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Global analyses of the dynamics of mammalian microRNA metabolism.

ABSTRACT: Rates of production and degradation together specify microRNA (miRNA) abundance and dynamics. Here, we used approach-to-steady-state metabolic labeling to assess these rates for 176 miRNAs in contact-inhibited mouse embryonic fibroblasts (MEFs), 182 miRNAs in dividing MEFs, and 127 miRNAs in mouse embryonic stem cells (mESCs). MicroRNA duplexes, each comprising a mature miRNA and its passenger strand, are produced at rates as fast as 110 ± 50 copies/cell/min, which exceeds rates reported for any mRNAs. These duplexes are rapidly loaded into Argonaute, with <30 min typically required for duplex loading and silencing-complex maturation. Within Argonaute, guide strands have stabilities that vary by 100-fold. Half-lives also vary globally between cell lines, with median values ranging from 11 to 34 h in mESCs and contact-inhibited MEFs, respectively. Moreover, relative half-lives for individual miRNAs vary between cell types, implying the influence of cell-specific factors in dictating turnover rate. The apparent influence of miRNA regions most important for targeting, together with the effect of one target on miR-7 accumulation, suggest that targets fulfill this role. Analysis of the tailing and trimming of miRNA 3' termini showed that the flux was typically greatest through the isoform tailed with a single uridine, although changes in this flux did not correspond to changes in stability, which suggested that the processes of tailing and trimming might be independent from that of decay. Together, these results establish a framework for describing the dynamics and regulation of miRNAs throughout their life cycle.

SUBMITTER: Kingston ER

PROVIDER: S-EPMC6836734 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Global analyses of the dynamics of mammalian microRNA metabolism.

Kingston Elena R ER Bartel David P DP

Genome research 20190913 11

Rates of production and degradation together specify microRNA (miRNA) abundance and dynamics. Here, we used approach-to-steady-state metabolic labeling to assess these rates for 176 miRNAs in contact-inhibited mouse embryonic fibroblasts (MEFs), 182 miRNAs in dividing MEFs, and 127 miRNAs in mouse embryonic stem cells (mESCs). MicroRNA duplexes, each comprising a mature miRNA and its passenger strand, are produced at rates as fast as 110 ± 50 copies/cell/min, which exceeds rates reported for any ...[more]

PMID: 31519739

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Project description:BackgroundAnthracnose is a damaging disease of sorghum caused by the fungal pathogen Colletotrichum sublineolum. Genome-wide mRNA and microRNA (miRNA) profiles of resistant and susceptible sorghum genotypes were studied to understand components of immune responses, and fungal induced miRNA and target gene networks.ResultsA total of 18 mRNA and 12 miRNA libraries from resistant and susceptible sorghum lines were sequenced prior to and after inoculation with C. sublineolum. Significant differences in transcriptomes of the susceptible and resistant genotypes were observed with dispersion distance and hierarchical cluster tree analyses. Of the total 33,032 genes predicted in the sorghum genome, 19,593 were induced by C. sublineolum, and 15,512 were differentially expressed (DEGs) between the two genotypes. The resistant line was marked by significant reprogramming of the transcriptome at 24 h post inoculation (hpi), and a decrease at 48 hpi, whereas the susceptible line displayed continued changes in gene expression concordant with elevated fungal growth in the susceptible genotype. DEGs encode proteins implicated in diverse functions including photosynthesis, synthesis of tetrapyrrole, carbohydrate and secondary metabolism, immune signaling, and chitin binding. Genes encoding immune receptors, MAPKs, pentatricopeptide repeat proteins, and WRKY transcription factors were induced in the resistant genotype. In a parallel miRNA profiling, the susceptible line displayed greater number of differentially expressed miRNAs than the resistant line indicative of a widespread suppression of gene expression. Interestingly, we found 75 miRNAs, including 36 novel miRNAs, which were differentially expressed in response to fungal inoculation. The expression of 50 miRNAs was significantly different between resistant and susceptible lines. Subsequently, for 35 differentially expressed miRNAs, the corresponding 149 target genes were identified. Expression of 56 target genes were significantly altered after inoculation, showing inverse expression with the corresponding miRNAs.ConclusionsWe provide insights into genome wide dynamics of mRNA and miRNA profiles, biological and cellular processes underlying host responses to fungal infection in sorghum. Resistance is correlated with early transcriptional reprogramming of genes in various pathways. Fungal induced genes, miRNAs and their targets with a potential function in host responses to anthracnose were identified, opening avenues for genetic dissection of resistance mechanisms.

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Global analyses of the dynamics of mammalian microRNA metabolism.

Publications

Global analyses of the dynamics of mammalian microRNA metabolism.

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