Moving from the most recent results on Foxg1 biology,we first summarize the available information on some special pleiotropic effectors of neurodevelopmental interest,involved in controlling both transcription and pos...Moving from the most recent results on Foxg1 biology,we first summarize the available information on some special pleiotropic effectors of neurodevelopmental interest,involved in controlling both transcription and post-transcriptional steps of gene expression.Then,after further analysis of the literature,we report evidence that,not strictly limited to neurodevelopmental effectors,such pleiotropy also applies to other transcription factors,involved in physiology and homeostasis.Furthermore,through the systematic analysis of a major public protein-protein interaction database,we gather strong evidence that the involvement of“canonical”transcription factors in post-transcriptional control of gene expression could be a pervasive phenomenon,characterizing hundreds of effectors.Finally,we discuss the biological significance of these findings and propose three evolutionary mechanisms that may have contributed to such an unexpected scenario.展开更多
Precursor mRNA(pre-mRNA)splicing is essential for gene expression in most eukaryotic organisms.Previous studies from mammals,Drosophila,and yeast show that the majority of splicing events occurs co-transcriptionally.I...Precursor mRNA(pre-mRNA)splicing is essential for gene expression in most eukaryotic organisms.Previous studies from mammals,Drosophila,and yeast show that the majority of splicing events occurs co-transcriptionally.In plants,however,the features of co-transcriptional splicing(CTS)and its regulation still remain largely unknown.Here,we used chromatin-bound RNA sequencing to study CTS in Arabidopsis thaliana.We found that CTS is widespread in Arabidopsis seedlings,with a large proportion of alternative splicing events determined co-transcriptionally.CTS efficiency correlated with gene expression level,the chromatin landscape and,most surprisingly,the number of introns and exons of individual genes,but is independent of gene length.In combination with enhanced crosslinking and immunoprecipitation sequencing analysis,we further showed that the hnRNP-like proteins RZ-1B and RZ-1C promote efficient CTS globally through direct binding,frequently to exonic sequences.Notably,this general effect of RZ-1B/1C on splicing promotion is mainly observed at the chromatin level,not at the mRNA level.RZ-1C promotes CTS of multiple-exon genes in association with its binding to regions both proximal and distal to the regulated introns.We propose that RZ-1C promotes efficient CTS of genes with multiple exons through cooperative interactions with many exons,introns,and splicing factors.Our work thus reveals important features of CTS in plants and provides methodologies for the investigation of CTS and RNA-binding proteins in plants.展开更多
RNA splicing and spliceosome assembly in eukaryotes occur mainly during transcription.However,co-transcriptional splicing has not yet been explored in plants.Here,we built transcriptomes of nascent chromatin RNAs in A...RNA splicing and spliceosome assembly in eukaryotes occur mainly during transcription.However,co-transcriptional splicing has not yet been explored in plants.Here,we built transcriptomes of nascent chromatin RNAs in Arabidopsis thaliana and showed that nearly all introns undergo co-transcriptional splicing,which occurs with higher efficiency for introns in protein-coding genes than for those in noncoding RNAs.Total intron number and intron position are two predominant features that correlate with co-transcriptional splicing efficiency,and introns with alternative 5′or 3′splice sites are less efficiently spliced.Furthermore,we found that mutations in genes encoding trans-acting proteins lead to more introns with increased splicing defects in nascent RNAs than in mature RNAs,and that introns with increased splicing defects in mature RNAs are inefficiently spliced at the co-transcriptional level.Collectively,our results not only uncovered widespread co-transcriptional splicing in Arabidopsis but also identified features that may affect or be affected by co-transcriptional splicing efficiency.展开更多
目的确定贾第虫滋养体内核糖核酸酶P(RNase P)RNA 3′端序列及其存在形式。方法提取贾第虫滋养体总RNA,大肠埃希菌(E.coli)Poly(A)聚合酶加polyA尾后,进行反转录,扩增出加polyA尾后的cDNA,经PCR及测序进行鉴定,确定其3′端序列。应用实...目的确定贾第虫滋养体内核糖核酸酶P(RNase P)RNA 3′端序列及其存在形式。方法提取贾第虫滋养体总RNA,大肠埃希菌(E.coli)Poly(A)聚合酶加polyA尾后,进行反转录,扩增出加polyA尾后的cDNA,经PCR及测序进行鉴定,确定其3′端序列。应用实时荧光定量PCR(RT-qPCR)分别检测RNase P-GLsR15共转录体与RNase PRNA成熟体的总表达量,两者之差即为RNase P RNA成熟体的表达量,确定贾第虫RNase P RNA的存在形式。结果 RNase P RNA 3′cDNA大小约300 nt,3′端序列与GLsR15 3′端序列一致;RNase P-GLsR15共转录体和RNaseP RNA成熟体的总表达量与RNase P-GLsR15共转录体表达量差异无统计学意义(P>0.05)。结论已成功克隆了RNase P RNA 3′端序列,证实RNase P RNA和GlsR15的共转录体即为RNase P RNA成熟体的存在形式。展开更多
基金supported by SISSA(intramural funding to AM)International FOXG1 Research Foundation(Grant to AM)+1 种基金Italian Ministery of University and Research(Grant PRIN222022M95RC7 to AM)Fondazione Telethon(Grant GMR22T2018 to AM).
文摘Moving from the most recent results on Foxg1 biology,we first summarize the available information on some special pleiotropic effectors of neurodevelopmental interest,involved in controlling both transcription and post-transcriptional steps of gene expression.Then,after further analysis of the literature,we report evidence that,not strictly limited to neurodevelopmental effectors,such pleiotropy also applies to other transcription factors,involved in physiology and homeostasis.Furthermore,through the systematic analysis of a major public protein-protein interaction database,we gather strong evidence that the involvement of“canonical”transcription factors in post-transcriptional control of gene expression could be a pervasive phenomenon,characterizing hundreds of effectors.Finally,we discuss the biological significance of these findings and propose three evolutionary mechanisms that may have contributed to such an unexpected scenario.
基金supported by Guangdong Innovative and Entrepreneurial Research Team Program(2016ZT06S172)the Shenzhen Sci-Tech Fund No.KYTDPT20181011104005the National Natural Science Foundation of China(31771365 to Z.W.and 31800268 to D.Z.).
文摘Precursor mRNA(pre-mRNA)splicing is essential for gene expression in most eukaryotic organisms.Previous studies from mammals,Drosophila,and yeast show that the majority of splicing events occurs co-transcriptionally.In plants,however,the features of co-transcriptional splicing(CTS)and its regulation still remain largely unknown.Here,we used chromatin-bound RNA sequencing to study CTS in Arabidopsis thaliana.We found that CTS is widespread in Arabidopsis seedlings,with a large proportion of alternative splicing events determined co-transcriptionally.CTS efficiency correlated with gene expression level,the chromatin landscape and,most surprisingly,the number of introns and exons of individual genes,but is independent of gene length.In combination with enhanced crosslinking and immunoprecipitation sequencing analysis,we further showed that the hnRNP-like proteins RZ-1B and RZ-1C promote efficient CTS globally through direct binding,frequently to exonic sequences.Notably,this general effect of RZ-1B/1C on splicing promotion is mainly observed at the chromatin level,not at the mRNA level.RZ-1C promotes CTS of multiple-exon genes in association with its binding to regions both proximal and distal to the regulated introns.We propose that RZ-1C promotes efficient CTS of genes with multiple exons through cooperative interactions with many exons,introns,and splicing factors.Our work thus reveals important features of CTS in plants and provides methodologies for the investigation of CTS and RNA-binding proteins in plants.
基金supported by the Fundamental Research Funds for the Central Universities,China and National Science Foundation of China(91740202).Y.W.was supported by a fellowship from Shenzhen Un iversity.
文摘RNA splicing and spliceosome assembly in eukaryotes occur mainly during transcription.However,co-transcriptional splicing has not yet been explored in plants.Here,we built transcriptomes of nascent chromatin RNAs in Arabidopsis thaliana and showed that nearly all introns undergo co-transcriptional splicing,which occurs with higher efficiency for introns in protein-coding genes than for those in noncoding RNAs.Total intron number and intron position are two predominant features that correlate with co-transcriptional splicing efficiency,and introns with alternative 5′or 3′splice sites are less efficiently spliced.Furthermore,we found that mutations in genes encoding trans-acting proteins lead to more introns with increased splicing defects in nascent RNAs than in mature RNAs,and that introns with increased splicing defects in mature RNAs are inefficiently spliced at the co-transcriptional level.Collectively,our results not only uncovered widespread co-transcriptional splicing in Arabidopsis but also identified features that may affect or be affected by co-transcriptional splicing efficiency.
文摘目的确定贾第虫滋养体内核糖核酸酶P(RNase P)RNA 3′端序列及其存在形式。方法提取贾第虫滋养体总RNA,大肠埃希菌(E.coli)Poly(A)聚合酶加polyA尾后,进行反转录,扩增出加polyA尾后的cDNA,经PCR及测序进行鉴定,确定其3′端序列。应用实时荧光定量PCR(RT-qPCR)分别检测RNase P-GLsR15共转录体与RNase PRNA成熟体的总表达量,两者之差即为RNase P RNA成熟体的表达量,确定贾第虫RNase P RNA的存在形式。结果 RNase P RNA 3′cDNA大小约300 nt,3′端序列与GLsR15 3′端序列一致;RNase P-GLsR15共转录体和RNaseP RNA成熟体的总表达量与RNase P-GLsR15共转录体表达量差异无统计学意义(P>0.05)。结论已成功克隆了RNase P RNA 3′端序列,证实RNase P RNA和GlsR15的共转录体即为RNase P RNA成熟体的存在形式。
