Non-coding RNA

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    New lncRNA annotation reveals extensive functional divergence of the transcriptome in maize
    Linqian Han, Zhenna Mu, Zi Luo, Qingchun Pan and Lin Li
    J Integr Plant Biol 2019, 61 (4): 394-405.  
    DOI: 10.1111/jipb.12708
    Abstract (Browse 258)  |   Save
    Long non-coding RNAs (lncRNAs), whose sequences are approximately 200 bp or longer and unlikely to encode proteins, may play an important role in eukaryotic gene regulation. Although the latest maize (Zea mays L.) reference genome provides an essential genomic resource, genome-wide annotations of maize lncRNAs have not been updated. Here, we report on a large transcriptomic dataset collected from 749 RNA sequencing experiments across different tissues and stages of the maize reference inbred B73 line and 60 from its wild relative teosinte. We identified 18,165 high-confidence lncRNAs in maize, of which 6,873 are conserved between maize and teosinte. We uncovered distinct genomic characteristics of conserved lncRNAs, non-conserved lncRNAs, and protein-coding transcripts. Intriguingly, Shannon entropy analysis showed that conserved lncRNAs are likely to be expressed similarly to protein-coding transcripts. Co-expression network analysis revealed significant variation in the degree of co-expression. Furthermore, selection analysis indicated that conserved lncRNAs are more likely than non-conserved lncRNAs to be located in regions subject to recent selection, indicating evolutionary differentiation. Our results provide the latest genome-wide annotation and analysis of maize lncRNAs and uncover potential functional divergence between protein-coding, conserved lncRNA, and non-conserved lncRNA genes, demonstrating the high complexity of the maize transcriptome.
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    Plant lncRNAs are enriched in and move systemically through the phloem in response to phosphate deficiency
    Zhaoliang Zhang, Yi Zheng, Byung-Kook Ham, Shupei Zhang, Zhangjun Fei and William J. Lucas
    J Integr Plant Biol 2019, 61 (4): 492-508.  
    DOI: 10.1111/jipb.12715
    Abstract (Browse 297)  |   Save

    In response to phosphate (Pi) deficiency, it has been shown that micro-RNAs (miRNAs) and mRNAs are transported through the phloem for delivery to sink tissues. Growing evidence also indicates that long non-coding RNAs (lncRNAs) are critical regulators of Pi homeostasis in plants. However, whether lncRNAs are present in and move through the phloem, in response to Pi deficiency, remains to be established. Here, using cucumber as a model plant, we show that lncRNAs are enriched in the phloem translocation stream and respond, systemically, to an imposed Pi-stress. A well-known lncRNA, IPS1, the target mimic (TM) of miRNA399, accumulates to a high level in the phloem, but is not responsive to early Pi deficiency. An additional 24 miRNA TMs were also detected in the phloem translocation stream; among them miRNA171 TMs and miR166 TMs were induced in response to an imposed Pi stress. Grafting studies identified 22 lncRNAs which move systemically into developing leaves and root tips. A CU-rich PTB motif was further identified in these mobile lncRNAs. Our findings revealed that lncRNAs respond to Pi deficiency, non-cell-autonomously, and may act as systemic signaling agents to coordinate early Pi deficiency signaling, at the whole-plant level.

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    Short Panicle 3 controls panicle architecture by upregulating APO2/RFL and increasing cytokinin content in rice
    Yong Huang, Xufeng Bai, Meifang Luo and Yongzhong Xing
    J Integr Plant Biol 2019, 61 (9): 987-999.  
    doi: 10.1111/jipb.12729
    Abstract (Browse 331)  |   Save

    Inflorescence architecture is a major determinant of spikelet numbers per panicle, a key component of grain yield in rice. In this study, Short Panicle 3 (SP3) was identified from a short panicle 3 (sp3) mutant in which T‐DNA was inserted in the promoter of SP3, resulting in a knockdown mutation. SP3 encodes a DNA binding with one finger (Dof) transcriptional activator. Quantitative real time (qRT)‐PCR and RNA in situ hybridization assays confirmed that SP3 is preferentially expressed in the young rice inflorescence, specifically in the branch primordial regions. SP3 acts as a negative regulator of inflorescence meristem abortion by upregulating APO2/RFL. SP3 both up‐ and downregulates expression of genes involved in cytokinin biosynthesis and catabolism, respectively. Consequently, cytokinin concentrations are decreased in young sp3 panicles, thereby leading to small panicles having fewer branches and spikelets. Our findings support a model in which SP3 regulates panicle architecture by modulating cytokinin homeostasis. Potential applications to rice breeding, through gene‐editing of the SP3 promoter are assessed.

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    TCP7 functions redundantly with several Class I TCPs and regulates endoreplication in Arabidopsis
    Guofang Zhang, Hongtao Zhao, Chunguang Zhang, Xiaoyun Li, Yuanyuan Lyu, Dongmei Qi, Yanwei Cui, Lin Hu, Zhenjie Wang, Zheng Liang and Sujuan Cui
    J Integr Plant Biol 2019, 61 (11): 1151-1170.  
    doi: 10.1111/jipb.12749
    Abstract (Browse 289)  |   Save

    TCP (TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR) proteins, a family of plant‐specific transcription factors, play important roles in many developmental processes. However, genetic and functional redundancy among class I TCP limits the analysis of their biological roles. Here, we identified a dominant‐negative mutant of Arabidopsis thaliana TCP7 named leaf curling‐upward (lcu), which exhibits smaller leaf cells and shorter hypocotyls than the wild type, due to defective endoreplication. A septuple loss‐of‐function mutant of TCP7, TCP8, TCP14, TCP15, TCP21, TCP22, and TCP23 displayed similar developmental defects to those of lcu. Genome‐wide RNA‐sequencing showed that lcu and the septuple mutant share many misexpressed genes. Intriguingly, TCP7 directly targets the CYCLIN D1;1 (CYCD1;1) locus and activates its transcription. We determined that the C‐terminus of TCP7 accounts for its transcriptional activation activity. Furthermore, the mutant protein LCU exhibited reduced transcriptional activation activity due to the introduction of an EAR‐like repressive domain at its C‐terminus. Together, these observations indicate that TCP7 plays important roles during leaf and hypocotyl development, redundantly, with at least six class I TCPs, and regulates the expression of CYCD1;1 to affect endoreplication in Arabidopsis.

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    OS1 functions in the allocation of nutrients between the endosperm and embryo in maize seeds
    Weibin Song, Jinjie Zhu, Haiming Zhao, Yingnan Li, Jiangtao Liu, Xiangbo Zhang, Liangliang Huang and Jinsheng Lai
    J Integr Plant Biol 2019, 61 (6): 706-727.  
    doi: 10.1111/jipb.12755
    Abstract (Browse 364)  |   Save
    Uncovering the genetic basis of seed development will provide useful tools for improving both crop yield and nutritional value. However, the genetic regulatory networks of maize (Zea mays) seed development remain largely unknown. The maize opaque endosperm and small germ 1 (os1) mutant has opaque endosperm and a small embryo. Here, we cloned OS1 and show that it encodes a putative transcription factor containing an RWP-RK domain. Transcriptional analysis indicated that OS1 expression is elevated in early endosperm development, especially in the basal endosperm transfer layer (BETL), conducting zone (CZ), and central starch endosperm (CSE) cells. RNA sequencing (RNA-Seq) analysis of the os1 mutant revealed sharp downregulation of certain genes in specific cell types, including ZmMRP-1 and Meg1 in BETL cells and a majority of zein- and starch-related genes in CSE cells. Using a haploid induction system, we show that wild-type endosperm could rescue the smaller size of os1 embryo, which suggests that nutrients are allocated by the wild-type endosperm. Therefore, our data imply that the network regulated by OS1 accomplishes a key step in nutrient allocation between endosperm and embryo within maize seeds. Identification of this network will help uncover the mechanisms regulating the nutritional balance between endosperm and embryo.
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    The F-box protein HAWAIIAN SKIRT is required for mimicry target-induced microRNA degradation in Arabidopsis
    Jun Mei, Ning Jiang and Guodong Ren
    J Integr Plant Biol 2019, 61 (11): 1121-1127.  
    doi: 10.1111/jipb.12761
    Abstract (Browse 366)  |   Save

    Mimicry target‐directed microRNA degradation is widespread and highly conserved among eukaryotes. However, little is known about its mechanism of action. In this letter, by using STTM160 (target mimic of miR160) as a reporter, we show that dysfunction of HAWAIIAN SKIRT (HWS) suppresses the pleiotropic phenotype of STTM160. Small RNA sequencing and Northern blot analyses suggested that HWS only affects a subset of microRNAs. Intriguingly, we identified a stable coexistence of miR160/miR399 and their mimicry targets within the AGO1 complex when HWS is compromised, pointing to a possible role of HWS in the clearance of RNA‐induced silencing complexes associated with mimicry target.

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    Comparative effect of allopolyploidy on transposable element composition and gene expression between Gossypium hirsutum and its two diploid progenitors
    Hua Cheng, Gaofei Sun, Shoupu He, Wenfang Gong, Zhen Peng, Ruiping Wang, Zhongxu Lin and Xiongming Du
    J Integr Plant Biol 2019, 61 (1): 45-59.  
    doi: 10.1111/jipb.12763
    Abstract (Browse 227)  |   Save
    An allopolyploidization event formed allotetraploid Gossypium species from an A-genome diploid species and a D-genome diploid species. To explore the responses of transposable elements (TEs) to allopolyploidy, we assembled parallel TE datasets from G. hirsutum, G. arboreum and G. raimondii and analyzed the TE types and the effects of TEs on orthologous gene expression in the three Gossypium genomes. Gypsy was the most abundant TE type and most TEs were located ~500 bp from genes in all three genomes. In G. hirsutum, 35.6% of genes harbored TE insertions, whereas insertions were more frequent in G. arboreum and G. raimondii. G. hirsutum had the highest proportion of uniquely matching 24-nt small interfering RNAs (siRNAs) that targeted TEs. TEs, particularly those targeted by 24-nt siRNAs, were associated with reduced gene expression, but the effect of TEs on orthologous gene expression varied substantially among species. Orthologous gene expression levels in G. hirsutum were intermediate between those of G. arboreum and G. raimondii, which did not experience TE expansion or reduction resulting from allopolyploidization. This study underscores the diversity of TEs co-opted by host genes and provides insights into the roles of TEs in regulating gene expression in Gossypium.
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    MicroRNAs transcriptionally regulate promoter activity in Arabidopsis thaliana
    Guodong Yang, Yuanyuan Li, Binjiang Wu, Kaiyue Zhang, Lei Gao and Chengchao Zheng
    J Integr Plant Biol 2019, 61 (11): 1128-1133.  
    doi: 10.1111/jipb.12775
    Abstract (Browse 426)  |   Save

    MicroRNAs (miRNAs) are vital regulators that repress gene expression in the cytoplasm in two main ways: mRNA degradation and translational inhibition. Several animal studies have shown that miRNAs also target promoters, thereby activating expression. Whether this miRNA action also occurs in plants is unknown. In this study, we demonstrated that several miRNAs regulate target promoters in Arabidopsis thaliana. For example, miR5658 was predominantly present in the nucleus and activated the expression of AT3G25290 directly by binding to its promoter. Our observations suggest that this mode of action may be a general feature of plant miRNAs, and thus provide insight into the vital roles of plant miRNAs in the nucleus.

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    miR164c and miR168a regulate seed vigor in rice
    Yan Zhou, Shiqi Zhou, Liping Wang, Duo Wu, Hailan Cheng, Xu Du, Dandan Mao, Chunlai Zhang and Xiaocheng Jiang
    J Integr Plant Biol 2020, 62 (4): 470-486.  
    doi: 10.1111/jipb.12792
    Abstract (Browse 744)  |   Save

    MicroRNAs (miRNAs) are key regulators of gene expression in many important biological processes of plants. However, few miRNAs have been shown to regulate seed vigor. Here, we conducted microarray assays to analyze miRNA expression levels in seeds of the rice (Oryza sativa L.) cultivar ZR02. Results showed significant differences in the expression of 11 miRNAs between artificially aged and untreated control seeds. Among these, osa‐miR164c was transcriptionally upregulated, while osa‐miR168a was downregulated in artificially aged seeds; this was verified by quantitative real‐time PCR analysis. Under the same aging condition, osa‐miR164c overexpression in OE164c transgenic seeds and osa‐miR168a silencing in MIM168a transgenic seeds of the rice cultivar Kasalath led to lower germination rates, whereas osa‐miR164c silencing in MIM164c and osa‐miR168a overexpression in OE168a resulted in higher seed germination rates compared with wild‐type seeds. Meanwhile, changes in cytomembrane permeability of seeds and in the expression level of osa‐miR164c target genes (OsPM27 and OsPSK5) and osa‐miR168a target genes (OsAGO1 and OsPTR2) under aging conditions coincided with changes in seed vigor induced by osa‐miR164c and osa‐miR168a. Thus, genetic manipulation of miRNAs has important implications in the development of crop cultivars with high vigor and extended life span of seeds.

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    Dek42 encodes an RNA-binding protein that affects alternative pre-mRNA splicing and maize kernel development
    Yi Zuo, Fan Feng, Weiwei Qi and Rentao Song
    J Integr Plant Biol 2019, 61 (6): 728-748.  
    doi: 10.1111/jipb.12798
    Abstract (Browse 342)  |   Save
    RNA-binding proteins (RBPs) play an important role in post-transcriptional gene regulation. However, the functions of RBPs in plants remain poorly understood. Maize kernel mutant dek42 has small defective kernels and lethal seedlings. Dek42 was cloned by Mutator tag isolation and further confirmed by an independent mutant allele and clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 materials. Dek42 encodes an RRM_RBM48 type RNA-binding protein that localizes to the nucleus. Dek42 is constitutively expressed in various maize tissues. The dek42 mutation caused a significant reduction in the accumulation of DEK42 protein in mutant kernels. RNA-seq analysis showed that the dek42 mutation significantly disturbed the expression of thousands of genes during maize kernel development. Sequence analysis also showed that the dek42 mutation significantly changed alternative splicing in expressed genes, which were especially enriched for the U12-type intron-retained type. Yeast two-hybrid screening identified SF3a1 as a DEK42-interacting protein. DEK42 also interacts with the spliceosome component U1-70K. These results suggested that DEK42 participates in the regulation of pre-messenger RNA splicing through its interaction with other spliceosome components. This study showed the function of a newly identified RBP and provided insights into alternative splicing regulation during maize kernel development.
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    Exploring the molecular basis of heterosis for plant breeding
    Jie Liu, Mengjie Li, Qi Zhang, Xin Wei and Xuehui Huang
    J Integr Plant Biol 2020, 62 (3): 287-298.  
    doi: 10.1111/jipb.12804
    Abstract (Browse 576)  |   Save

    Since approximate a century ago, many hybrid crops have been continually developed by crossing two inbred varieties. Owing to heterosis (hybrid vigor) in plants, these hybrids often have superior agricultural performances in yield or disease resistance succeeding their inbred parental lines. Several classical hypotheses have been proposed to explain the genetic causes of heterosis. During recent years, many new genetics and genomics strategies have been developed and used for the identifications of heterotic genes in plants. Heterotic effects of the heterotic loci and molecular functions of the heterotic genes are being investigated in many plants such as rice, maize, sorghum, Arabidopsis and tomato. More and more data and knowledge coming from the molecular studies of heterotic loci and genes will serve as a valuable resource for hybrid breeding by molecular design in future. This review aims to address recent advances in our understanding of the genetic and molecular mechanisms of heterosis in plants. The remaining scientific questions on the molecular basis of heterosis and the potential applications in breeding are also proposed and discussed.

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    The role of miR156 in rejuvenation in Arabidopsis thaliana
    Bin-Bin Ye, Ke Zhang and Jia-Wei Wang
    J Integr Plant Biol 2020, 62 (5): 550-555.  
    doi: 10.1111/jipb.12855
    Abstract (Browse 413)  |   Save

    Rejuvenation refers to the process enabling plants to regain physiological and molecular characteristics lost after entering the adult phase. The underlying molecular mechanism is poorly understood. Previous studies have revealed that microRNA156 (miR156) is highly accumulated at juvenile stage and maintains juvenile traits by repressing a group of SQUAMOSA PROMOTER BINDING PROTEIN‐LIKE (SPL) transcription factors. Here, we found that induction of miR156 expression in adult leaves can only restore some aspects of juvenile traits, such as loss of epidermal leaf hairs on the lower side of leaves and absence of serration at the leaf edges, but is incapable of delaying flowering and promoting adventitious root production.

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    SMALL KERNEL4 is required for mitochondrial cox1 transcript editing and seed development in maize
    Hong‐Chun Wang, Aqib Sayyed, Xin‐Yuan Liu, Yan‐Zhuo Yang, Feng Sun, Yong Wang, Miaodi Wang and Bao‐Cai Tan
    J Integr Plant Biol 2020, 62 (6): 777-792.  
    DOI: 10.1111/jipb.12856
    Abstract (Browse 449)  |   Save

    In land plants, cytidine‐to‐uridine (C‐to‐U) editing of organellar transcripts is an important post‐transcriptional process, which is considered to remediate DNA genetic mutations to restore the coding of functional proteins. Pentatricopeptide repeat (PPR) proteins have key roles in C‐to‐U editing. Owing to its large number, however, the biological functions of many PPR proteins remain to be identified. Through characterizing a small kernel4 (smk4 ) mutant, here we report the function of Smk4 and its role in maize growth and development. Null mutation of Smk4 slows plant growth and development, causing small plants, delayed flowering time, and small kernels. Cloning revealed that Smk4 encodes a new E‐subclass PPR protein, and localization indicated that SMK4 is exclusively localized in mitochondria. Loss of Smk4 function abolishes C‐to‐U editing at position 1489 of the cytochrome c oxidase1 (cox1 ) transcript, causing an amino acid change from serine to proline at 497 in Cox1. Cox1 is a core component of mitochondrial complex IV. Indeed, complex IV activity is reduced in the smk4 , along with drastically elevated expression of alternative oxidases (AOX). These results indicate that SMK4 functions in the C‐to‐U editing of cox1 ‐1489, and this editing is crucial for mitochondrial complex IV activity, plant growth, and kernel development in maize.

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    Osa-miR1873 fine-tunes rice immunity against Magnaporthe oryzae and yield traits
    Shi-Xin Zhou, Yong Zhu, Liang-Fang Wang, Ya-Ping Zheng, Jin-Feng Chen, Ting-Ting Li, Xue-Mei Yang, He Wang, Xu-Pu Li, Xiao-Chun Ma, Ji-Qun Zhao, Mei Pu, Hui Feng, Yan Li, Jing Fan, Ji-Wei Zhang, Yan-Yan Huang and Wen-Ming Wang
    J Integr Plant Biol 2020, 62 (8): 1213-1226.  
    doi: 10.1111/jipb.12900
    Abstract (Browse 524)  |   Save

    MicroRNAs (miRNAs) are known to fine‐tune growth, development, and stress‐induced responses. Osa‐miR1873 is a rice‐specific miRNA targeting LOC_Os05g01790 . Here, we show that Osa‐miR1873 fine‐tunes rice immunity against Magnaporthe oryzae and yield traits via LOC_Os05g01790 . Osa‐miR1873 was significantly upregulated in a susceptible accession but downregulated in a resistance accession at 24 h post‐inoculation (hpi) of M. oryzae . Overexpressing Osa‐miR1873 enhanced susceptibility to M . oryzae and compromised induction of defense responses. In contrast, blocking Osa‐miR1873 through target mimicry compromised susceptibility to M . oryzae and enhanced induction of defense responses. Altered expression of Osa‐miR1873 also resulted in some defects in yield traits, including grain numbers and seed setting rate. Moreover, overexpression of the target gene LOC_Os05g01790 increased rice blast disease resistance but severely penalized growth and yield. Taken together, we demonstrate that Osa‐miR1873 fine‐tunes the rice immunity‐growth trade‐off via LOC_Os05g01790 , and blocking Osa‐miR1873 could improve blast disease resistance without significant yield penalty. Thus, the Osa‐miR1873‐LOC_Os05g01790 regulatory module is valuable in balancing yield traits and blast resistance.

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    The heterochronic gene Oryza sativa LIKE HETEROCHROMATIN PROTEIN 1 modulates miR156b/c/i/e levels
    Yongtao Cui, Jingfei Cheng, Shuang Ruan, Peipei Qi, Wei Liu, Hongwu Bian, Luhuan Ye, Yuping Zhang, Jiang Hu, Guojun Dong, Longbiao Guo, Yijing Zhang, Qian Qian and Xingming Hu
    J Integr Plant Biol 2020, 62 (12): 1839-1852.  
    DOI: 10.1111/jipb.12991
    Abstract (Browse 271)  |   Save

    The juvenile‐to‐adult transition in plants involves changes in vegetative growth and plant architecture; the timing of this transition has important implications for agriculture. The microRNA miR156 regulates this transition and shoot maturation in plants. In Arabidopsis thaliana, deposition of histone H3 trimethylation on lysine 27 (H3K27me3, a repressive mark) at the MIR156A/C loci is regulated by Polycomb Repressive Complex 1 (PRC1) or PRC2, depending on the developmental stage. The levels of miR156 progressively decline during shoot maturation. The amount of H3K27me3 at MIR156A/C loci affects miR156 levels; however, whether this epigenetic regulation is conserved remains unclear. Here, we found that in rice (Oryza sativa), the putative PRC1 subunit LIKE HETEROCHROMATIN PROTEIN 1 (OsLHP1), with the miR156–SQUAMOSA PROMOTER BINDING PROTEIN‐LIKE (SPL) module, affects developmental phase transitions. Loss of OsLHP1 function results in ectopic expression of MIR156B/C/I/E, phenocopy of miR156 overexpression, and reduced H3k27me3 levels at MIR156B/C/I/E. This indicates that OsLHP1 has functionally diverged from Arabidopsis LHP1. Genetic and transcriptome analyses of wild‐type, miR156b/c‐overexpression, and Oslhp1‐2 mutant plants suggest that OsLHP1 acts upstream of miR156 and SPL during the juvenile‐to‐adult transition. Therefore, modifying the OsLHP1–miR156–SPL pathway may enable alteration of the vegetative period and plant architecture.

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    Profiling of circular RNA N6‐methyladenosine in moso bamboo (Phyllostachys edulis) using nanopore‐based direct RNA sequencing
    Yongsheng Wang, Huihui Wang, Feihu Xi, Huiyuan Wang, Ximei Han, Wentao Wei, Hangxiao Zhang, Qianyue Zhang, Yushan Zheng, Qiang Zhu, Markus V. Kohnen, Anireddy S. N. Reddy and Lianfeng Gu
    J Integr Plant Biol 2020, 62 (12): 1823-1838.  
    DOI: 10.1111/jipb.13002
    Abstract (Browse 385)  |   Save

    N6‐methyladenosine (m6A) is a prevalent modification in messenger RNAs and circular RNAs that play important roles in regulating various aspects of RNA metabolism. However, the occurrence of the m6A modification in plant circular RNAs has not been reported. A widely used method to identify m6A modifications relies on m6A‐specific antibodies followed by next‐generation sequencing of precipitated RNAs (MeRIP‐Seq). However, one limitation of MeRIP‐Seq is that it does not provide the precise location of m6A at single‐nucleotide resolution. Although more recent sequencing techniques such as Nanopore‐based direct RNA sequencing (DRS) can overcome such limitations, the technology does not allow sequencing of circular RNAs, as these molecules lack a poly(A) tail. Here, we developed a novel method to detect the precise location of m6A modifications in circular RNAs using Nanopore DRS. We first enriched our samples for circular RNAs, which we then fragmented and sequenced on the Nanopore platform with a customized protocol. Using this method, we identified 470 unique circular RNAs from DRS reads based on the back‐spliced junction region. Among exonic circular RNAs, about 10% contained m6A sites, which mainly occurred around acceptor and donor splice sites. This study demonstrates the utility of our antibody‐independent method in identifying total and methylated circular RNAs using Nanopore DRS. This method has the additional advantage of providing the exact location of m6A sites at single‐base resolution in circular RNAs or linear transcripts from non‐coding RNA without poly(A) tails.

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    The pre‐mRNA splicing factor RDM16 regulates root stem cell maintenance in Arabidopsis
    Bingsheng Lv, Kongqin Hu, Te Tian, Kaijing Wei, Feng Zhang, Yuebin Jia, Huiyu Tian and Zhaojun Ding
    J Integr Plant Biol 2021, 63 (4): 662-678.  
    DOI: 10.1111/jipb.13006
    Abstract (Browse 440)  |   Save
    Pre‐mRNA (messenger RNA) splicing participates in the regulation of numerous biological processes in plants. For example, alternative splicing shapes transcriptomic responses to abiotic and biotic stress, and controls developmental programs. However, no study has revealed a role for splicing in maintaining the root stem cell niche. Here, a screen for defects in root growth in Arabidopsis thaliana identified an ethyl methane sulfonate mutant defective in pre‐mRNA splicing (rdm16‐4). The rdm16‐4 mutant displays a short‐root phenotype resulting from fewer cells in the root apical meristem. The PLETHORA1 (PLT1) and PLT2 transcription factor genes are important for root development and were alternatively spliced in rdm16‐4 mutants, resulting in a disordered root stem cell niche and retarded root growth. The root cap of rdm16‐4 contained reduced levels of cytokinins, which promote differentiation in the developing root. This reduction was associated with the alternative splicing of genes encoding cytokinin signaling factors, such as ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN5 and ARABIDOPSIS RESPONSE REGULATORS (ARR1, ARR2, and ARR11). Furthermore, expression of the full‐length coding sequence of ARR1 or exogenous cytokinin application partially rescued the short‐root phenotype of rdm16‐4. This reveals that the RDM16‐mediated alternative splicing of cytokinin signaling components contributes to root growth.
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    Genome-wide profiling of circular RNAs, alternative splicing, and R-loops in stem-differentiating xylem of Populus trichocarpa
    Xuqing Liu, Yubang Gao, Jiakai Liao, Miao Miao, Kai Chen, Feihu Xi, Wentao Wei, Huihui Wang, Yongsheng Wang, Xi Xu, Anireddy S.N. Reddy and Lianfeng Gu
    J Integr Plant Biol 2021, 63 (7): 1294-1308.  
    DOI: 10.1111/jipb.13081
    Abstract (Browse 286)  |   Save
    Circular RNAs (circRNAs) are a recently discovered type of non-coding RNA derived from pre-mRNAs. R-loops consist of a DNA:RNA hybrid and the associated single-stranded DNA. In Arabidopsis thaliana, circRNA:DNA R-loops regulate alternative splicing (AS) of SEPALLATA3 (SEP3). However, the occurrence and functions of circRNAs and R-loops in Populus trichocarpa are largely unexplored. Here, we performed circRNA-enriched sequencing in the stem-differentiating xylem (SDX) of P. trichocarpa and identified 2,742 distinct circRNAs, including circ-CESA4, circ-IRX7, and circ-GUX1, which are generated from genes involved in cellulose, and hemicellulose biosynthesis, respectively. To investigate the roles of circRNAs in modulating alternative splicing (AS), we detected 7,836 AS events using PacBio Iso-Seq and identified 634 circRNAs that overlapped with 699 AS events. Furthermore, using DNA:RNA hybrid immunoprecipitation followed by sequencing (DRIP-seq), we identified 8,932 R-loop peaks that overlapped with 181 circRNAs and 672 AS events. Notably, several SDX-related circRNAs overlapped with R-loop peaks, pointing to their possible roles in modulating AS in SDX. Indeed, overexpressing circ-IRX7 increased the levels of R-loop structures and decreased the frequency of intron retention in linear IRX7 transcripts. This study provides a valuable R-loop atlas resource and uncovers the interplay between circRNAs and AS in SDX of P. trichocarpa.
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    Plant transfer RNA-derived fragments: Biogenesis and functions
    Xuan Ma, Chunyan Liu and Xiaofeng Cao
    J Integr Plant Biol 2021, 63 (8): 1399-1409.  
    doi: 10.1111/jipb.13143
    Abstract (Browse 269)  |   Save
    Processing of mature transfer RNAs (tRNAs) produces complex populations of tRNA-derived fragments (tRFs). Emerging evidence shows that tRFs have important functions in bacteria, animals, and plants. Here, we review recent advances in understanding plant tRFs, focusing on their biological and cellular functions, such as regulating stress responses, mediating plant–pathogen interactions, and modulating post-transcriptional gene silencing and translation. We also review sequencing strategies and bioinformatics resources for studying tRFs in plants. Finally, we discuss future directions for plant tRF research, which will expand our knowledge of plant non-coding RNAs.
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