LncRNA/circRNA–miRNA–mRNA networks regulate the development of root and shoot meristems of Populus

Liu, Sian; Wu, Ling; Qi, Haoran; Xu, Meng

doi:10.1016/j.indcrop.2019.03.048

Cited by 58 publications

(44 citation statements)

References 61 publications

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“…In addition, the circRNA circ_001350 regulates glioma cell proliferation, apoptosis, and metastatic properties by acting as a miRNA sponge [64]. In plants, circRNA-miRNA-mRNA networks have been identified, but they have not been confirmed by experiments [31,65]. To reveal whether DEcircRNAs can target miRNAs and participate in the transcriptional regulation of genes, we identified 385 DEcircRNAs predicted to contain miRNA decoy sites.…”

Section: Discussionmentioning

confidence: 99%

“…Recent studies have suggested that plant circRNAs play functional roles in developmental processes and stress responses, including the responses to drought, chilling injury, nutrient deficiency, and pathogen invasion [19,20,22,24,25,30]. Based on the functions of animal circRNAs, circRNA-miRNA-mRNA networks have been generated for plants; these networks suggest that plant circRNAs may act as miRNA sponges to regulate functional gene expression [23,25,31]. Additionally, plant circRNAs are involved in the regulation of their parental genes.…”

Section: Introductionmentioning

confidence: 99%

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Identification and Characterization of circRNAs Responsive to Methyl Jasmonate in Arabidopsis thaliana

Zhang

Liu

Zhu

et al. 2020

IJMS

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Circular RNAs (circRNAs) are endogenous noncoding RNAs with covalently closed continuous loop structures that are formed by 3 -5 ligation during splicing. These molecules are involved in diverse physiological and developmental processes in eukaryotic cells. Jasmonic acid (JA) is a critical hormonal regulator of plant growth and defense. However, the roles of circRNAs in the JA regulatory network are unclear. In this study, we performed high-throughput sequencing of Arabidopsis thaliana at 24 h, 48 h, and 96 h after methyl JA (MeJA) treatment. A total of 8588 circRNAs, which were distributed on almost all chromosomes, were identified, and the majority of circRNAs had lengths between 200 and 800 bp. We identified 385 differentially expressed circRNAs (DEcircRNAs) by comparing data between MeJA-treated and untreated samples. Gene Ontology (GO) enrichment analysis of the host genes that produced the DEcircRNAs showed that the DEcircRNAs are mainly involved in response to stimulation and metabolism. Additionally, some DEcircRNAs were predicted to act as miRNA decoys. Eight DEcircRNAs were validated by qRT-PCR with divergent primers, and the junction sites of five DEcircRNAs were validated by PCR analysis and Sanger sequencing. Our results provide insight into the potential roles of circRNAs in the MeJA regulation network.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Identification and Characterization of circRNAs Responsive to Methyl Jasmonate in Arabidopsis thaliana

Zhang

Liu

Zhu

et al. 2020

IJMS

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“…In addition, the transcription, splicing patterns, and secondary structure of lncRNAs are also regulated by RNA modification, DNA methylation, and histone modification [8,9]. For miRNAs, the target gene can be determined by complementary pairing with the target sequence [10,11]; however, the regulatory mechanisms of lncRNAs are complex and diverse, and a target gene may be regulated by both cis-action (short-range) and trans-action (long-distance). Wang et al [12] classified various functions of lncRNAs into four regulatory mechanisms.…”

Section: The Regulatory Mechanisms Of Lncrnamentioning

confidence: 99%

“…The growth and stress response mechanisms of trees are more complex than those of herbaceous plants. In recent years, lncRNAs in trees have also emerged based on high-throughput sequencing and biological information prediction [48,49], and lncRNAs have been found in various stages of tree growth and stress response processes [10,48,50]. The authenticity identification and annotation of these lncRNAs have been enormously challenging, and there is still a long way to go for further experimental verification and validation.…”

Section: The Extensive Involvement Of Lncrnas In Plant Growth and Devmentioning

confidence: 99%

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Research Progress on Plant Long Non-Coding RNA

Liu

et al. 2020

Plants

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Non-coding RNAs (ncRNAs) that were once considered “dark matter” or “transcriptional noise” in genomes are research hotspots in the field of epigenetics. The most well-known microRNAs (miRNAs) are a class of short non-coding, small molecular weight RNAs with lengths of 20–24 nucleotides that are highly conserved throughout evolution. Through complementary pairing with the bases of target sites, target gene transcripts are cleaved and degraded, or translation is inhibited, thus regulating the growth and development of organisms. Unlike miRNAs, which have been studied thoroughly, long non-coding RNAs (lncRNAs) are a group of poorly conserved RNA molecules with a sequence length of more than 200 nucleotides and no protein encoding capability; they interact with large molecules, such as DNA, RNA, and proteins, and regulate protein modification, chromatin remodeling, protein functional activity, and RNA metabolism in vivo through cis- or trans-activation at the transcriptional, post-transcriptional, and epigenetic levels. Research on plant lncRNAs is just beginning and has gradually emerged in the field of plant molecular biology. Currently, some studies have revealed that lncRNAs are extensively involved in plant growth and development and stress response processes by mediating the transmission and expression of genetic information. This paper systematically introduces lncRNA and its regulatory mechanisms, reviews the current status and progress of lncRNA research in plants, summarizes the main techniques and strategies of lncRNA research in recent years, and discusses existing problems and prospects, in order to provide ideas for further exploration and verification of the specific evolution of plant lncRNAs and their biological functions.

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Plant Organ Primordia

Campbell¹,

Adams²

2020

Encyclopedia of Life Sciences

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The shoot apical meristem (SAM) in plants is composed of totipotent cells that generate the major plant organs including leaves and flowers. Within the SAM synthesis and movement of auxin creates a hormonal flux. In production of leaf primordia, the hormonal flux alters a series small ribonucleic acids (RNAs) that impact the expression of homeotic genes. This results in the generation of a WUSCHEL/CLAVATA feedback loop that generate niches that result in the placement of leaf primordia. This placement of leaf primordia generates the overall phyllotaxis and nodal architecture that defines the major plant body. In perennial plants, seasonal cues alter primordia development resulting in shifts between true leaves and bud scales creating the overwintering meristem. How the transition between bud scales and leaf primordia occurs in unclear. Key Concepts The initiation of leaf primordia at nodes is regulated by an auxin gradient within the SAM. A series of homeotic genes are associated with both SAM formation and establishment of leaf primordia and leaf organ symmetry including Knotted1, WUSCHEL‐RELATED Homeobox 1 and CLAVAT‐type (CLV) homoeotic genes. Small RNAs play a critical role in the developmental processes associated with the SAM development. Auxin flux is directed by PIN1 transporter polarity controlled by MONOPTEROS . Responses to seasonal variation alter leaf primordia development.

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LncRNA/circRNA–miRNA–mRNA networks regulate the development of root and shoot meristems of Populus

Cited by 58 publications

References 61 publications

Identification and Characterization of circRNAs Responsive to Methyl Jasmonate in Arabidopsis thaliana

Identification and Characterization of circRNAs Responsive to Methyl Jasmonate in Arabidopsis thaliana

Research Progress on Plant Long Non-Coding RNA

Plant Organ Primordia

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