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Pipeline for circRNA annotation. A flowchart of the computational pipeline used for circRNA identification. (PDF 138 kb)

Two videos developed by Pedro Miura about bioinformatics at UNR

C. elegans aging paradigm. Protocol for collecting total RNA during C. elegans aging. Wild-type animals were fed E. coli OP50 and grown at 15°C. Gravid adults were bleached and populations were synchronized as L1 larvae and grown for an additional 4 days. At the L4 larval stage (Day 0), animals were either collected or transferred to FUdR containing NGM agar plates seeded with E. coli OP50, and were allowed to continue growth at 15°C. Total RNA was collected at different age time-points (L4, D-1, D-7, and D-10). (PDF 107 kb)

Using photoshop and illustrator from tif file to make a figure

Complete Supplemental Figures. Figure S1. Affinity-purified nuclear RNA is enriched for photoreceptor-expressed genes. Figure S2. Rh1-Gal4 drives GFP expression in antennal sensory neurons. Figure S3. Relative sensory neuron proportions and yields of affinity-purified nuclear RNA do not change with age. Figure S4. qPCR of selected age-regulated genes. Figure S5. K-means clustering of age-regulated genes based on temporal expression pattern. Figure S6. Top promoter motifs that predict age-related expression changes. Figure S7. Promoter motifs with the best predictive power co-occur frequently with a variety of other motifs. Figure S8. Distribution of the top motifs in age upregulated genes. Figure S9. Distribution of the top motifs in age upregulated genes. Figure S10. Distribution of the top motifs between expression clusters. Figure S11. Downregulated gene clusters are enriched for longer, more highly expressed and more heavily spliced genes. Figure S12. qPCR of selected age-regulated circRNAs. Figure S13. circRNA-containing host genes are enriched for longer and more heavily spliced genes. (PDF 4807 kb)

Duchenne Muscular Dystrophy (DMD) is a fatal, neuromuscular disorder caused by mutations/deletions in the dystrophin gene. In skeletal muscle, dystrophin is expressed along the sarcolemma, providing a mechanical link between the cytoskeleton and the extracellular matrix; loss of dystrophin results in disrupted sarcolemmal integrity and progressive muscle wasting. Utrophin is the autosomal homologue of dystrophin and is present in skeletal muscles of DMD patients, although its expression is primarily restricted to the neuromuscular junction of mature skeletal muscle fibers. Enhancing expression of utrophin in skeletal muscles of DMD animal models prevents the dystrophic pathology; thus, it is of considerable interest to identify the mechanisms controlling utrophin expression in skeletal muscle, with the ultimate goal of identifying drugs that can stimulate utrophin levels in DMD patients. Utrophin A expression is regulated by transcriptional mechanisms that are associated with the slow myogenic program. Here we uncovered that expression of utrophin A can be transcriptionally enhanced via its promoter by GW501516-mediated activation of the nuclear receptor PPARbeta/delta, a known regulator of the slow myogenic program. Treatment of dystrophin-deficient mdx mice with GW501516 stimulated utrophin A expression at the sarcolemma and mitigated the dystrophic phenotype, as evidenced by increased sarcolemmal stability and decreased susceptibility of skeletal muscles to lengthening contractions. Under multiple physiologically relevant conditions, enhancement of utrophin A protein levels in skeletal muscle are not accompanied by similar increases in mRNA levels, suggesting a role for post-transcriptional control. We identified that utrophin A expression is enhanced via Internal Ribosome Entry Site (IRES)-mediated translation in response to skeletal-muscle regeneration and glucocorticoid treatment. Using transgenic reporter mice, we found that IRES-mediated translation of utrophin A occurs exclusively in skeletal muscle fibers and no other tissues. Finally, we identified that a trans-acting factor, eEF1A2, interacts with the utrophin A 5'-UTR and is involved in regulating IRES-mediated translation of utrophin A. This work has identified novel transcriptional and translational mechanisms controlling expression of utrophin A in skeletal muscle. Our results suggest that GW501516 treatment might constitute a viable pharmacological therapy for DMD patients and IRES-mediated translational of utrophin A could serve as a new therapeutic target.