Plant microRNAs: Biogenesis, Homeostasis, and Degradation

Wang, Junli; Mei, Jun; Ren, Guodong

doi:10.3389/fpls.2019.00360

Cited by 189 publications

(137 citation statements)

References 167 publications

Supporting

Mentioning

132

Contrasting

Unclassified

Order By: Relevance

“…sRNA turnover is a key but poorly understood mechanism that determines the accumulation of sRNAs [3,11]. The plant exoribonuclease that conducts 5'-3' sRNA degradation has not been identified.…”

Section: Discussionmentioning

confidence: 99%

“…SDN mutants accumulate higher levels of miRNAs and purified GST-SDN1 protein degrades single-strand sRNA in vitro with size of 17,18,20,21,22,23,24 and 27nt and yield an approximately 8-9 nt end products [9]. In animals, a number of 3 -5 exribonucleases have been reported to function in small RNA 3 processing and degradation including MUT-7 and Poly(A)-specific Ribonuclease (PARN-1) in C. elegans, Nibbler in Drosophila [10,11]. RRP41degrades miR382 and some miRNAs in human embryonic kidney (HEK293T) cells [12].…”

mentioning

confidence: 99%

See 1 more Smart Citation

AtXRN4 Affects the Turnover of Chosen miRNA*s in Arabidopsis

Liu

Gao

et al. 2020

Plants

View full text Add to dashboard Cite

Small RNA (sRNA) turnover is a key but poorly understood mechanism that determines the homeostasis of sRNAs. Animal XRN genes contribute the degradation of sRNAs, AtXRN2 and AtXRN3 also contribute the pri-miRNA processing and miRNA loop degradation in plants. However, the possible functions of the plant XRN genes in sRNA degradation are far from known. Here, we find that AtXRN4 contributes the turnover of plant sRNAs in Arabidopsis thaliana mainly by sRNA-seq, qRT-PCR and Northern blot. The mutation of AtXRN4 alters the sRNA profile and the accumulation of 21 nt sRNAs was increased. Some miRNA*s levels are significantly increased in xrn4 mutant plants. However, the accumulation of the primary miRNAs (pri-miRNAs) and miRNA precursors (pre-miRNAs) were generally unchanged in xrn4 mutant plants which indicates that AtXRN4 contributes the degradation of some miRNA*s. Moreover, AtXRN4 interacts with Arabidopsis Argonaute 2 (AtAGO2). This interaction takes place in Processing bodies (P-bodies). Taken together, our observations identified the interaction between XRN4 with AtAGO2 and suggested that plant XRN4 also contributes the turnover of sRNAs.

show abstract

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

AtXRN4 Affects the Turnover of Chosen miRNA*s in Arabidopsis

Liu

Gao

et al. 2020

Plants

View full text Add to dashboard Cite

show abstract

“…Based on High-Throughput Sequencing that miRNAs play key roles in gene expression regulation at the post-transcriptional level through direct cleavage of transcripts, translational repression [6], or, in some cases, methylation at the transcriptional level in plants. Therefore, miRNAs can facilitate the identification of relevant targets for disease diagnosis and treatment.…”

Section: Analysis Of Panax Ginseng Mirnas and Their Target Predictionmentioning

confidence: 99%

Analysis of Panax ginseng miRNAs and Their Target Prediction Based on High-Throughput Sequencing

et al. 2019

View full text Add to dashboard Cite

Panax ginseng has been widely and effectively used as medicine for thousands of years. However, only limited studies have been conducted to date on ginseng miRNAs. In the present study, we collected 3 ginseng samples from the Changbai Mountain in China. Small RNA libraries were constructed and sequenced on the Illumina HiSeq platform. Sequencing analyses identified 3798 miRNAs, including 298 known miRNAs and 3500 potentially novel miRNAs. The miR166, miR159, and miR396 families were among the most highly expressed miRNAs in all libraries. The results of miRNA expression analyses were validated by qRT-PCR. Target gene prediction through computational and pathway annotation analyses revealed that the primary pathways were related to plant development, including metabolic processes and single-organism processes. It has been reported that plant miRNAs might be one of the hidden bioactive ingredients in medicinal plants. Based on the combined use of RNAhybrid, Miranda, and TargetScan software, a total of 50,992 potential human genes were predicted as the putative targets of 2868 miRNAs. Interestingly, the enriched KEGG pathways were associated with some human diseases, especially cancer, immune system diseases, and neurological disorders, and this could support the clinical use of ginseng. However, the human targets of ginseng miRNAs should be confirmed by further experimental validation. Our results provided valuable insight into ginseng miRNAs and the putative roles of these miRNAs.

show abstract

“…MicroRNAs (miRNAs) are a large class of small noncoding RNAs of 20 to 24 nucleotides (nt) in length [36,43,44]. The miRNA and its target mRNA can form the miRNAinduced silencing RISC complex, which inhibits the protein of its target genes by either destabilizing the mRNA or by inhibiting its translation [43,44]. The RISC complex negatively regulates gene expression at the posttranscriptional level.…”

Section: Introductionmentioning

confidence: 99%

Temporal responses of conserved miRNAs to drought and their associations with drought tolerance and productivity in rice

Xia

Kong

et al. 2020

BMC Genomics

View full text Add to dashboard Cite

Background: Plant miRNAs play crucial roles in responses to drought and developmental processes. It is essential to understand the association of miRNAs with drought-tolerance (DT), as well as their impacts on growth, development, and reproduction (GDP). This will facilitate our utilization of rice miRNAs in breeding. Results: In this study, we investigated the time course of miRNA responses to a long-term drought among six rice genotypes by high-throughput sequencing. In total, 354 conserved miRNAs were drought responsive, representing obvious genotype-and stage-dependent patterns. The drought-responsive miRNAs (DRMs) formed complex regulatory network via their coexpression and direct/indirect impacts on the rice transcriptome. Based on correlation analyses, 211 DRMs were predicted to be associated with DT and/or GDP. Noticeably, 14.2% DRMs were inversely correlated with DT and GDP. In addition, 9 pairs of mature miRNAs, each derived from the same pre-miRNAs, were predicted to have opposite roles in regulating DT and GDP. This suggests a potential yield penalty if an inappropriate miRNA/ pre-miRNA is utilized. miRNAs have profound impacts on the rice transcriptome reflected by great number of correlated drought-responsive genes. By regulating these genes, a miRNA could activate diverse biological processes and metabolic pathways to adapt to drought and have an influence on its GDP. Conclusion: Based on the temporal pattern of miRNAs in response to drought, we have described the complex network between DRMs. Potential associations of DRMs with DT and/or GDP were disclosed. This knowledge provides valuable information for a better understanding in the roles of miRNAs play in rice DT and/or GDP, which can facilitate our utilization of miRNA in breeding.

show abstract

Plant microRNAs: Biogenesis, Homeostasis, and Degradation

Cited by 189 publications

References 167 publications

AtXRN4 Affects the Turnover of Chosen miRNA*s in Arabidopsis

AtXRN4 Affects the Turnover of Chosen miRNA*s in Arabidopsis

Analysis of Panax ginseng miRNAs and Their Target Prediction Based on High-Throughput Sequencing

Temporal responses of conserved miRNAs to drought and their associations with drought tolerance and productivity in rice

Contact Info

Product

Resources

About