这个家族在水稻中有12个成员,在45个不同的植物中均发现了miR156,且其在植物界中高度保守。研究表明,miR156的靶基因为SPL,是一种包含SBP盒的植物特异性转录因子。在位于水稻6条染色体上的12个miR156家族成员中,miR156b和miR156e基因(以下称为MIR156b/c)是位于1号染色体上的串联基因。一个全长cDNA(AK110797)同时编码这两个miRNA。miR156b的过表达导致水稻和玉米中的多分蘖和丛生性状。序列分析表明,MIR156b/c基因座位在禾本科作物中具有高度保守性,但是在双子叶植物中并不保守。同时,基因组倍增事件在miR156家族的进化过程中有重要影响。本研究对30个栽培稻和15个野生稻的MIR156b/c座位进行了测序。遗传多样性研究表明,栽培稻中MIR156b/c基因座位只保留了野生稻(Oryza rufipogon)约9%的核苷酸多样性。Tajima's JD检验以及Fu and Li's D~*和F~*检验的结果拒绝了中性假设(P＜0.05),表明MIR156b/c基因座位在O.rufipogon中受到了显著的自然选择。在栽培稻中检测到强的正向选择信号,表明栽培稻也经历了显著的自然或驯化选择过程。
为了获得水稻小RNA在基因组水平上的分布等特征,我们对前期所测定的680多万条水稻种子发育过程中产生的小RNA序列在水稻基因组上的分布和表达等进行了分析。结果表明,小RNA主要产生于重复序列和基因间隔区,且基因组不同区域上小RNA的产生量有非常大的差异,提示小RNA的产生有基因组区域上的特异性。水稻基因组倍增块之间小RNA分布的差异分析表明,基因组倍增事件在小RNA的进化过程中扮演重要的角色。
It has been known that most eukaryotes contain a diversified set of small RNA-guided pathways that negatively regulate or control genes,repeated sequences, and viruses at the transcriptional and posttranscriptional levels.Owing to the development of better experimental and computational approaches,an ever increasing number of small RNAs are uncovered in different plant genomes.There are two major classes of small RNAs that are found in the plant kingdom,namely small interfering RNAs(siRNAs),microRNAs(miRNAs),each derived from distinct modes of biogenesis and genomic loci.Small RNA-generating loci,especially those producing predominantly 24-nt siRNAs,were found to be highly correlated with repetitive elements across the genome.It was found that there are many different components, such as RNA-dependent RNA polymerase(RDR),Dicer-like enzyme(DCL), Supressor of Gene Silencing(SGS)and Argonaute(AGO),are involved in diverse small RNA pathway in plant.All forms of silencing by small RNAs require an effector protein of the AGO family.Recent advances in technology permit practical deep sequencing of small RNA populations.Several studies applying high-throughput sequencing methods have helped on both qualitative discovery of new small RNAs or small RNA classes,as well as quantitative profiling of small RNA populations. Although our understanding of the diversity,biogenesis and function of these regulatory RNAs is growing rapidly,their evolutionary process is not well understood. Genome duplication is one of the primary accelerators of evolution.It provide a source of genetic material for mutation,drift,and selection to act upon,making new evolutionary opportunities possible.Ancient genome duplication events have been identified in diverse organisms,such as yeast,vertebrates,Arabidopsis and Poaceae (Gramineae,grass family).Recent investigations found that duplication events played an important role in the main mechanisms involved in the diversification and evolution of several Arabidopsis miRNA families,such as the miR159 and miR395 families.
Here,we adopt the approach combining experimental and computational methods, to infer the evolution of two typical small RNA family,TAS3 and miR156 in grass family.Using the small RNA data generated from our high-throughput sequencing of small RNA populations of developing rice grain,we analyzed the distribution and expression divergence of small RNA-generating loci in rice genome.
trans-acting siRNAs(tasiRNAs)are a plant-specific class of 21-nt endogenous siRNA.It function in a similar manner to miRNAs,cleave target mRNAs via interaction with a target site with non-perfect complementarity.Each tasiRNA locus (known as a TAS gene)produces a non-coding transcript,a portion of which is converted into dsRNA,this in turn is successively cleaved into mostly 21-nt tasiRNAs phased in a 21-nt register.The production of tasiRNAs requires SGS3/RDR6/DCL4 pathway,miRNA function is required to set the phasing register for tasiRNA production.Over ten TAS genes have been characterized to date,from one locus in rice(TAS3)to four loci in Arabidopsis(TAS1-4).Biological functions have been assigned to a TAS3 family tasiRNA,tasiARF,tasiARF downregulates mRNAs encoding Auxin Response Factors(ARFs),including ARF2,ARF3 and ARF4,and is involved in the proper timing of vegetative shoot development and establishment of leaf polarity.The TAS3 family is distinguished from other TAS loci by the dual miR390 complementary sites flanking the tasiRNA region.TAS3 loci have been reported in rice and other seed plants based on their conserved tasiARFs and dual miR390 complementary sites.Computational procedures have also been successfully used to identify small RNAs based on evolutionary conservation.In this study,56 putative TAS3 genes were identified by database mining and PCR amplification. Phylogenetic analysis indicated that at least three genome/gene duplication events have been involved in the expansion of TAS3 genes and that many TAS3 genes have been lost during evolution in the grass family.Sequence analysis reveals that a high conservation of 21-nt changes in length between tasiARF and the 3' miR390 binding site and the presence of TAS3-like loci in a miR390-targeted protein-coding gene (LRR kinase)in rice and Arabidopsis.We discussed the origin and potential mechanisms for the biogenesis of TAS3 genes in the light of these findings。
miRNAs are～21-24 nt long.They derive from hairpin structured miRNA precursors(pre-miRNAs)that are processed by DCL1 from primary miRNAs (pri-miRNAs)transcribed by RNA polymeraseⅡ.miRNAs post-transcriptionally down-regulate gene expression by cleavage or translational repression of target mRNAs.In rice,hundreds of miRNAs have been identified by cloning or computational prediction.It was found that duplication was also one of the main mechanisms involved in the evolution of several miRNA families in Arabidopsis.The miR156 family was one of the first characterized miRNA families in plants,and has 12 members in rice.It is highly conserved in the plant kingdom and has been identified in 45 different plant species,miR156 has been demonstrated to target SPL genes,which are plant specific transcription factors containing an SBP box.Of 12 miR156 family members located on six chromosomes in rice genome,miR156b and miR156c gene(MIR156b/c hereafter)are tandem genes on chromosome 1.A full-length cDNA(AK110797)encodes both miRNAs.Over-expression of miR156b resulted in multiple-tillers and bushy phenotype in maize and flee.MIR156b/c locus was highly conserved among cereals,but not in dicots.Genome duplication events played an important role in the evolution of the miR156 family.We performed sequencing on the miR156b/c loci from 45 diverse Oryza accessions,with 15 accessions of O.rufipogon and 30 domesticated lines of O.sativa(15 indica and 15 japonica cultivars).Genetic diversity investigation at the locus indicated that only～9%of nucleotide diversity observed in wild rice(O.rufigogon)was maintained in the cultivated rice and the neutral model was rejected(P＜0.05)based on Tajima's D and Fu and Li's D~* and F~* tests.These results indicated that the MIR156b/c locus experienced strong natural selection in O.rufipogon,and natural and/or domestication selection in the cultivated rice.
To study the distribution and expression divergence of small RNA-generating loci in rice genome,we analyzed the small RNA data generated from our high-throughput sequencing of small RNA populations in developing rice grain.Our results showed that small RNA-generating loci from the repeat associated and intergenic region are most abundant and highly active.Scrolling-window analysis along each chromosome showed that some regions spawn relatively high numbers of small RNA.The significant distribution difference of small RNA populations between duplicated segmental pairs in rice genome was found.It suggested that duplication events played an important role in diversification and evolution of small RNA.
引文
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