A repertoire of intronic lariat RNAs reveals tissue-specific regulation and target mimicry potential in plants

Lariat RNA is concomitantly produced by excised intron during RNA splicing,which is usually debranched by DBR1,an RNA debranching enzyme.However,increasing evidence showed that some lariat RNA could escape debranching.Little is known about how and why these lariat RNAs could be retained.By comparing the atlas of lariat RNAs between the non-dividing cell(mature pollen)and three actively dividing tissues(young shoot apex,young seeds,and young roots),we identified hundreds to thousands of lariat RNA naturally retained in each tissue,and the incidence of lariat RNA retention is much less in shoot apex while much more in pollen.Many lariat RNAs derived from the same intron or different lariat RNAs from the same pre-m RNA could be retained in one tissue while degraded in the other tissues.By deciphering lariat RNA sequences,we identified an AG-rich(RAAAAVAAAR)motif and a UC-rich(UCUCUYUCUC)motif for pollen-specific and the other three tissues-retained lariat RNAs,respectively.Reconstitution of the pollen-specific AG-rich motif indeed enhanced lariat RNA retention in plants.Biologically,hundreds of lariat RNAs harbored mi RNA binding sites,and dual-luciferase reporter assay showed that these natural lariat RNAs had the potential to protect expression of mi RNA target genes.Collectively,our results uncover that selective retention of lariat RNA is an actively regulatory process,and provide new insights into understanding how lariat RNA metabolism may impact mi RNA activity.

The chromatin remodeling complex imitation of switch controls stamen filament elongation by promoting jasmonic acid biosynthesis in Arabidopsis

Plant reproduction requires the coordinated development of both male and female reproductive organs.Jasmonic acid(JA)plays an essential role in stamen filament elongation.However,the mechanism by which the JA biosynthesis genes are regulated to promote stamen elongation remains unclear.Here,we show that the chromatin remodeling complex Imitation of Switch(ISWI)promotes stamen filament elongation by regulating JA biosynthesis.We show that AT-Rich Interacting Domain 5(ARID5)interacts with CHR11,CHR17,and RLT1,several known subunits of ISWI.Mutations in ARID5 and RLTs caused a reduced seed set due to greatly shortened stamen filaments.RNA-seq analyses reveal that the expression of key genes responsible for JA biosynthesis is significantly down-regulated in the arid5 and rlt mutants.Consistently,the JA levels are drastically decreased in both arid5 and rlt mutants.Chromatin immunoprecipitationquantitative PCR analyses further show that ARID5 is recruited to the chromatin of JA biosynthesis genes.Importantly,exogenous JA treatments can fully rescue the defects of stamen filament elongation in both arid5 and rlt mutants,leading to the partial recovery of fertility.Our results provide a clue how JA biosynthesisis positively regulated by the chromatin remodeling complex ISWI,thereby promoting stamen filament elongation in Arabidopsis.

A lariat-derived circular RNA is required for plant development in Arabidopsis

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.