Growing Diversity of Plant MicroRNAs and MIR-Derived Small RNAs

Gozmanova, Mariyana; Baev, Vesselin; Apostolova, Elena; Sablok, Gaurav; Yahubyan, Galina

doi:10.1007/978-3-319-55520-1_3

Cited by 6 publications

(4 citation statements)

References 107 publications

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“…The same length class was described in animal germ line cells as the PIWI-interacting small RNA (piRNAs), not known to be present in plants (Siomi et al, 2011). In plants, a speci c class of 23-27 nt long miRNAs was previously reported inArabidopsis thaliana (Gozmanova et al, 2017). Similarly, 27-30 nt sRNAs are present in unicellular eukaryotes (Lee and Collins, 2006), green algae (Li et al, 2023) and pathogenic fungi (Wang et al, 2016;Jia et al, 2017).…”

Section: Introductionmentioning

confidence: 75%

Novel long small RNAs (lsRNAs) are evolutionary conserved in plants and differentially expressed during epitype inducing conditions in Norway spruce embryos

Yakovlev,

Nakamura,

Viejo

et al. 2023

Preprint

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Small non-coding RNA (sRNA) and the various other RNA species have tissue specific expression profiles. However, some size fractions may be missed or left out in the sequencing library preparation process, sequence data processing and downstream bioinformatic analysis. Here, we performed sRNA profiling in embryonic and vegetative tissues to elucidate a more complete picture of the gymnosperm sRNA populations than previously reported. We detected a novel group of sRNA between 31–34 nt in our Norway spruce sequencing data, with a prevalence in the 32–33 nt fraction, defined as the long small RNAs (lsRNAs). These lsRNAs were predominantly present in embryonic samples of Norway spruce. An in-silico analysis indicated that these lsRNA could originate from transfer RNAs (tRNA) and other non-coding transcripts and thus may target other non-coding RNAs (including tRNAs) or target repetitive elements such as transposons. We identified 18 putative orthologs of genes involved in Piwi-interacting RNA (piRNA) biogenesis but no spruce proteins were true homologs to the animal Piwi-proteins, thus lsRNAs cannot be considered as plant analogs to the animal piRNAs. Among the lsRNAs, tRNA-derived sequences from Asp, Glu and His iso-acceptors were in a majority and these sequences showed 3’ or 5’- bias dependent on the iso-acceptor type putatively targeted. The lsRNA sized fraction was detected in seeds of all the gymnosperms examined and in Arabidopsis thaliana, suggesting that these comprise a conserved type of sRNAs between gymnosperms and angiosperms. lsRNA levels differed significantly among tissue types and developmental stages, and interestingly their expression was impacted by epitype-inducing temperature conditions. The lsRNAs add to the complexity of the small RNA world and may play a role in epigenetic regulation of gene expression in plants.

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Section: Introductionmentioning

confidence: 75%

Novel long small RNAs (lsRNAs) are evolutionary conserved in plants and differentially expressed during epitype inducing conditions in Norway spruce embryos

Yakovlev,

Nakamura,

Viejo

et al. 2023

Preprint

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“…By mapping all small RNAs identified in small RNA libraries from rice tissues (leaves, roots) (Baldrich et al., 2015 ), a centred distribution of sequences mapping to the opposite arms of this structure (or isomiRs) was observed (Figure S1 ). miRNA isomers are known to be produced during miRNA biogenesis and have been proposed to be caused by DCL slippage (Gozmanova et al., 2017 ). Most of the small RNAs mapping to the stem‐loop region of this precursor were 24 nt in length (Figure S1 ).…”

Section: Resultsmentioning

confidence: 99%

A novel Transposable element‐derived microRNA participates in plant immunity to rice blast disease

Campo

Sánchez-Sanuy

Camargo-Ramírez

et al. 2021

Plant Biotechnology Journal

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Summary MicroRNAs (miRNAs) are small non‐coding RNAs that direct post‐transcriptional gene silencing in plant development and stress responses through cleavage or translational repression of target mRNAs. Here, we report the identification and functional characterization of a new member of the miR812 family in rice (named as miR812w) involved in disease resistance. miR812w is present in cultivated Oryza species, both japonica and indica subspecies, and wild rice species within the Oryza genus, but not in dicotyledonous species. miR812w is a 24nt‐long that requires DCL3 for its biogenesis and is loaded into AGO4 proteins. Whereas overexpression of miR812w increased resistance to infection by the rice blast fungus Magnaporthe oryzae, CRISPR/Cas9‐mediated MIR812w editing enhances disease susceptibility, supporting that miR812w plays a role in blast resistance. We show that miR812w derives from the Stowaway type of rice MITEs (Miniature Inverted‐Repeat Transposable Elements). Moreover, miR812w directs DNA methylation in trans at target genes that have integrated a Stowaway MITE copy into their 3′ or 5′ untranslated region (ACO3, CIPK10, LRR genes), as well as in cis at the MIR812w locus. The target genes of miR812 were found to be hypo‐methylated around the miR812 recognition site, their expression being up‐regulated in transgene‐free CRISPR/Cas9‐edited miR812 plants. These findings further support that, in addition to post‐transcriptional regulation of gene expression, miRNAs can exert their regulatory function at the transcriptional level. This relationship between miR812w and Stowaway MITEs integrated into multiple coding genes might eventually create a network for miR812w‐mediated regulation of gene expression with implications in rice immunity.

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“…Altogether, DNA and histone modifications and noncoding DNA can regulate gene transcription in the positive or negative sense, as well as selective formation of splice variants by long noncoding RNA. This is the view achieved on the background information from higher eukaryotes, as outlined by Allis and Jenuwein (2016) and Harvey et al (2018); they provide a survey of general aspects in animal cells, while Gozmanova et al (2017) describe this for plant cells.…”

Section: I L I At E S -A Pr Ec Ious Mode L For Epigen Et Ic Smentioning

confidence: 99%

Ciliate research: From myth to trendsetting science

Plattner

2022

J Eukaryotic Microbiology

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This special issue of the Journal of Eukaryotic Microbiology (JEM) summarizes achievements obtained by generations of researchers with ciliates in widely different disciplines. In fact, ciliates range among the first cells seen under the microscope centuries ago. Their beauty made them an object of scientia amabilis, and their manifold reactions made them attractive for college experiments and finally challenged causal analyses at the cellular level. Some of this work was honored by a Nobel Prize. Some observations yielded a baseline for additional novel discoveries, occasionally facilitated by specific properties of some ciliates. This also offers some advantages in the exploration of closely related parasites (malaria). Articles contributed here by colleagues from all over the world encompass a broad spectrum of ciliate life, from genetics to evolution, from molecular cell biology to ecology, from intercellular signaling to epigenetics, etc. This introductory chapter, largely based on my personal perception, aims at integrating work presented in this special issue of JEM into a broader historical context up to current research.

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Growing Diversity of Plant MicroRNAs and MIR-Derived Small RNAs

Cited by 6 publications

References 107 publications

Novel long small RNAs (lsRNAs) are evolutionary conserved in plants and differentially expressed during epitype inducing conditions in Norway spruce embryos

Novel long small RNAs (lsRNAs) are evolutionary conserved in plants and differentially expressed during epitype inducing conditions in Norway spruce embryos

A novel Transposable element‐derived microRNA participates in plant immunity to rice blast disease

Ciliate research: From myth to trendsetting science

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