Direct Nanopore Sequencing of Individual Full Length tRNA Strands

We describe a method for direct tRNA sequencing using the Oxford Nanopore MinION. The principal technical advance is custom adapters that facilitate end-to-end sequencing of individual transfer RNA (tRNA) molecules at subnanometer precision. A second advance is a nanopore sequencing pipeline optimized for tRNA. We tested this method using purified E. coli tRNA^fMet, tRNA^Lys, and tRNA^Phe samples. 76-92% of individual aligned tRNA sequence reads were full length. As a proof of concept, we showed that nanopore sequencing detected all 43 expected isoacceptors in total E. coli MRE600 tRNA as well as isodecoders that further define that tRNA population. Alignment-based comparisons between the three purified tRNAs and their synthetic controls revealed systematic nucleotide miscalls that were diagnostic of known modifications. Systematic miscalls were also observed proximal to known modifications in total E. coli tRNA alignments, including a highly conserved pseudouridine in the T loop. This work highlights the potential of nanopore direct tRNA sequencing as well as improvements needed to implement tRNA sequencing for human healthcare applications.

Direct Nanopore Sequencing of Individual Full Length tRNA Strands

We describe a method for direct tRNA sequencing using the Oxford Nanopore MinION. The principal technical advance is custom adapters that facilitate end-to-end sequencing of individual transfer RNA (tRNA) molecules at subnanometer precision. A second advance is a nanopore sequencing pipeline optimized for tRNA. We tested this method using purified E. coli tRNA^fMet, tRNA^Lys, and tRNA^Phe samples. 76-92% of individual aligned tRNA sequence reads were full length. As a proof of concept, we showed that nanopore sequencing detected all 43 expected isoacceptors in total E. coli MRE600 tRNA as well as isodecoders that further define that tRNA population. Alignment-based comparisons between the three purified tRNAs and their synthetic controls revealed systematic nucleotide miscalls that were diagnostic of known modifications. Systematic miscalls were also observed proximal to known modifications in total E. coli tRNA alignments, including a highly conserved pseudouridine in the T loop. This work highlights the potential of nanopore direct tRNA sequencing as well as improvements needed to implement tRNA sequencing for human healthcare applications.

IMP-L3, A 20-hydroxyecdysone-responsive gene encodes Drosophila lactate dehydrogenase: structural characterization and developmental studies

IMP-L3, a gene isolated as a potential mediator of imaginal disc morphogenesis in Drosophila melanogaster, encodes lactate dehydrogenase (LDH). The predicted amino acid sequence of IMP-L3 is 58-61% identical to those of human LDHs. In cultured imaginal discs, IMP-L3 transcript levels and LDH enzyme activity increase in response to the steroid hormone, 20-hydroxyecdysone. In embryos, IMP-L3 transcript and LDH activity appear in developing somatic muscles by late stage 13, well before the onset of muscular contraction. High levels of transcript and LDH activity persist throughout embryogenesis and throughout larval development. The gene has been localized by in situ hybridization and deficiency mapping to 65A7-65B2 on the third chromosome. LDH activity is reduced to approximately 50% of wild type in animals heterozygous for a deficiency that removes the 65A-B region. Embryos deficient for the 65A-b region lack LDH activity. We conclude that IMP-L3 is the only gene that encodes LDH in Drosophila.