Next-generation RNA sequencing has been successfully used for identification of transcript assembly,evaluation of gene expression levels,and detection of post-transcriptional modifications.Despite these large-scale st...Next-generation RNA sequencing has been successfully used for identification of transcript assembly,evaluation of gene expression levels,and detection of post-transcriptional modifications.Despite these large-scale studies,additional comprehensive RNA-seq data from different subregions of the human brain are required to fully evaluate the evolutionary patterns experienced by the human brain transcriptome.Here,we provide a total of 6.5 billion RNA-seq reads fromdifferent subregions of the human brain.A significant correlation was observed between the levels of alternative splicing and RNA editing,which might be explained by a competition between the molecularmachineries responsible for the splicing and editing of RNA.Younghuman protein-coding genesdemonstrate biased expression to the neocortical and non-neocortical regions during evolution on the lineage leading to humans.Wealso found that a significantly greater number of young human protein-coding genes are expressed in the putamen,a tissue that was also observed to have the highest level of RNA-editing activity.The putamen,which previously received little attention,plays an important role in cognitive ability,and our data suggest a potential contribution of the putamen to human evolution.展开更多
MicroRNA （miRNA）-mediated RNA silencing and nonsense-rnediated decay （NMD） are two conserved RNA-level regulatory path-ways. Although they are mechanically different, both can regulate target genes by RNA degradat...MicroRNA （miRNA）-mediated RNA silencing and nonsense-rnediated decay （NMD） are two conserved RNA-level regulatory path-ways. Although they are mechanically different, both can regulate target genes by RNA degradation and translational repression. Moreover, studies of individual target genes indicated that these two pathways can be involved in the same processes （e.g., development and stress responses）. These facts raise an important question that whether these two systems are cooperative, interchangeable or optimal for regulation of different sorts of genes. We addressed this by comparing miRNA and NMD targets in Arabidopsis thaliana at the genome-wide scale. We find no more overlap in the genes targeted by both systems than expected by chance. Moreover, the sorts of genes or pathways regulated by these systems are categorically different on several cross-correlating fronts. While miRNA targets show enrichment in the process of development, metabolism and transcription, NMD targets are associated with stress responses but otherwise poorly annotated. Validated miRNA targets are more highly expressed, less variably expressed and slower evolving. These differences suggest that the modes of regulation need not be interchangeable. Instead, we suggest that miRNA genes are commonly dose-sensitive and require line control of levels through weak pull-down by miRNAs. This is consistent with miRNA-regulated genes being more likely to be involved in protein-protein interactions. Many NMD-regulated genes, by contrast, have properties consistent with them being rapid emergency response ＂＇fire-fighter＇＂ genes. If true, the lack of annotation of NMD targets suggests that we poorly understand the emer-gencies plants lace in the wild.展开更多
Ⅰ类内含子(group I intron)是研究RNAs结构与功能关系的理想元件,在解释RNA折叠理论、催化机制等方面起着重要作用;对其结构与功能关系的研究也因此成为一个非常重要的课题.本研究建立了一个基于卡那霉素抗性进行Ⅰ类内含子结构与功能...Ⅰ类内含子(group I intron)是研究RNAs结构与功能关系的理想元件,在解释RNA折叠理论、催化机制等方面起着重要作用;对其结构与功能关系的研究也因此成为一个非常重要的课题.本研究建立了一个基于卡那霉素抗性进行Ⅰ类内含子结构与功能关系研究系统,将源于海洋蓝细菌Nostoc punctiforme(Npu)核糖核酸还原酶基因(ribonucleotide reductase,Rir)中的1个Ⅰ类内含子插入到pDrive质粒的卡那霉素抗性基因(kanamycin resistance gene,KanR)内构建得pKR12质粒并转化大肠杆菌(E.coli).只有内含子剪接的阳性克隆才能生成KanR蛋白并在Kan抗性平板上生长.结果显示,pKR12转入E.coli后不能在Kan抗性平板上生长,RT-PCR检测仅可见前体带,表明插入到KanR中的Npu Rir内含子没有发生剪接.随后通过易错PCR建立内含子的随机突变库并用Kan抗性筛选进行定向演化,产生有剪接活性的内含子突变体,RT-PCR检测显示剪接发生.由于内含子剪接活性的改变可通过Kan抗性变化在LB平板上得以反映,因此该系统有望成为简单快速地研究Ⅰ类内含子结构与功能关系的有利工具.展开更多
基金supported by grants from the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB13000000)the National Natural Science Foundation of China(31271339,31301042).
文摘Next-generation RNA sequencing has been successfully used for identification of transcript assembly,evaluation of gene expression levels,and detection of post-transcriptional modifications.Despite these large-scale studies,additional comprehensive RNA-seq data from different subregions of the human brain are required to fully evaluate the evolutionary patterns experienced by the human brain transcriptome.Here,we provide a total of 6.5 billion RNA-seq reads fromdifferent subregions of the human brain.A significant correlation was observed between the levels of alternative splicing and RNA editing,which might be explained by a competition between the molecularmachineries responsible for the splicing and editing of RNA.Younghuman protein-coding genesdemonstrate biased expression to the neocortical and non-neocortical regions during evolution on the lineage leading to humans.Wealso found that a significantly greater number of young human protein-coding genes are expressed in the putamen,a tissue that was also observed to have the highest level of RNA-editing activity.The putamen,which previously received little attention,plays an important role in cognitive ability,and our data suggest a potential contribution of the putamen to human evolution.
基金partially supported by the National Basic Research Program of China(No.2011CB510100 to X.K.)the National Natural Science Foundation of China(No.81030015 to X.K.)
文摘MicroRNA （miRNA）-mediated RNA silencing and nonsense-rnediated decay （NMD） are two conserved RNA-level regulatory path-ways. Although they are mechanically different, both can regulate target genes by RNA degradation and translational repression. Moreover, studies of individual target genes indicated that these two pathways can be involved in the same processes （e.g., development and stress responses）. These facts raise an important question that whether these two systems are cooperative, interchangeable or optimal for regulation of different sorts of genes. We addressed this by comparing miRNA and NMD targets in Arabidopsis thaliana at the genome-wide scale. We find no more overlap in the genes targeted by both systems than expected by chance. Moreover, the sorts of genes or pathways regulated by these systems are categorically different on several cross-correlating fronts. While miRNA targets show enrichment in the process of development, metabolism and transcription, NMD targets are associated with stress responses but otherwise poorly annotated. Validated miRNA targets are more highly expressed, less variably expressed and slower evolving. These differences suggest that the modes of regulation need not be interchangeable. Instead, we suggest that miRNA genes are commonly dose-sensitive and require line control of levels through weak pull-down by miRNAs. This is consistent with miRNA-regulated genes being more likely to be involved in protein-protein interactions. Many NMD-regulated genes, by contrast, have properties consistent with them being rapid emergency response ＂＇fire-fighter＇＂ genes. If true, the lack of annotation of NMD targets suggests that we poorly understand the emer-gencies plants lace in the wild.
