Transcriptome and Degradome Profiling Reveals a Role of miR530 in the Circadian Regulation of Gene Expression in Kalanchoë marnieriana

Hu, Zhikang; Nie, Ziyan; Yan, Chao; Huang, Hu; Ma, Xianjin; Wang, Yupeng; Ye, Ning; Tuskan, Gerald A.; Yang, Xiaohan; Yin, Hengfu

doi:10.3390/cells10061526

Cited by 5 publications

(2 citation statements)

References 52 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Evidence for targets of miR530 have been varied in the literature; for example, predicted miR530 target ARGONAUTE1 (Shao & Lu, 2013;Sunitha et al, 2019) has not been established experimentally. Yang, Du et al (2015) claimed miR530 targets Knotted-Like1 in poplar, and we previously documented slicing activity for Ribosomal protein L10A and zinc knuckle Plus-3 domain/PL3 in grapevine (Sunitha et al, 2019), where PL3 homologues predicted in poplar and chickpea (Kohli et al, 2014;Lu et al, 2008) have been validated in strawberry, rice, poplar, and Kalanchoë marnieriana (Ding et al, 2022;Hu et al, 2021;Sun et al, 2020;Xia et al, 2015). These convergent evidences support the PL3 gene family as a canonical miR530 target, supporting our finding of four degradome-supported zinc knuckle/Plus3 domain target genes (7CP98C, TEF2FC, YIX0R7, SM0BS0; Supporting Information S4a).…”

Section: Validation Of Mirna Cognate and Novel Noncanonical Targets B...mentioning

confidence: 87%

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

et al. 2023

View full text Add to dashboard Cite

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.

show abstract

Section: Validation Of Mirna Cognate and Novel Noncanonical Targets B...mentioning

confidence: 87%

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

et al. 2023

View full text Add to dashboard Cite

show abstract

“…The regulatory gene-expression network in plants involves several layers of regulatory components that control the biogenesis of genes, including signal transduction, chromatin remodeling, transcription factors, transcription, post-transcription, and translation [ 8 , 9 , 10 , 11 , 12 , 13 ]. MicroRNA (miRNA) is one of the critical components in regulating gene expression at the post-transcriptional level, playing essential roles in various molecular and developmental processes [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

Overview of Repressive miRNA Regulation by Short Tandem Target Mimic (STTM): Applications and Impact on Plant Biology

Othman

Mustaffa

Che-Othman

et al. 2023

Plants

View full text Add to dashboard Cite

The application of miRNA mimic technology for silencing mature miRNA began in 2007. This technique originated from the discovery of the INDUCED BY PHOSPHATE STARVATION 1 (IPS1) gene, which was found to be a competitive mimic that prevents the cleavage of the targeted mRNA by miRNA inhibition at the post-transcriptional level. To date, various studies have been conducted to understand the molecular mimic mechanism and to improve the efficiency of this technology. As a result, several mimic tools have been developed: target mimicry (TM), short tandem target mimic (STTM), and molecular sponges (SPs). STTM is the most-developed tool due to its stability and effectiveness in decoying miRNA. This review discusses the application of STTM technology on the loss-of-function studies of miRNA and members from diverse plant species. A modified STTM approach for studying the function of miRNA with spatial–temporal expression under the control of specific promoters is further explored. STTM technology will enhance our understanding of the miRNA activity in plant-tissue-specific development and stress responses for applications in improving plant traits via miRNA regulation.

show abstract

Exploration of plant transcriptomes reveals five putative novel poleroviruses and an enamovirus

Sidharthan

Nagendran²,

Baranwal³

2022

Virus Genes

View full text Add to dashboard Cite

Transcriptome datasets available in public domain serve as valuable resource for identi cation and characterization of novel viral genomes. Poleroviruses are economically important plant-infecting RNA viruses belonging to the family Luteoviridae. In the present study, we explored the plant transcriptomes available in public domain and identi ed ve putative novel poleroviruses tentatively named as Foeniculum vulgare polerovirus (FvPV), Kalanchoe marnieriana polerovirus (KmPV), Paspalum notatum polerovirus (PnPV), Piper methysticum polerovirus (PmPV), Trachyspermum ammi polerovirus (TaPV) and a novel enamovirus named as Celmisia lyallii enamovirus (ClEV) in Foeniculum vulgare, Kalanchoe marnieriana, Paspalum notatum, Piper methysticum, Trachyspermum ammi and Celmisia lyallii, respectively. Coding-complete genomes (5.56−5.74 kb) of CIEV, KmPV, PnPV, PmPV and TaPV were recovered while only the partial genome of FvPV could be recovered. The genome organization of identi ed viruses except ClEV is 5'−P0−P1−P2−P3a−P3−P4−P5−3' while that of ClEV is 5'−P0−P1−P2−P3− P5−3'. Phylogenetic analysis and genome organization revealed the relatedness of FvPV, KmPV, PnPV, PmPV and TaPV to other poleroviruses and ClEV to other enamoviruses.

show abstract

Transcriptome and Degradome Profiling Reveals a Role of miR530 in the Circadian Regulation of Gene Expression in Kalanchoë marnieriana

Cited by 5 publications

References 52 publications

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

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

Overview of Repressive miRNA Regulation by Short Tandem Target Mimic (STTM): Applications and Impact on Plant Biology

Exploration of plant transcriptomes reveals five putative novel poleroviruses and an enamovirus

Contact Info

Product

Resources

About