Long noncoding RNAs(lncRNAs)are emerging as pivotal regulators in gene expression networks,charac-terized by their structural flexibility and functional versatility.In plants,lncRNAs have gained increasing attention d...Long noncoding RNAs(lncRNAs)are emerging as pivotal regulators in gene expression networks,charac-terized by their structural flexibility and functional versatility.In plants,lncRNAs have gained increasing attention due to accumulating evidence of their roles in modulating developmental plasticity and agro-nomic traits.In this review,we focus on the origin,classification,and mechanisms of action of plant lncRNAs,with a particular emphasis on their involvement in developmental processes.We also compre-hensively analyze the relationship between plant lncRNAs and their responses to environmental stimuli,discussing how environmental cues influence their expressions and regulatory functions.We then highlight the importance of the advanced technologies driving their functional exploration.Finally,we discuss recent discoveries of specific long noncoding transcripts that encode functional small peptides,revealing an additional layer of regulatory complexity to these transcripts.Overall,this review discuss the fascinating relationship between the dynamic transcription of lncRNAs and plant developmental plasticity,as well as environmental responses,and emphasizes the need for further research to uncover the underlying mo-lecular mechanisms and exploit the potential of noncoding transcripts for RNA-based strategies in crop improvementandmolecularbreeding.展开更多
Plant long noncoding RNAs(lncRNAs)have emerged as important regulators of chromatin dynamics,impacting on transcriptional programs leading to different developmental outputs.The lncRNA AUXIN-REGULATED PROMOTER LOOP(AP...Plant long noncoding RNAs(lncRNAs)have emerged as important regulators of chromatin dynamics,impacting on transcriptional programs leading to different developmental outputs.The lncRNA AUXIN-REGULATED PROMOTER LOOP(APOLO)directly recognizes multiple independent loci across the Arabidopsis genome and modulates their three-dimensional chromatin conformation,leading to transcriptional shifts.Here,we show that APOLO recognizes the locus encoding the root hair(RH)master regulator ROOT HAIR DEFECTIVE 6(RHD6)and controls RHD6 transcriptional activity,leading to cold-enhanced RH elongation through the consequent activation of the transcription factor gene RHD6-like RSL4.Furthermore,we demonstrate that APOLO interacts with the transcription factor WRKY42 and modulates its binding to the RHD6 promoter.WRKY42 is required for the activation of RHD6 by low temperatures and WRKY42 deregulation impairs cold-induced RH expansion.Collectively,our results indicate that a novel ribonucleoprotein complex with APOLO and WRKY42 forms a regulatory hub to activate RHD6 by shaping its epigenetic environment and integrate signals governing RH growth and development.展开更多
Clustered organization of biosynthetic non-homologous genes is emerging as a characteristic feature of plant genomes.The co-regulation of clustered genes seems to largely depend on epigenetic reprogram-ming and three-...Clustered organization of biosynthetic non-homologous genes is emerging as a characteristic feature of plant genomes.The co-regulation of clustered genes seems to largely depend on epigenetic reprogram-ming and three-dimensional chromatin conformation.In this study,we identified the long non-coding RNA(lncRNA)MARneral Silencing(MARS),localized inside the Arabidopsis marneral cluster,which con-trols the local epigenetic activation of its surrounding region in response to abscisic acid(ABA).MARS modulates the POLYCOMB REPRESSIVE COMPLEX 1(PRC1)component LIKE HETEROCHROMATIN PROTEIN 1(LHP1)binding throughout the cluster in a dose-dependent manner,determining H3K27me3 deposition and chromatin condensation.In response to ABA,MARS decoys LHP1 away from the cluster and promotes the formation of a chromatin loop bringing together the MARNERAL SYNTHASE 1(MRN1)locus and a distal ABA-responsive enhancer.The enrichment of co-regulated lncRNAs in clustered meta-bolic genes in Arabidopsis suggests that the acquisition of novel non-coding transcriptional units may constitute an additional regulatory layer driving the evolution of biosynthetic pathways.展开更多
基金supported by the National Natural Science Foundation of China(Nos.U24A20386 to Y.-Q.C.and 32470605 to D.W.)the Jiangxi Province Outstanding Youth Fund Project(20242BAB23062 to D.W.)+3 种基金the National Ten Thousand Talent Program(2022WRQB007 to Y.-C.Z.)Guangdong Province(2022B1515020018 to Y.-C.Z.)Agencia I+D+i,ICGEB,to F.A.and the AXA Research Fund(AXA Chair,2025-2029 to F.A.).
文摘Long noncoding RNAs(lncRNAs)are emerging as pivotal regulators in gene expression networks,charac-terized by their structural flexibility and functional versatility.In plants,lncRNAs have gained increasing attention due to accumulating evidence of their roles in modulating developmental plasticity and agro-nomic traits.In this review,we focus on the origin,classification,and mechanisms of action of plant lncRNAs,with a particular emphasis on their involvement in developmental processes.We also compre-hensively analyze the relationship between plant lncRNAs and their responses to environmental stimuli,discussing how environmental cues influence their expressions and regulatory functions.We then highlight the importance of the advanced technologies driving their functional exploration.Finally,we discuss recent discoveries of specific long noncoding transcripts that encode functional small peptides,revealing an additional layer of regulatory complexity to these transcripts.Overall,this review discuss the fascinating relationship between the dynamic transcription of lncRNAs and plant developmental plasticity,as well as environmental responses,and emphasizes the need for further research to uncover the underlying mo-lecular mechanisms and exploit the potential of noncoding transcripts for RNA-based strategies in crop improvementandmolecularbreeding.
基金supported by grants from ANPCyT(PICT2016-0132 and PICT2017-0066)Instituto Milenio iBio-Iniciativa Cientffica Milenio,MINECON to J.M.E.
文摘Plant long noncoding RNAs(lncRNAs)have emerged as important regulators of chromatin dynamics,impacting on transcriptional programs leading to different developmental outputs.The lncRNA AUXIN-REGULATED PROMOTER LOOP(APOLO)directly recognizes multiple independent loci across the Arabidopsis genome and modulates their three-dimensional chromatin conformation,leading to transcriptional shifts.Here,we show that APOLO recognizes the locus encoding the root hair(RH)master regulator ROOT HAIR DEFECTIVE 6(RHD6)and controls RHD6 transcriptional activity,leading to cold-enhanced RH elongation through the consequent activation of the transcription factor gene RHD6-like RSL4.Furthermore,we demonstrate that APOLO interacts with the transcription factor WRKY42 and modulates its binding to the RHD6 promoter.WRKY42 is required for the activation of RHD6 by low temperatures and WRKY42 deregulation impairs cold-induced RH expansion.Collectively,our results indicate that a novel ribonucleoprotein complex with APOLO and WRKY42 forms a regulatory hub to activate RHD6 by shaping its epigenetic environment and integrate signals governing RH growth and development.
基金supported by a BBSRC grant(BB/L016966/1)to J.G.-M.and Saclay Plant Sciences-SPS(ANR-17-EUR-0007)and CNRS(Labora-toire International Associe NOCOSYM)to M.C.and F.A..T.R.was awarded a PhD scholarship from the French“Ministere de I'Enseignement superieur,de la Recherche et de I'nnovation.”。
文摘Clustered organization of biosynthetic non-homologous genes is emerging as a characteristic feature of plant genomes.The co-regulation of clustered genes seems to largely depend on epigenetic reprogram-ming and three-dimensional chromatin conformation.In this study,we identified the long non-coding RNA(lncRNA)MARneral Silencing(MARS),localized inside the Arabidopsis marneral cluster,which con-trols the local epigenetic activation of its surrounding region in response to abscisic acid(ABA).MARS modulates the POLYCOMB REPRESSIVE COMPLEX 1(PRC1)component LIKE HETEROCHROMATIN PROTEIN 1(LHP1)binding throughout the cluster in a dose-dependent manner,determining H3K27me3 deposition and chromatin condensation.In response to ABA,MARS decoys LHP1 away from the cluster and promotes the formation of a chromatin loop bringing together the MARNERAL SYNTHASE 1(MRN1)locus and a distal ABA-responsive enhancer.The enrichment of co-regulated lncRNAs in clustered meta-bolic genes in Arabidopsis suggests that the acquisition of novel non-coding transcriptional units may constitute an additional regulatory layer driving the evolution of biosynthetic pathways.
