Ensemble Analysis of Primary MicroRNA Structure Reveals an Extensive Capacity To Deform near the Drosha Cleavage Site

Quarles, Kaycee A.; Sahu, Debashish; Havens, Mallory A.; Forsyth, Ellen R.; Wostenberg, Christopher; Hastings, Michelle L.; Showalter, Scott A.

doi:10.1021/bi301452a

Cited by 23 publications

(42 citation statements)

References 55 publications

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“…This was confirmed experimentally by selective 2′-hydroxyl acylation by primer extension chemistry in miR-16-1, miR-30a and miR-107 (37). Furthermore, variants of these three miRNAs that stabilize this region were shown to mature less efficiently than their corresponding endogenous miRNAs in vitro (37). This flexible hot spot in the vicinity of the Drosha cleavage site is required for processing and its exact location can vary in different miRNAs.…”

Section: Resultsmentioning

confidence: 64%

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Structural dynamics control the MicroRNA maturation pathway

et al. 2016

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MicroRNAs (miRNAs) are crucial gene expression regulators and first-order suspects in the development and progression of many diseases. Comparative analysis of cancer cell expression data highlights many deregulated miRNAs. Low expression of miR-125a was related to poor breast cancer prognosis. Interestingly, a single nucleotide polymorphism (SNP) in miR-125a was located within a minor allele expressed by breast cancer patients. The SNP is not predicted to affect the ground state structure of the primary transcript or precursor, but neither the precursor nor mature product is detected by RT-qPCR. How this SNP modulates the maturation of miR-125a is poorly understood. Here, building upon a model of RNA dynamics derived from nuclear magnetic resonance studies, we developed a quantitative model enabling the visualization and comparison of networks of transient structures. We observed a high correlation between the distances between networks of variants with that of their respective wild types and their relative degrees of maturation to the latter, suggesting an important role of transient structures in miRNA homeostasis. We classified the human miRNAs according to pairwise distances between their networks of transient structures.

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Section: Resultsmentioning

confidence: 64%

“…Recently, the structural requirements for DROSHA processing of a few pri-miRNAs were shown to be subject to the flexibility of a specific region (37). We asked whether we could link miRNA processing to transition networks and use the metrics described above to predict variations in overall maturation efficiencies.…”

Section: Resultsmentioning

confidence: 99%

Structural dynamics control the MicroRNA maturation pathway

et al. 2016

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“…3B). As bulged-structures that bend pri-miRNA stems have been shown to enhance processing efficiency (Quarles et al 2013), the position of the internal loop within the SV40 primiRNA and resulting bend in the pri-miRNA stem could facilitate an optimal Drosha-DGCR8/pri-miRNA interaction, dictating the Drosha-DGCR8-binding position and cleavage site. Although many mammalian pri-miRNAs contain internal loops/bulges within the pri-miRNA stems, whether these structures similarly influence Drosha cleavage site selection and processing efficiency remains to be tested.…”

Section: Discussionmentioning

confidence: 99%

A central role for the primary microRNA stem in guiding the position and efficiency of Drosha processing of a viral pri-miRNA

Burke

Kelenis

Kincaid

et al. 2014

RNA

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Processing of primary microRNA (pri-miRNA) stem-loops by the Drosha-DGCR8 complex is the initial step in miRNA maturation and crucial for miRNA function. Nonetheless, the underlying mechanism that determines the Drosha cleavage site of pri-miRNAs has remained unclear. Two prevalent but seemingly conflicting models propose that Drosha-DGCR8 anchors to and directs cleavage a fixed distance from either the basal single-stranded (ssRNA) or the terminal loop. However, recent studies suggest that the basal ssRNA and/or the terminal loop may influence the Drosha cleavage site dependent upon the sequence/structure of individual pri-miRNAs. Here, using a panel of closely related pri-miRNA variants, we further examine the role of pri-miRNA structures on Drosha cleavage site selection in cells. Our data reveal that both the basal ssRNA and terminal loop influence the Drosha cleavage site within three pri-miRNAs, the Simian Virus 40 (SV40) pri-miRNA, pri-miR-30a, and pri-miR-16. In addition to the flanking ssRNA regions, we show that an internal loop within the SV40 pri-miRNA stem strongly influences Drosha cleavage position and efficiency. We further demonstrate that the positions of the internal loop, basal ssRNA, and the terminal loop of the SV40 pri-miRNA cooperatively coordinate Drosha cleavage position and efficiency. Based on these observations, we propose that the pri-miRNA stem, defined by internal and flanking structural elements, guides the binding position of Drosha-DGCR8, which consequently determines the cleavage site. This study provides mechanistic insight into primiRNA processing in cells that has numerous biological implications and will assist in refining Drosha-dependent shRNA design.

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“…It was recently shown that microRNAs (miRNAs) may play a major role in regulating myocardial ischemia reperfusion (Shapiro et al, 2011;Chang et al, 2012;Tu et al, 2013). miRNAs are small, endogenous, single-stranded, non-coding RNAs usually 22 nucleotides in length and function as regulators of protein expression by binding to mRNA and preventing translation (Liu et al, 2012;Quarles et al, 2013). The number of studies reporting on important roles for miRNAs in disease occurrence and development is steadily increasing and a number of studies have suggested a role for miRNAs in cardiovascular disease (Corsten et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Effect and mechanism of miR-126 in myocardial ischemia reperfusion

Huang

2015

Genet. Mol. Res.

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ABSTRACT.Multiple studies have shown microRNAs to play an important role in disease occurrence and development. The role of miRNAs in ischemia-reperfusion injury, however, requires further investigation and the aim of this study was therefore to assess miR-126 expression in myocardial ischemia reperfusion and the effects of miR-126 on myocardial ischemia-reperfusion injury. An in vitro model of ischemia-reperfusion injury was established using rat myocardial H9c2 cells and miR-126 expression in these cells was assessed by real-time PCR. The miR-126 mimic and inhibitor were transfected into H9c2 cells before the injury was induced. Flow cytometry and western blotting were used to assess myocardial cell apoptosis. The triphenyltetrazolium chloride method was used to assess the infarction area and a TUNEL assay was used to analyze myocardial cell apoptosis. The results of the western blot analyses indicate that the miR-126 mimic and inhibitor increase and decrease caspase 3 degradation in myocardial cells, respectively. The in vivo experiments, moreover, revealed that the miR-126 mimic and inhibitor increase and reduce the myocardial infarction area, respectively. The TUNEL assay results showed increases and decreases in apoptotic myocardial cell numbers after infusion with the miR-126 mimic or inhibitor, respectively. These findings indicate that miRmiR-126 in myocardial ischemia reperfusion 18991©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (4): 18990-18998 (2015) 126 is down-regulated in myocardial ischemia-reperfusion injury and that the inhibition of miR-126 may protect against myocardial cell apoptosis caused by ischemia-reperfusion.

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Ensemble Analysis of Primary MicroRNA Structure Reveals an Extensive Capacity To Deform near the Drosha Cleavage Site

Cited by 23 publications

References 55 publications

Structural dynamics control the MicroRNA maturation pathway

Structural dynamics control the MicroRNA maturation pathway

A central role for the primary microRNA stem in guiding the position and efficiency of Drosha processing of a viral pri-miRNA

Effect and mechanism of miR-126 in myocardial ischemia reperfusion

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