A lariat-derived circular RNA is required for plant development in Arabidopsis
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摘要
Lariat RNA is produced during pre-mRNA splicing, and it is traditionally thought as by-products, due to the quick turnover by debranching followed by degradation. However, recent findings identified many lariat RNAs accumulate with a circular form in higher eukaryotes. Although the remarkable accumulation, biological consequence of lariat-derived circular RNAs(here we name laciRNAs) remains largely unknown. Here, we report that a specific laciRNA from At5 g37720 plays an essential role in plant development by regulating gene expression globally. We focus on 17 laciRNAs with accumulation in wild type plants by circular RNA sequencing in Arabidopsis. To determine biological functions of these laciRNAs, we constructed one pair of transgenic plants for each laciRNA, in which the local gene with or without introns was over-expressed in wild type plants,respectively. By comparing morphological phenotypes and transcriptomic profiles between two classes of transgenic plants, we show that over-expression of the laciRNA derived from the 1 st intron of At5 g37720 causes pleiotropic phenotypes, including curly and clustered leaf, late flowering, reduced fertility, and accompanied with altered expression of approximately 800 genes.Our results provide another example that a specific plant circular RNA regulates gene expression in a similar manner to that of other non-coding RNAs under physiological conditions.
Lariat RNA is produced during pre-mRNA splicing, and it is traditionally thought as by-products, due to the quick turnover by debranching followed by degradation. However, recent findings identified many lariat RNAs accumulate with a circular form in higher eukaryotes. Although the remarkable accumulation, biological consequence of lariat-derived circular RNAs(here we name laciRNAs) remains largely unknown. Here, we report that a specific laciRNA from At5 g37720 plays an essential role in plant development by regulating gene expression globally. We focus on 17 laciRNAs with accumulation in wild type plants by circular RNA sequencing in Arabidopsis. To determine biological functions of these laciRNAs, we constructed one pair of transgenic plants for each laciRNA, in which the local gene with or without introns was over-expressed in wild type plants,respectively. By comparing morphological phenotypes and transcriptomic profiles between two classes of transgenic plants, we show that over-expression of the laciRNA derived from the 1 st intron of At5 g37720 causes pleiotropic phenotypes, including curly and clustered leaf, late flowering, reduced fertility, and accompanied with altered expression of approximately 800 genes.Our results provide another example that a specific plant circular RNA regulates gene expression in a similar manner to that of other non-coding RNAs under physiological conditions.
Lariat RNA is produced during pre-mRNA splicing, and it is traditionally thought as by-products, due to the quick turnover by debranching followed by degradation. However, recent findings identified many lariat RNAs accumulate with a circular form in higher eukaryotes. Although the remarkable accumulation, biological consequence of lariat-derived circular RNAs(here we name laciRNAs) remains largely unknown. Here, we report that a specific laciRNA from At5 g37720 plays an essential role in plant development by regulating gene expression globally. We focus on 17 laciRNAs with accumulation in wild type plants by circular RNA sequencing in Arabidopsis. To determine biological functions of these laciRNAs, we constructed one pair of transgenic plants for each laciRNA, in which the local gene with or without introns was over-expressed in wild type plants,respectively. By comparing morphological phenotypes and transcriptomic profiles between two classes of transgenic plants, we show that over-expression of the laciRNA derived from the 1 st intron of At5 g37720 causes pleiotropic phenotypes, including curly and clustered leaf, late flowering, reduced fertility, and accompanied with altered expression of approximately 800 genes.Our results provide another example that a specific plant circular RNA regulates gene expression in a similar manner to that of other non-coding RNAs under physiological conditions.
引文
Armakola,M.,Higgins,M.J.,Figley,M.D.,Barmada,S.J.,Scarborough,E.A.,Diaz,Z.,Fang,X.,Shorter,J.,Krogan,N.J.,Finkbeiner,S.,Farese,R.V.,and Gitler,A.D.(2012).Inhibition of RNA lariat debranching enzyme suppresses TDP-43 toxicity in ALS disease models.Nat Genet 44,1302-1309.
Ashwal-Fluss,R.,Meyer,M.,Pamudurti,N.R.,Ivanov,A.,Bartok,O.,Hanan,M.,Evantal,N.,Memczak,S.,Rajewsky,N.,and Kadener,S.(2014).circRNA biogenesis competes with pre-mRNA splicing.Mol Cell 56,55-66.
Conn,V.M.,Hugouvieux,V.,Nayak,A.,Conos,S.A.,Capovilla,G.,Cildir,G.,Jourdain,A.,Tergaonkar,V.,Schmid,M.,Zubieta,C.,and Conn,S.J.(2017).A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R-loop formation.Nat Plants 3,17053.
Hansen,T.B.,Jensen,T.I.,Clausen,B.H.,Bramsen,J.B.,Finsen,B.,Damgaard,C.K.,and Kjems,J.(2013).Natural RNA circles function as efficient microRNA sponges.Nature 495,384-388.
Jeck,W.R.,and Sharpless,N.E.(2014).Detecting and characterizing circular RNAs.Nat Biotechnol 32,453-461.
Karst,S.M.,Rütz,M.L.,and Menees,T.M.(2000).The yeast retrotransposons Ty1 and Ty3 require the RNA lariat debranching enzyme,Dbr1p,for efficient accumulation of reverse transcripts.Biochem Biophys Res Commun 268,112-117.
Kim,H.C.,Kim,G.M.,Yang,J.M.,and Ki,J.W.(2001).Cloning,expression,and complementation test of the RNA lariat debranching enzyme cDNA from mouse.Mol Cells 11,198-203.
Kim,J.W.,Kim,H.C.,Kim,G.M.,Yang,J.M.,Boeke,J.D.,and Nam,K.(2000).Human RNA lariat debranching enzyme cDNA complements the phenotypes of Saccharomyces cerevisiae dbr1 and Schizosaccharomyces pombe dbr1 mutants.Nucleic Acids Res 28,3666-3673.
Li,Z.,Huang,C.,Bao,C.,Chen,L.,Lin,M.,Wang,X.,Zhong,G.,Yu,B.,Hu,W.,Dai,L.,Zhu,P.,Chang,Z.,Wu,Q.,Zhao,Y.,Jia,Y.,Xu,P.,Liu,H.,and Shan,G.(2015).Exon-intron circular RNAs regulate transcription in the nucleus.Nat Struct Mol Biol 22,256-264.
Li,Z.,Wang,S.,Cheng,J.,Su,C.,Zhong,S.,Liu,Q.,Fang,Y.,Yu,Y.,Lv,H.,Zheng,Y.,and Zheng,B.(2016).Intron lariat RNA inhibits microRNAbiogenesis by sequestering the Dicing complex in Arabidopsis.PLoS Genet 12,e1006422.
Lu,T.,Cui,L.,Zhou,Y.,Zhu,C.,Fan,D.,Gong,H.,Zhao,Q.,Zhou,C.,Zhao,Y.,Lu,D.,Luo,J.,Wang,Y.,Tian,Q.,Feng,Q.,Huang,T.,and Han,B.(2015).Transcriptome-wide investigation of circular RNAs in rice.RNA 21,2076-2087.
Memczak,S.,Jens,M.,Elefsinioti,A.,Torti,F.,Krueger,J.,Rybak,A.,Maier,L.,Mackowiak,S.D.,Gregersen,L.H.,Munschauer,M.,Loewer,A.,Ziebold,U.,Landthaler,M.,Kocks,C.,le Noble,F.,and Rajewsky,N.(2013).Circular RNAs are a large class of animal RNAs with regulatory potency.Nature 495,333-338.
Quinlan,A.R.,and Hall,I.M.(2010).BEDTools:a flexible suite of utilities for comparing genomic features.Bioinformatics 26,841-842.
Piwecka,M.,Gla瀉r,P.,Hernandez-Miranda,L.R.,Memczak,S.,Wolf,S.A.,Rybak-Wolf,A.,Filipchyk,A.,Klironomos,F.,Cerda Jara,C.A.,Fenske,P.,Trimbuch,T.,Zywitza,V.,Plass,M.,Schreyer,L.,Ayoub,S.,Kocks,C.,Kühn,R.,Rosenmund,C.,Birchmeier,C.,and Rajewsky,N.(2017).Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function.Science 357,eaam8526.
Robinson,M.D.,McCarthy,D.J.,and Smyth,G.K.(2010).edgeR:a Bioconductor package for differential expression analysis of digital gene expression data.Bioinformatics 26,139-140.
Ruskin,B.,Krainer,A.R.,Maniatis,T.,and Green,M.R.(1984).Excision of an intact intron as a novel lariat structure during pre-mRNA splicing in vitro.Cell 38,317-331.
Suzuki,H.,Zuo,Y.,Wang,J.,Zhang,M.Q.,Malhotra,A.,and Mayeda,A.(2006).Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing.Nucleic Acids Res 34,e63.
Trapnell,C.,Roberts,A.,Goff,L.,Pertea,G.,Kim,D.,Kelley,D.R.,Pimentel,H.,Salzberg,S.L.,Rinn,J.L.,and Pachter,L.(2012).Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.Nat Protoc 7,562-578.
Wang,H.,Hill,K.,and Perry,S.E.(2004).An Arabidopsis RNA lariat debranching enzyme is essential for embryogenesis.J Biol Chem 279,1468-1473.
Wang,P.L.,Bao,Y.,Yee,M.C.,Barrett,S.P.,Hogan,G.J.,Olsen,M.N.,Dinneny,J.R.,Brown,P.O.,and Salzman,J.(2014).Circular RNA is expressed across the eukaryotic tree of life.PLoS ONE 9,e90859.
Ye,C.Y.,Chen,L.,Liu,C.,Zhu,Q.H.,and Fan,L.(2015).Widespread noncoding circular RNAs in plants.New Phytol 208,88-95.
Zhang,Y.,Zhang,X.O.,Chen,T.,Xiang,J.F.,Yin,Q.F.,Xing,Y.H.,Zhu,S.,Yang,L.,and Chen,L.L.(2013).Circular intronic long noncoding RNAs.Mol Cell 51,792-806.
Ashwal-Fluss,R.,Meyer,M.,Pamudurti,N.R.,Ivanov,A.,Bartok,O.,Hanan,M.,Evantal,N.,Memczak,S.,Rajewsky,N.,and Kadener,S.(2014).circRNA biogenesis competes with pre-mRNA splicing.Mol Cell 56,55-66.
Conn,V.M.,Hugouvieux,V.,Nayak,A.,Conos,S.A.,Capovilla,G.,Cildir,G.,Jourdain,A.,Tergaonkar,V.,Schmid,M.,Zubieta,C.,and Conn,S.J.(2017).A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R-loop formation.Nat Plants 3,17053.
Hansen,T.B.,Jensen,T.I.,Clausen,B.H.,Bramsen,J.B.,Finsen,B.,Damgaard,C.K.,and Kjems,J.(2013).Natural RNA circles function as efficient microRNA sponges.Nature 495,384-388.
Jeck,W.R.,and Sharpless,N.E.(2014).Detecting and characterizing circular RNAs.Nat Biotechnol 32,453-461.
Karst,S.M.,Rütz,M.L.,and Menees,T.M.(2000).The yeast retrotransposons Ty1 and Ty3 require the RNA lariat debranching enzyme,Dbr1p,for efficient accumulation of reverse transcripts.Biochem Biophys Res Commun 268,112-117.
Kim,H.C.,Kim,G.M.,Yang,J.M.,and Ki,J.W.(2001).Cloning,expression,and complementation test of the RNA lariat debranching enzyme cDNA from mouse.Mol Cells 11,198-203.
Kim,J.W.,Kim,H.C.,Kim,G.M.,Yang,J.M.,Boeke,J.D.,and Nam,K.(2000).Human RNA lariat debranching enzyme cDNA complements the phenotypes of Saccharomyces cerevisiae dbr1 and Schizosaccharomyces pombe dbr1 mutants.Nucleic Acids Res 28,3666-3673.
Li,Z.,Huang,C.,Bao,C.,Chen,L.,Lin,M.,Wang,X.,Zhong,G.,Yu,B.,Hu,W.,Dai,L.,Zhu,P.,Chang,Z.,Wu,Q.,Zhao,Y.,Jia,Y.,Xu,P.,Liu,H.,and Shan,G.(2015).Exon-intron circular RNAs regulate transcription in the nucleus.Nat Struct Mol Biol 22,256-264.
Li,Z.,Wang,S.,Cheng,J.,Su,C.,Zhong,S.,Liu,Q.,Fang,Y.,Yu,Y.,Lv,H.,Zheng,Y.,and Zheng,B.(2016).Intron lariat RNA inhibits microRNAbiogenesis by sequestering the Dicing complex in Arabidopsis.PLoS Genet 12,e1006422.
Lu,T.,Cui,L.,Zhou,Y.,Zhu,C.,Fan,D.,Gong,H.,Zhao,Q.,Zhou,C.,Zhao,Y.,Lu,D.,Luo,J.,Wang,Y.,Tian,Q.,Feng,Q.,Huang,T.,and Han,B.(2015).Transcriptome-wide investigation of circular RNAs in rice.RNA 21,2076-2087.
Memczak,S.,Jens,M.,Elefsinioti,A.,Torti,F.,Krueger,J.,Rybak,A.,Maier,L.,Mackowiak,S.D.,Gregersen,L.H.,Munschauer,M.,Loewer,A.,Ziebold,U.,Landthaler,M.,Kocks,C.,le Noble,F.,and Rajewsky,N.(2013).Circular RNAs are a large class of animal RNAs with regulatory potency.Nature 495,333-338.
Quinlan,A.R.,and Hall,I.M.(2010).BEDTools:a flexible suite of utilities for comparing genomic features.Bioinformatics 26,841-842.
Piwecka,M.,Gla瀉r,P.,Hernandez-Miranda,L.R.,Memczak,S.,Wolf,S.A.,Rybak-Wolf,A.,Filipchyk,A.,Klironomos,F.,Cerda Jara,C.A.,Fenske,P.,Trimbuch,T.,Zywitza,V.,Plass,M.,Schreyer,L.,Ayoub,S.,Kocks,C.,Kühn,R.,Rosenmund,C.,Birchmeier,C.,and Rajewsky,N.(2017).Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function.Science 357,eaam8526.
Robinson,M.D.,McCarthy,D.J.,and Smyth,G.K.(2010).edgeR:a Bioconductor package for differential expression analysis of digital gene expression data.Bioinformatics 26,139-140.
Ruskin,B.,Krainer,A.R.,Maniatis,T.,and Green,M.R.(1984).Excision of an intact intron as a novel lariat structure during pre-mRNA splicing in vitro.Cell 38,317-331.
Suzuki,H.,Zuo,Y.,Wang,J.,Zhang,M.Q.,Malhotra,A.,and Mayeda,A.(2006).Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing.Nucleic Acids Res 34,e63.
Trapnell,C.,Roberts,A.,Goff,L.,Pertea,G.,Kim,D.,Kelley,D.R.,Pimentel,H.,Salzberg,S.L.,Rinn,J.L.,and Pachter,L.(2012).Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.Nat Protoc 7,562-578.
Wang,H.,Hill,K.,and Perry,S.E.(2004).An Arabidopsis RNA lariat debranching enzyme is essential for embryogenesis.J Biol Chem 279,1468-1473.
Wang,P.L.,Bao,Y.,Yee,M.C.,Barrett,S.P.,Hogan,G.J.,Olsen,M.N.,Dinneny,J.R.,Brown,P.O.,and Salzman,J.(2014).Circular RNA is expressed across the eukaryotic tree of life.PLoS ONE 9,e90859.
Ye,C.Y.,Chen,L.,Liu,C.,Zhu,Q.H.,and Fan,L.(2015).Widespread noncoding circular RNAs in plants.New Phytol 208,88-95.
Zhang,Y.,Zhang,X.O.,Chen,T.,Xiang,J.F.,Yin,Q.F.,Xing,Y.H.,Zhu,S.,Yang,L.,and Chen,L.L.(2013).Circular intronic long noncoding RNAs.Mol Cell 51,792-806.