Accessibility of microRNA binding sites in metastable RNA secondary structures in the presence of SNPs

Expression Localization of the KRT32 Gene and Its Association of Genetic Variation with Wool Traits

Changes in keratin gene expression and spatiotemporal regulation determine the compositional content and cellular localization of wool keratin, thereby affecting wool traits. Therefore, keratin gene family member 32 (KRT32) was selected for a study using RT-qPCR, immunofluorescence, and penta-primer amplification refractory mutation system (PARMS) techniques. The results showed that KRT32 mRNA was highly expressed in the skin and localized to the inner root sheath (IRS), outer root sheath (ORS) and dermal papilla (DP). Sequencing results identified eight SNPs in KRT32, and association analyses revealed that the variations were significantly associated with multiple traits in wool (p < 0.05), including MFD, CF and MFC. The constructed haplotype combination H2H3 has higher CF and smaller MFD than other haplotype combination (p < 0.05). In conclusion, KRT32 can be used as a candidate gene for molecular genetic improvement of wool in Gansu Alpine Fine-wool sheep.

Conformational Dynamics of the RNA G-Quadruplex and its Effect on Translation Efficiency

During translation, intracellular mRNA folds co-transcriptionally and must refold following the passage of ribosome. The mRNAs can be entrapped in metastable structures during these folding events. In the present study, we evaluated the conformational dynamics of the kinetically favored, metastable, and hairpin-like structure, which disturbs the thermodynamically favored G-quadruplex structure, and its effect on co-transcriptional translation in prokaryotic cells. We found that nascent mRNA forms a metastable hairpin-like structure during co-transcriptional folding instead of the G-quadruplex structure. When the translation progressed co-transcriptionally before the metastable hairpin-like structure transition to the G-quadruplex, function of the G-quadruplex as a roadblock of the ribosome was sequestered. This suggested that kinetically formed RNA structures had a dominant effect on gene expression in prokaryotes. The results of this study indicate that it is critical to consider the conformational dynamics of RNA-folding to understand the contributions of the mRNA structures in controlling gene expression.

A new heuristic method for approximating the number of local minima in partial RNA energy landscapes

The analysis of energy landscapes plays an important role in mathematical modelling, simulation and optimisation. Among the main features of interest are the number and distribution of local minima within the energy landscape. Granier and Kallel proposed in 2002 a new sampling procedure for estimating the number of local minima. In the present paper, we focus on improved heuristic implementations of the general framework devised by Granier and Kallel with regard to run-time behaviour and accuracy of predictions. The new heuristic method is demonstrated for the case of partial energy landscapes induced by RNA secondary structures. While the computation of minimum free energy RNA secondary structures has been studied for a long time, the analysis of folding landscapes has gained momentum over the past years in the context of co-transcriptional folding and deeper insights into cell processes. The new approach has been applied to ten RNA instances of length between 99 nt and 504 nt and their respective partial energy landscapes defined by secondary structures within an energy offset ΔE above the minimum free energy conformation. The number of local minima within the partial energy landscapes ranges from 1440 to 3441. Our heuristic method produces for the best approximations on average a deviation below 3.0% from the true number of local minima.

Identification of a new target of miR-16, Vacuolar Protein Sorting 4a

Rationale

The rationale was to utilize a bioinformatics approach to identify miRNA binding sites in genes with single nucleotide mutations (SNPs) to discover pathways in heart failure (HF).

Objective

The objective was to focus on the genes containing miRNA binding sites with miRNAs that were significantly altered in end-stage HF and in response to a left ventricular assist device (LVAD).

Methods and Results

BEDTools v2.14.3 was used to discriminate SNPs within predicted 3′UTR miRNA binding sites. A member of the miR-15/107 family, miR-16, was decreased in the circulation of end-stage HF patients and increased in response to a LVAD (p<0.001). MiR-16 decreased Vacuolar Protein Sorting 4a (VPS4a) expression in HEK 293T cells (p<0.01). The SNP rs16958754 was identified in the miR-15/107 family binding site of VPS4a which abolished direct binding of miR-16 to the 3′UTR of VPS4a (p<0.05). VPS4a was increased in the circulation of end-stage HF patients (p<0.001), and led to a decrease in the number of HEK 293T cells in vitro (p<0.001).

Conclusions

We provide evidence that miR-16 decreases in the circulation of end-stage HF patients and increases with a LVAD. Modeling studies suggest that miR-16 binds to and decreases expression of VPS4a. Overexpression of VPS4a decreases cell number. Together, these experiments suggest that miR-16 and VPS4a expression are altered in end-stage HF and in response to unloading with a LVAD. This signaling pathway may lead to reduced circulating cell number in HF.