RNA editing is a post-transcriptional process that results in modifications of ribonucleotides at specific locations. In land plants editing can occur in both mitochondria and chloroplasts and most commonly involves C...RNA editing is a post-transcriptional process that results in modifications of ribonucleotides at specific locations. In land plants editing can occur in both mitochondria and chloroplasts and most commonly involves C-to-U changes, especially in seed plants. Using prediction and experimental determination, we investigated RNA editing in 40 protein-coding genes from the chloroplast genome of Cycas taitungensis. A total of 85 editing sites were identified in 25 transcripts. Comparison analysis of the published editotypes of these 25 transcripts in eight species showed that RNA editing events gradually disappear during plant evolution. The editing in the first and third codon position disappeared quicker than that in the second codon position, ndh genes have the highest editing frequency while serine and proline codons were more frequently edited than the codons of other amino acids. These results imply that retained RNA editing sites have imbalanced distribution in genes and most of them may function by changing protein structure or interaction. Mitochondrion protein-coding genes have three times the editing sites compared with chloroplast genes of Cycas, most likely due to slower evolution speed.展开更多
In Papilionoideae legume, Lotusjaponicus, the development of dorsal-ventral （DV） asymmetric flowers is mainly controlled by two TB1/CYCLOIDEA/PCF （TCP） genes, SQUARED STANDARD （SQU） and KEELED WINGS IN LOTUS （...In Papilionoideae legume, Lotusjaponicus, the development of dorsal-ventral （DV） asymmetric flowers is mainly controlled by two TB1/CYCLOIDEA/PCF （TCP） genes, SQUARED STANDARD （SQU） and KEELED WINGS IN LOTUS （KEW）, which determine dorsal and lateral identities, respectively. However, the molecular basis of how these two highly homologous genes orchestrate their diverse functions remains unclear. Here, we analyzed their expression levels, and investigated the transcriptional activities of SQUand KEW. We demonstrated that SQU possesses both activation and repression activities, while KEW acts only as an activator. They form homo- and heterodimers, and then collaboraUvely regulate their expression at the transcription level. Furthermore, we identified two types of post-transcriptional modifications, phosphor- ylation and ATP/GTP binding, both of which could affect their transcriptional activities. Mutations in ATP/ GTP binding motifs of SQU and KEW lead to failure of phosphorylation, and transgenic plants bearing the mutant proteins display defective DV asymmetric flower development, indicating that the two conjugate modifications are essential for their diverse functions. Altogether, SQU and KEW activities are precisely modulated at both transcription and post-transcription levels, which might link DV asymmetric flower development to different physiological status and/or signaling pathways.展开更多
The induction of genes encoded in the open reading frames (ORFs) of chloroplast genomes have been posited to be influenced by ambient light condition. The current study focused on determining which of the six ORFs, en...The induction of genes encoded in the open reading frames (ORFs) of chloroplast genomes have been posited to be influenced by ambient light condition. The current study focused on determining which of the six ORFs, encoding the genes ycf 1, ycf 2, psbD (photosystem II), rbcl (Rubisco), matK (Maturase K) and rpoC1 (RNA polymerase) were influenced by light. Characterization of gene expression at the whole plant level and callus stage facilitates the identification of transcripts which are differentially regulated under these environmental conditions. Specificity of these primers was tested against genomic DNA and total RNA. Transcripts of six targeted genes were detected in all three replicates of the green and white callus under light and dark conditions, except for ycf 2 gene in green callus under light. The result showed that a partial transcript of the gene ycf 2 located on the J. curcas chloroplast genome was not detectable using reverse transcription PCR. This finding was then validated using quantitative real-time PCR. The gene was suspected to be post-transcriptionally modified. The transcripts of the remaining five ORFs could be detected using quantitative real-time PCR. Specific transcripts can be identified for application as biomarkers for selection of callus for plantlet regeneration.展开更多
目的探讨m^(6)A结合蛋白YTHDC2在结直肠癌发展过程中的分子机制及其所参与的信号通路。方法通过The Human Protein Atlas和GEPIA网站分析肿瘤基因组图谱(TCGA)数据库中YTHDC2与结直肠癌的关系,探究相关的信号转导途径和生物学过程。体...目的探讨m^(6)A结合蛋白YTHDC2在结直肠癌发展过程中的分子机制及其所参与的信号通路。方法通过The Human Protein Atlas和GEPIA网站分析肿瘤基因组图谱(TCGA)数据库中YTHDC2与结直肠癌的关系,探究相关的信号转导途径和生物学过程。体外培养结直肠癌HCT116和Caco2细胞系,对YTHDC2进行过表达或敲低后,采用RT-PCR和Western blot检测p38MAPK、p-p38MAPK及其下游凋亡相关蛋白在丝裂原活化蛋白激酶(MAPK)信号通路中的表达,流式细胞术检测细胞凋亡率。结果The Human Protein Atlas和GEPIA分析结果表明,肿瘤组织中YTHDC2表达水平较癌旁组织存在降低趋势,YTHDC2的表达增加与结直肠癌患者总体生存率提高呈正相关。基于cBioPortal和Xena数据库中结直肠癌相关的基因表达量和临床数据以及KEGG和GO数据库中的注释基因集,基因集富集分析(GSEA)提示,YTHDC2具有调控MAPK信号通路的作用。流式细胞术检测结果显示,敲除YTHDC2时细胞凋亡比率显著减少,过表达时则显著增加,Western blot检测结果显示,p38MAPK表达未见显著变化,p-p38MAPK在YTHDC2过表达时显著升高,敲除时显著降低。基因表达谱交互分析(GEPIA)结果提示,凋亡蛋白的表达与YTHDC2的表达呈正相关,与RT-PCR和Western blot检测结果相符合。结论YTHDC2激活p38MAPK信号途径中外源性死亡受体和内源性线粒体凋亡通路调控结直肠癌细胞的凋亡。展开更多
MicroRNAs(miRNAs)are a highly conserved class of small(18–24 nucleotides)non-coding RNAs that regulate a broad spectrum of biological processes.Aberrations or corruptions of miRNA functions may lead to deregulated ce...MicroRNAs(miRNAs)are a highly conserved class of small(18–24 nucleotides)non-coding RNAs that regulate a broad spectrum of biological processes.Aberrations or corruptions of miRNA functions may lead to deregulated cell proliferation,tumorigenesis,and ultimately,cancer.Increasing evidences suggested that a large fraction of miRNAs is regulated at the posttranscriptional stage,which impacts on the level and function of miRNAs during cell development and human diseases.Recently,several distinct mechanisms are emerging to regulate the biogenesis,stability and function of miRNAs at post-transcriptional level,such as specific binding to terminal loops of miRNA precursors(primiRNAs or pre-miRNAs)by RNA-binding proteins and 3’-terminal modifications by particular enzymes.Signaling cascades and post-translational modifications of the core components of RNA machinery also take part in the posttranscriptional regulation of miRNAs.展开更多
Voltage-gated sodium channels(VGSCs)are transiently expressed in cochlear hair cells before hearing onset and play an indispensable role in shaping spontaneous activity.In this study,we showed that Na^+currents shaped...Voltage-gated sodium channels(VGSCs)are transiently expressed in cochlear hair cells before hearing onset and play an indispensable role in shaping spontaneous activity.In this study,we showed that Na^+currents shaped the spontaneous action potentials in developing mouse inner hair cells(IHCs)by decreasing the time required for the membrane potential to reach the action-potential threshold.In immature IHCs,we identified 9 known VGSC subtypes(Navl.la-l.9ot),among which Navl.7a was the most highly expressed subtype and the main contributor to Na+currents in developing hair cells.Electrophysiological recordings of two cochlea-specific Navi.7 variants(CbmNavl.7a and CbmNavl.7b)revealed a novel loss-of-function mutation(C934R)at the extracellular linker between segments 5 and 6 of domain II.In addition,post-transcriptional modification events,such as alternative splicing and RNA editing,amended the gating properties and kinetic features of CbmNavl.7a(C934).These results provide molecular and functional characteristics of VGSCs in mammalian IHCs and their contributions to spontaneous physiological activity during cochlear maturation.展开更多
Histone methylation is one of the most widely studied post-transcriptional modifications. It is thought to be an important epigenetic event that is closely associated with cell fate determination and differentiation. ...Histone methylation is one of the most widely studied post-transcriptional modifications. It is thought to be an important epigenetic event that is closely associated with cell fate determination and differentiation. To explore the spatiotemporal expression of histone H3 lysine 4trimethylation（H3K4me3） and histone H3 lysine 27 trimethylation（H3K27me3） epigenetic marks and methylation or demethylation transferases in tooth organ development, we measured the expression of SET7, EZH2, KDM5 B and JMJD3 via immunohistochemistry and quantitative polymerase chain reaction（qP CR） analysis in the first molar of BALB/c mice embryos at E13.5, E15.5, E17.5, P0 and P3, respectively. We also measured the expression of H3K4me3 and H3K27me3 with immunofluorescence staining. During murine tooth germ development, methylation or demethylation transferases were expressed in a spatial–temporal manner. The bivalent modification characterized by H3K4me3 and H3K27me3 can be found during the tooth germ development, as shown by immunofluorescence. The expression of SET7, EZH2 as methylation transferases and KDM5 B and JMJD3 as demethylation transferases indicated accordingly with the expression of H3K4me3 and H3K27me3 respectively to some extent. The bivalent histone may play a critical role in tooth organ development via the regulation of cell differentiation.展开更多
核受体亚家族4A组成员1(nuclear receptor subfamily 4 group A member 1,NR4A1)是由多种应激源诱导的早期转录因子,参与细胞生理活动与病理进程,尤其是在炎症相关的肺部疾病中发挥关键的调节作用,且其活性表达受转录后修饰的调节。文...核受体亚家族4A组成员1(nuclear receptor subfamily 4 group A member 1,NR4A1)是由多种应激源诱导的早期转录因子,参与细胞生理活动与病理进程,尤其是在炎症相关的肺部疾病中发挥关键的调节作用,且其活性表达受转录后修饰的调节。文章探讨了NR4A1在哮喘、急性肺损伤(acute lung injury,ALI)、肺动脉高压(pulmonary arterial hypertension,PAH)和慢性阻塞性肺疾病(chronic obstructive pulmonary diseases,COPD)中的调控作用,并对其小泛素相关修饰物(small ubiquitin‑like modifier,SUMO)修饰、磷酸化、乙酰化转录后修饰调节机制进行综述,为进一步明确NR4A1在肺实质性疾病中转录后修饰的调控机制及寻找临床肺实质相关疾病的防治靶点提供理论依据。展开更多
基金supported by the Fundamental Research Fund for the Central Universities (Grant No. GK200902028)
文摘RNA editing is a post-transcriptional process that results in modifications of ribonucleotides at specific locations. In land plants editing can occur in both mitochondria and chloroplasts and most commonly involves C-to-U changes, especially in seed plants. Using prediction and experimental determination, we investigated RNA editing in 40 protein-coding genes from the chloroplast genome of Cycas taitungensis. A total of 85 editing sites were identified in 25 transcripts. Comparison analysis of the published editotypes of these 25 transcripts in eight species showed that RNA editing events gradually disappear during plant evolution. The editing in the first and third codon position disappeared quicker than that in the second codon position, ndh genes have the highest editing frequency while serine and proline codons were more frequently edited than the codons of other amino acids. These results imply that retained RNA editing sites have imbalanced distribution in genes and most of them may function by changing protein structure or interaction. Mitochondrion protein-coding genes have three times the editing sites compared with chloroplast genes of Cycas, most likely due to slower evolution speed.
基金This work was supported by National Natural Science Foundation of China （Grant Noa. 30930009） and Science and Technology Planning Project of Guangdong Province, China （Grant Nos, 2011A020201008）.
文摘In Papilionoideae legume, Lotusjaponicus, the development of dorsal-ventral （DV） asymmetric flowers is mainly controlled by two TB1/CYCLOIDEA/PCF （TCP） genes, SQUARED STANDARD （SQU） and KEELED WINGS IN LOTUS （KEW）, which determine dorsal and lateral identities, respectively. However, the molecular basis of how these two highly homologous genes orchestrate their diverse functions remains unclear. Here, we analyzed their expression levels, and investigated the transcriptional activities of SQUand KEW. We demonstrated that SQU possesses both activation and repression activities, while KEW acts only as an activator. They form homo- and heterodimers, and then collaboraUvely regulate their expression at the transcription level. Furthermore, we identified two types of post-transcriptional modifications, phosphor- ylation and ATP/GTP binding, both of which could affect their transcriptional activities. Mutations in ATP/ GTP binding motifs of SQU and KEW lead to failure of phosphorylation, and transgenic plants bearing the mutant proteins display defective DV asymmetric flower development, indicating that the two conjugate modifications are essential for their diverse functions. Altogether, SQU and KEW activities are precisely modulated at both transcription and post-transcription levels, which might link DV asymmetric flower development to different physiological status and/or signaling pathways.
文摘The induction of genes encoded in the open reading frames (ORFs) of chloroplast genomes have been posited to be influenced by ambient light condition. The current study focused on determining which of the six ORFs, encoding the genes ycf 1, ycf 2, psbD (photosystem II), rbcl (Rubisco), matK (Maturase K) and rpoC1 (RNA polymerase) were influenced by light. Characterization of gene expression at the whole plant level and callus stage facilitates the identification of transcripts which are differentially regulated under these environmental conditions. Specificity of these primers was tested against genomic DNA and total RNA. Transcripts of six targeted genes were detected in all three replicates of the green and white callus under light and dark conditions, except for ycf 2 gene in green callus under light. The result showed that a partial transcript of the gene ycf 2 located on the J. curcas chloroplast genome was not detectable using reverse transcription PCR. This finding was then validated using quantitative real-time PCR. The gene was suspected to be post-transcriptionally modified. The transcripts of the remaining five ORFs could be detected using quantitative real-time PCR. Specific transcripts can be identified for application as biomarkers for selection of callus for plantlet regeneration.
文摘目的探讨m^(6)A结合蛋白YTHDC2在结直肠癌发展过程中的分子机制及其所参与的信号通路。方法通过The Human Protein Atlas和GEPIA网站分析肿瘤基因组图谱(TCGA)数据库中YTHDC2与结直肠癌的关系,探究相关的信号转导途径和生物学过程。体外培养结直肠癌HCT116和Caco2细胞系,对YTHDC2进行过表达或敲低后,采用RT-PCR和Western blot检测p38MAPK、p-p38MAPK及其下游凋亡相关蛋白在丝裂原活化蛋白激酶(MAPK)信号通路中的表达,流式细胞术检测细胞凋亡率。结果The Human Protein Atlas和GEPIA分析结果表明,肿瘤组织中YTHDC2表达水平较癌旁组织存在降低趋势,YTHDC2的表达增加与结直肠癌患者总体生存率提高呈正相关。基于cBioPortal和Xena数据库中结直肠癌相关的基因表达量和临床数据以及KEGG和GO数据库中的注释基因集,基因集富集分析(GSEA)提示,YTHDC2具有调控MAPK信号通路的作用。流式细胞术检测结果显示,敲除YTHDC2时细胞凋亡比率显著减少,过表达时则显著增加,Western blot检测结果显示,p38MAPK表达未见显著变化,p-p38MAPK在YTHDC2过表达时显著升高,敲除时显著降低。基因表达谱交互分析(GEPIA)结果提示,凋亡蛋白的表达与YTHDC2的表达呈正相关,与RT-PCR和Western blot检测结果相符合。结论YTHDC2激活p38MAPK信号途径中外源性死亡受体和内源性线粒体凋亡通路调控结直肠癌细胞的凋亡。
文摘MicroRNAs(miRNAs)are a highly conserved class of small(18–24 nucleotides)non-coding RNAs that regulate a broad spectrum of biological processes.Aberrations or corruptions of miRNA functions may lead to deregulated cell proliferation,tumorigenesis,and ultimately,cancer.Increasing evidences suggested that a large fraction of miRNAs is regulated at the posttranscriptional stage,which impacts on the level and function of miRNAs during cell development and human diseases.Recently,several distinct mechanisms are emerging to regulate the biogenesis,stability and function of miRNAs at post-transcriptional level,such as specific binding to terminal loops of miRNA precursors(primiRNAs or pre-miRNAs)by RNA-binding proteins and 3’-terminal modifications by particular enzymes.Signaling cascades and post-translational modifications of the core components of RNA machinery also take part in the posttranscriptional regulation of miRNAs.
基金We thank Prof.Lin Chen(University of Science and Technology of China)and Dr.Juanmei Yang(Eye and ENT Hospital of Fudan University)for valuable help with cochlear microscopic anatomy.This work was supported by the National Natural Science Foundation of China(31571032,31771191.81730028)the National Basic Research Development Program of China(SQ2017YFSF080012)the Postdoctoral Science Foundation of China(2018M640407).
文摘Voltage-gated sodium channels(VGSCs)are transiently expressed in cochlear hair cells before hearing onset and play an indispensable role in shaping spontaneous activity.In this study,we showed that Na^+currents shaped the spontaneous action potentials in developing mouse inner hair cells(IHCs)by decreasing the time required for the membrane potential to reach the action-potential threshold.In immature IHCs,we identified 9 known VGSC subtypes(Navl.la-l.9ot),among which Navl.7a was the most highly expressed subtype and the main contributor to Na+currents in developing hair cells.Electrophysiological recordings of two cochlea-specific Navi.7 variants(CbmNavl.7a and CbmNavl.7b)revealed a novel loss-of-function mutation(C934R)at the extracellular linker between segments 5 and 6 of domain II.In addition,post-transcriptional modification events,such as alternative splicing and RNA editing,amended the gating properties and kinetic features of CbmNavl.7a(C934).These results provide molecular and functional characteristics of VGSCs in mammalian IHCs and their contributions to spontaneous physiological activity during cochlear maturation.
基金supported by National Science Foundation of China (Grant No. 81371136) to Xue-Dong ZhouNational Science Foundation of China (Grant No. 81200760 and 81470711) to Li-Wei Zheng
文摘Histone methylation is one of the most widely studied post-transcriptional modifications. It is thought to be an important epigenetic event that is closely associated with cell fate determination and differentiation. To explore the spatiotemporal expression of histone H3 lysine 4trimethylation（H3K4me3） and histone H3 lysine 27 trimethylation（H3K27me3） epigenetic marks and methylation or demethylation transferases in tooth organ development, we measured the expression of SET7, EZH2, KDM5 B and JMJD3 via immunohistochemistry and quantitative polymerase chain reaction（qP CR） analysis in the first molar of BALB/c mice embryos at E13.5, E15.5, E17.5, P0 and P3, respectively. We also measured the expression of H3K4me3 and H3K27me3 with immunofluorescence staining. During murine tooth germ development, methylation or demethylation transferases were expressed in a spatial–temporal manner. The bivalent modification characterized by H3K4me3 and H3K27me3 can be found during the tooth germ development, as shown by immunofluorescence. The expression of SET7, EZH2 as methylation transferases and KDM5 B and JMJD3 as demethylation transferases indicated accordingly with the expression of H3K4me3 and H3K27me3 respectively to some extent. The bivalent histone may play a critical role in tooth organ development via the regulation of cell differentiation.
