DEAD-box helicases modulate dicing body formation in
            <i>Arabidopsis</i>

Li, Qi; Liu, Ningkun; Liu, Qing; Zheng, Xingguo; Lu, Lu; Gao, Wenrui; Liu, Yang; Liu, Yan; Zhang, Shicheng; Wang, Qian; Pan, Jing; Chen, Chen; Mi, Yingjie; Yang, Meiling; Cheng, Xiaofei; Ren, Guodong; Yuan, Yao‐Wu; Zhang, Xiaoming

doi:10.1126/sciadv.abc6266

Cited by 34 publications

(30 citation statements)

References 78 publications

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“…Finally, in M. polymoprha we identified Serrate Associated Protein 1 (Mp SEAP1 ) gene which encodes an ortholog of A. thaliana SEAP1 protein. In Arabidopsis SEAP1 interacts with SE and affects the splicing and early biogenesis stages of a set of miRNAs ( M. Li et al , 2021 ).…”

Section: Higher Plant Mirna Biogenesis Proteins Are Encoded Within Th...mentioning

confidence: 99%

“…For instance, genes encoding Small 1 (SMA1) and RNA helicase 8 (RH8) have been identified as Mp SMA1 and Mp RH8 within the M. polymorpha genome. According to Q. Li et al (2021) , Arabidopsis RH8 (together with RH6 and RH12) controls the formation of dicing-bodies (D-bodies) by interacting with the SE protein ( Li et al , 2018 ). However, we did not identify RH6 and RH12 in the M. polymorpha genome.…”

Section: Higher Plant Mirna Biogenesis Proteins Are Encoded Within Th...mentioning

confidence: 99%

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Biogenesis, conservation, and function of miRNA in liverworts

Pietrykowska

Sierocka

Zieleziński

et al. 2022

Journal of Experimental Botany

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Micro RNAs (miRNAs) are small, non-coding endogenous RNA molecules of 18–24 nucleotides in length that control multiple gene regulatory pathways via posttranscriptional gene silencing in eukaryotes. To develop a comprehensive picture of the evolutionary history of miRNA biogenesis and action in land plants, new studies on bryophyte representatives are needed. Here, we review the current understanding of MIR gene structure, miRNA biogenesis, and function. In addition, we focus on representatives of two liverwort lineages: the simple thalloid Pellia endiviifolia and the complex thalloid Marchantia polymorpha. The purpose of this review is to bring readers up to date on what is known about conserved and non-conserved miRNAs, their targets, and the functional implications of miRNA action in Marchantia and Pellia. We also note that most Marchantia miRNAs are encoded within protein-coding genes and provide the data for 23 MIR gene structures recognized as independent transcriptional units. Furthermore, we identify Marchantia genes involved in miRNA biogenesis, that are homologous to those identified in higher plants. These genes include those that encode core microprocessor components as well as other auxiliary and regulatory proteins that influence the stability, folding, and processing of pri-miRNAs. We analyzed miRNA biogenesis proteins and found similar domain architecture in majority of the cases. Taken together, our data support the hypothesis that almost all miRNA biogenesis factors known in higher plants are also present in liverworts, suggesting that they emerged early during land plant evolution.

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Section: Higher Plant Mirna Biogenesis Proteins Are Encoded Within Th...mentioning

confidence: 99%

Section: Higher Plant Mirna Biogenesis Proteins Are Encoded Within Th...mentioning

confidence: 99%

Biogenesis, conservation, and function of miRNA in liverworts

Pietrykowska

Sierocka

Zieleziński

et al. 2022

Journal of Experimental Botany

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“…SE-mediated phase separation is necessary for the formation of D-bodies, in which accurate and efficient miRNA processing occurs (Xie et al, 2021). A recent study also reported that several RNA helicase RH6/8/12 interact with SE and promote the phase separation and the formation of D-bodies (Li Q. et al, 2021).…”

Section: Regulation Of Microrna Processingmentioning

confidence: 99%

Mechanisms of MicroRNA Biogenesis and Stability Control in Plants

Zhang

Xiang²,

Chen³

et al. 2022

Front. Plant Sci.

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MicroRNAs (miRNAs), a class of endogenous, non-coding RNAs, which is 20–24 nucleotide long, regulate the expression of its target genes post-transcriptionally and play critical roles in plant normal growth, development, and biotic and abiotic stresses. In cells, miRNA biogenesis and stability control are important in regulating intracellular miRNA abundance. In addition, research on these two aspects has achieved fruitful results. In this review, we focus on the recent research progress in our understanding of miRNA biogenesis and their stability control in plants.

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“…AtRH27, a DEAD-box RNA helicase in Arabidopsis , has been shown to interact with the biogenesis components of miRNAs (microRNAs) like RNA binding proteins (DAWDLE, HYPONASTIC LEAVES 1 and SERRATE) and regulates miRNA biogenesis 9 . In a recent study which bolsters the association between miRNAs and DEAD-box helicases, it was reported that the DEAD-box helicases modulate the formation of nuclear organelles, the dicing bodies (D bodies) in Arabidopsis , a site where miRNAs are processed 10 .…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification, in silico characterization and expression analysis of the RNA helicase gene family in chickpea (C. arietinum L.)

Yadav

Yadava

Kohli

et al. 2022

Sci Rep

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The RNA helicases are an important class of enzymes which are known to influence almost every aspect of RNA metabolism. The majority of RNA helicases belong to the SF2 (superfamily 2) superfamily, members of which are further categorized into three separate subfamilies i.e., the DEAD, DEAH and DExD/H-box subfamilies. In chickpea, these RNA helicases have not been characterized until now. A genome-wide analysis across the chickpea genome led to the identification of a total of 150 RNA helicase genes which included 50 DEAD, 33 DEAH and 67 DExD/H-box genes. These were distributed across all the eight chromosomes, with highest number on chromosome 4 (26) and least on chromosome 8 (8). Gene duplication analysis resulted in identification of 15 paralogous gene pairs with Ka/Ks values < 1, indicating towards the genes being under purifying selection during the course of evolution. The promoter regions of the RNA helicase genes were enriched in cis-acting elements like the light and ABA-responsive elements. The drought responsiveness of the genes was analysed by studying the expression profiles of few of these genes, in two different genotypes, the cultivated variety ICC 8261 (kabuli, C. arietinum) and the wild accession ILWC 292 (C. reticulatum), through qRT-PCR. These genotypes were selected based on their drought responsiveness in a field experiment, where it was observed that the percentage (%) reduction in relative water content (RWC) and membrane stability index (MSI) for the drought stressed plants after withholding water for 24 days, over the control or well-watered plants, was least for both the genotypes. The genes CaDEAD50 and CaDExD/H66 were identified as drought-responsive RNA helicase genes in chickpea. The protein encoded by the CaDExD/H66 gene shares a high degree of homology with one of the CLSY (CLASSY) proteins of A. thaliana. We hypothesize that this gene could possibly be involved in regulation of DNA methylation levels in chickpea by regulating siRNA production, in conjunction with other proteins like the Argonaute, RNA dependent RNA polymerases and Dicer-like proteins.

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DEAD-box helicases modulate dicing body formation in Arabidopsis

Cited by 34 publications

References 78 publications

Biogenesis, conservation, and function of miRNA in liverworts

Biogenesis, conservation, and function of miRNA in liverworts

Mechanisms of MicroRNA Biogenesis and Stability Control in Plants

Genome-wide identification, in silico characterization and expression analysis of the RNA helicase gene family in chickpea (C. arietinum L.)

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