Interplay and transition between small RNA-directed posttranscriptional and transcriptional gene silencing in plants

Xie, Zhixin; Cheng, Hua

doi:10.1007/s40502-017-0337-5

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“…(iv) Degradome libraries drawn upon are often from different tissues (in our application: above and below ground [3d] gynophores, and mature seed), whereas the query sRNA libraries used to assay miRNA‐triggered events including transitivity/amplification of RNAi are drawn from many tissue sources. Bona fide interactions may be difficult to establish experimentally because of transient changes in miRNA abundance render the effect subtle, limited to specific cell types not assayed, and/or via buffering/epigenetic/target‐mimic mechanisms that indirectly influence gene expression (Franco‐Zorilla et al., 2007; Xie & Cheng, 2017).…”

Section: Resultsmentioning

confidence: 99%

“…Annotated MIRNA loci account for a small fraction of the genome that actively produces 20–24 nt small RNAs whereas the polyA + RNA sequencing (RNA‐Seq) space is largely explained by existing gene annotations. There exists an annotation gap between the empirical knowledge of small RNA (sRNA) expression and the annotations of sRNAs involved in epigenetic phenomena which account for 2%–10% of plant genomes (Coruh et al., 2014; Xie & Cheng, 2017). Understanding miRNA‐triggered phased, small‐interfering RNA loci ( PHAS s) is a major challenge in plant biology (Fei, Yu et al., 2018; Li, Reichel et al., 2014).…”

Section: Introductionmentioning

confidence: 99%

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The role of microRNAs in responses to drought and heat stress in peanut (Arachis hypogaea)

et al. 2023

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MicroRNAs (miRNAs) are 21–24 nt small RNAs (sRNAs) that negatively regulate protein‐coding genes and/or trigger phased small‐interfering RNA (phasiRNA) production. Two thousand nine hundred miRNA families, of which ∼40 are deeply conserved, have been identified in ∼80 different plant species genomes. miRNA functions in response to abiotic stresses is less understood than their roles in development. Only seven peanut MIRNA families are documented in miRBase, yet a reference genome assembly is now published and over 480 plant‐like MIRNA loci were predicted in the diploid peanut progenitor Arachis duranensis genome. We explored by computational analysis of a leaf sRNA library and publicly available sRNA, degradome, and transcriptome datasets the miRNA and phasiRNA space associated with drought and heat stresses in peanut. We characterized 33 novel candidate and 33 ancient conserved families of MIRNAs and present degradome evidence for their cleavage activities on mRNA targets, including several noncanonical targets and novel phasiRNA‐producing noncoding and mRNA loci with validated novel targets such as miR1509 targeting serine/threonine‐protein phosphatase7 and miRc20 and ahy‐miR3514 targeting penta‐tricopeptide repeats (PPRs), in contradistinction to other claims of miR1509/173/7122 superfamily miRNAs indirectly targeting PPRs via TAS‐like noncoding RNA loci. We characterized the inverse correlations of significantly differentially expressed drought‐ and heat‐regulated miRNAs, assayed by sRNA blots or transcriptome datasets, with target mRNA expressions in the same datasets. Meta‐analysis of an expression atlas and over representation of miRNA target genes in co‐expression networks suggest that miRNAs have functions in unique aspects of peanut gynophore development. Genome‐wide MIRNA annotation of the published allopolyploid peanut genome can facilitate molecular breeding of value‐added traits.

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Section: Resultsmentioning

confidence: 99%