Integration of Expressed Sequence Tag Data Flanking Predicted RNA Secondary Structures Facilitates Novel Non-Coding RNA Discovery

Many computational methods have been used to predict novel non-coding RNAs (ncRNAs), but none, to our knowledge, have explicitly investigated the impact of integrating existing cDNA-based Expressed Sequence Tag (EST) data that flank structural RNA predictions. To determine whether flanking EST data can assist in microRNA (miRNA) prediction, we identified genomic sites encoding putative miRNAs by combining functional RNA predictions with flanking ESTs data in a model consistent with miRNAs undergoing cleavage during maturation. In both human and mouse genomes, we observed that the inclusion of flanking ESTs adjacent to and not overlapping predicted miRNAs significantly improved the performance of various methods of miRNA prediction, including direct high-throughput sequencing of small RNA libraries. We analyzed the expression of hundreds of miRNAs predicted to be expressed during myogenic differentiation using a customized microarray and identified several known and predicted myogenic miRNA hairpins. Our results indicate that integrating ESTs flanking structural RNA predictions improves the quality of cleaved miRNA predictions and suggest that this strategy can be used to predict other non-coding RNAs undergoing cleavage during maturation

Discrimination between messenger ribonucleic acids by a mammalian translation initiation factor.

A factor from rabbit-reticulocyte ribosome, which stimulates by 5-fold initiation of hemoglobin mRNA translation in Krebs ascites cell extracts, was purified to homogeneity. The factor, a protein of about 65,000 molecular weight in sodium dodecyl sulfate, discriminates between various mRNAs: it stimulates translation of α globin mRNA and of tobacco mosaic virus RNA, but has only a small effect on β globin mRNA and no effect at all on Mengo virus RNA translation

The nucleotide sequence of a rat myosin light chain 2 gene.

A rat myosin light chain 2 gene was characterized by nucleotide sequence and S1 mapping analyses. It contains seven exons separated by six introns. The corresponding mRNA is predicted to be 654 nucleotides long (excluding polyA sequences), with 5'-nontranslated, coding, and 3'-nontranslated lengths of 56, 510, and 88 nucleotides, respectively. The predicted amino acid sequence is identical to that from rabbit except that the rat sequence lacks one of two Gly residues located at positions 12 and 13 in the rabbit sequence. From the nucleotide sequence, nascent rat myosin light chain 2 is predicted to have Met Ala preceding Pro at the N-terminal end

Acute pathophysiological effects of muscle-expressed Dp71 transgene on normal and dystrophic mouse muscle

Wieneke S, Heimann P, Leibovitz S, Nudel U, Jockusch H. Acute pathophysiological effects of muscle-expressed Dp71 transgene on normal and dystrophic mouse muscle. Journal of Applied Physiology. 2003;95(5):1861-1866.The products of the dystrophin gene range from the 427-kDa full-length dystrophin to the 70.8-kDa Dp71. Dp427 is expressed in skeletal muscle, where it links the actin cytoskeleton with the extracellular matrix via a complex of dystrophin-associated proteins (DAPs). Dystrophin deficiency disrupts the DAP complex and causes muscular dystrophy in humans and the mdx mouse. Dp71, the major nonmuscle product, consists of the COOH-terminal part of dystrophin, including the binding site for the DAP complex but lacks binding sites for microfilaments. Dp71 transgene (Dp71tg) expressed in mdx muscle restores the DAP complex but does not prevent muscle degeneration. In wild-type (WT) mouse muscle, Dp71tg causes a mild muscular dystrophy. In this study, we tested, using isolated extensor digitorum longus muscles, whether Dp71tg exerts acute influences on force generation and sarcolemmal stress resistance. In WT muscles, there was no effect on isometric twitch and tetanic force generation, but with a cytomegalovirus promotor-driven transgene, contraction with stretch led to sarcolemmal ruptures and irreversible loss of tension. In MDX muscle, Dp71tg reduced twitch and tetanic tension but did not aggravate sarcolemmal fragility. The adverse effects of Dp71 in muscle are probably due to its competition with dystrophin and utrophin ( in MDX muscle) for binding to the DAP complex