microRNAs and Their Roles in Plant Development

Dong, Qingkun; Hu, Binbin; Zhang, Cui

doi:10.3389/fpls.2022.824240

Cited by 86 publications

(65 citation statements)

References 237 publications

(219 reference statements)

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“…In plants and animals, microRNAs (miRNAs) direct Argonaute (AGO) proteins to repress mRNA expression by inhibiting translation or marking the RNA for destruction (Chen, 2009; Bartel, 2018; Dong et al, 2022; Zhang et al, 2022). In animals, miRNA biogenesis begins in the nucleus with the excision of a pre-miRNA stem loop from a primary miRNA transcript by the ribonuclease III enzyme Drosha, aided by a partner protein with multiple double-stranded RNA-binding domains (dsRBDs) (Lee et al, 2003; Denli et al, 2004; Gregory et al, 2004; Han et al, 2004; Han et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

Structural Basis of MicroRNA Biogenesis by Dicer-1 and Its Partner Protein Loqs-PB

Jouravleva

Golovenko

Demo

et al. 2022

Preprint

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SUMMARYIn animals and plants, Dicer enzymes collaborate with double-stranded RNA-binding proteins to convert precursor-microRNAs (pre-miRNAs) into miRNA duplexes. We report six cryo-EM structures of Drosophila Dicer-1 and its partner Loqs-PB. The structures show Dicer-1•Loqs-PB (1) before binding pre-miRNA, (2) after binding and in a catalytically competent state, (3) after nicking one arm of the pre-miRNA, (4) following complete dicing and initial product release. Our reconstructions suggest that pre-miRNA binds a rare, open conformation of the Dicer-1•Loqs-PB heterodimer, enabling conformational proofreading. The Dicer-1 dsRBD and three Loqs-PB dsRBD domains form a tight belt around the pre-miRNA, distorting the RNA helix to place the scissile phosphodiester bonds in the RNase III active sites. Pre-mRNA cleavage shifts the RNA- binding domains and tightens Dicer-1, promoting product release. Our data suggest a model for how the Dicer-1•Loqs-PB complex effects a complete cycle of pre-miRNA recognition, stepwise endonuclease cleavage, and sequential product release.

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Section: Introductionmentioning

confidence: 99%

Structural Basis of MicroRNA Biogenesis by Dicer-1 and Its Partner Protein Loqs-PB

Jouravleva

Golovenko

Demo

et al. 2022

Preprint

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“…They exert a negative regulation on the expression of target genes through sequence-based complementarity, resulting in mRNA cleavage or translation repression ( Chen et al, 2015 ; Song et al, 2019 ; Wang M et al, 2021 ). Studies have shown that miRNAs play important roles in plant growth and development, including organ morphogenesis, hormone secretion, and stress response ( Aukerman and Sakai, 2003 ; Sunkar et al, 2012 ; Dong et al, 2022 ). For example, in Osmanthus fragrans , miR858 affects flavonoid content in flower tissues by negatively regulating the MYB1 gene ( Shi et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Integrated mRNA and Small RNA Sequencing Reveals microRNAs Associated With Xylem Development in Dalbergia odorifera

Zhao

Meng

et al. 2022

Front. Genet.

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Dalbergia odorifera is a rare and precious rosewood specie, whose wood is a very high-quality material for valuable furniture and carving crafts. However, limited information is available about the process of wood formation in D. odorifera. To determine genes that might be closely associated with the xylem differentiation process, we analyzed the differentially expressed genes (DEGs) and microRNAs (miRNAs) from specific xylem tissues of D. odorifera by RNA sequencing (RNA-seq) and small RNA sequencing (small RNA-seq). In total, we obtained 134,221,955 clean reads from RNA-seq and 90,940,761 clean reads from small RNA-seq. By comparing the transition zone (Dotz) and sapwood (Dosw) samples, a total of 395 DEGs were identified. Further analysis revealed that DEGs encoded for WRKY transcription factors (eight genes), lignin synthesis (PER47, COMT, CCR2), cell wall composition (UXS2), gibberellin synthesis (KAO2, GA20OX1), jasmonic acid synthesis (OPR2, CYP74A), and synthesis of flavonoids (PAL2) and terpenoids (CYP71A1). Subsequently, a preliminary analysis by small RNA-seq showed that the expressions of 14 miRNAs (such as miR168a-5p, miR167f-5p, miR167h-5p, miR167e, miR390a, miR156g, novel_52, and novel_9) were significantly different between Dotz and Dosw. Further analysis revealed that the target genes of these differentially expressed miRNAs were enriched in the GO terms “amino acid binding,” “cellulase activity,” and “DNA beta-glucosyltransferase activity”. Further, KEGG pathway annotation showed significant enrichment in “fatty acid elongation” and “biosynthesis of unsaturated fatty acids”. These processes might be participating in the xylem differentiation of D. odorifera. Next, expression correlation analysis showed that nine differentially expressed miRNAs were significantly negatively associated with 21 target genes, which encoded for proteins such as pyrH, SPL6, SPL12, GCS1, and ARF8. Overall, this is the first study on miRNAs and their potential functions in the xylem development of D. odorifera, which provides a stepping stone for a detailed functional investigation of D. odorifera miRNAs.

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“…Some miRNAs are shown to function in chromatin modi cation by mediating DNA methylation and also regulate gene expression by targeting their promoters [3,4]. Plant miRNAs play key roles in almost all aspects of growth and development, ranging from embryogenesis, vegetative growth, organ formation, juvenile-to-adult transition, owering time determination and senescence and death [5][6][7].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification of auxin-responsive microRNAs in the poplar stem

Yang

Ping

et al. 2022

Preprint

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Background Wood (secondary xylem) of forests is widely used used in construction, paper making, furniture, and as a feedstock for biofuels. Wood development is strictly regulated by the phytohormone auxin and MicroRNAs (miRNAs). Currently, the regulatory mechanisms of auxin-induced miRNAs during wood formation in tree species remain unclear.Methods and results Here, we investigated the effect of auxin application on wood development in poplar and identified miRNAs in the stems treated with different concentrations (0 mg/L, CK; 5 mg/L, Low; 10 mg/L, High) of indol-3-butyric acid (IBA). High-throughput sequencing showed that the 24-nt sRNAs were the most abundant classes in three types of small RNA libraries. A total of 118 known miRNAs and 134 novel miRNAs were obtained. Sixty-nine unique developmental-related miRNAs exhibited specific expression patterns in response to auxin, which was consistent with the influence of auxin on wood development. 269 target genes of 69 auxin-responsive miRNAs were predicted. Of them, three novel miRNAs had the most number (≥9) of target genes, which correspondingly belong to SPL, GRF and ARF families. The evolutionary relationships and tissue expression patterns of these target genes were further analyzed. The relative expression levels of four representative miRNAs and their partial target genes were confirmed by using RT-qPCR.Conclusions The present study provides new insights into auxin-responsive miRNAs during wood development in trees.

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microRNAs and Their Roles in Plant Development

Cited by 86 publications

References 237 publications

Structural Basis of MicroRNA Biogenesis by Dicer-1 and Its Partner Protein Loqs-PB

Structural Basis of MicroRNA Biogenesis by Dicer-1 and Its Partner Protein Loqs-PB

Integrated mRNA and Small RNA Sequencing Reveals microRNAs Associated With Xylem Development in Dalbergia odorifera

Genome-wide identification of auxin-responsive microRNAs in the poplar stem

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