Single-nucleotide-resolution sequencing of human N6-methyldeoxyadenosine reveals strand-asymmetric clusters associated with SSBP1 on the mitochondrial genome

N6-methyldeoxyadenosine (6mA) is a well-characterized DNA modification in prokaryotes but reports on its presence and function in mammals have been controversial. To address this issue, we established the capacity of 6mA-Crosslinking-Exonuclease-sequencing (6mACE-seq) to detect genome-wide 6mA at single-nucleotide-resolution, demonstrating this by accurately mapping 6mA in synthesized DNA and bacterial genomes. Using 6mACE-seq, we generated a human-genome-wide 6mA map that accurately reproduced known 6mA enrichment at active retrotransposons and revealed mitochondrial chromosome-wide 6mA clusters asymmetrically enriched on the heavy-strand. We identified a novel putative 6mA-binding protein in single-stranded DNA-binding protein 1 (SSBP1), a mitochondrial DNA (mtDNA) replication factor known to coat the heavy-strand, linking 6mA with the regulation of mtDNA replication. Finally, we characterized AlkB homologue 1 (ALKBH1) as a mitochondrial protein with 6mA demethylase activity and showed that its loss decreases mitochondrial oxidative phosphorylation. Our results show that 6mA clusters play a previously unappreciated role in regulating human mitochondrial function, despite 6mA being an uncommon DNA modification in the human genome.

Specificity of DnaK-peptide binding

The sequence specificity of DnaK substrate binding has been studied using a peptide display library. Based on the amino acid patterns that appeared in this selection, short peptides were synthesized for direct measurements of DnaK affinity. The results show that peptides enriched in internal hydrophobic residues are preferential DnaK substrates, and negatively charged peptides have poor affinity. The isolated C-terminal domain of DnaK binds peptides. Peptide dissociation studies indicate that bound peptides are released from the C-terminal fragment and from DnaK at identical rates. ATP stimulates peptide dissociation from DnaK but not from the C-terminal fragment.

Effect of preanesthetic medication on ease of endoscopic intubation of the duodenum in anesthetized dogs

The effects of preanesthetic medication on ease of duodenal endoscopic intubation in dogs was evaluated. One of 12 combinations of preanesthetic medications (using atropine, glycopyrrolate, morphine, meperidine, acepromazine, and 0.9% NaCl solution) was administered IM to each of 12 dogs in a trial. Twelve endoscopic trials were performed so that each dog received each treatment combination once. Anesthesia was induced with thiamylal administered IV and maintained with halothane vaporized in oxygen. Electrocardiographic recordings, indirect blood pressure measurements, end-tidal carbon dioxide partial pressures, and halothane concentrations were monitored during the anesthetic period. The ease with which the fiberoptic endoscope was passed into the proximal portion of the duodenum was qualitatively score on the basis of time and maneuvering effort. None of the preanesthetic combinations made intubation of the duodenum significantly easier than that with 0.9% NaCl solution (control). Only the combination of morphine and atropine induced gastro-pyloric conditions that resulted in significantly higher (more difficult) endoscopic scores than those after preanesthetic medication with 0.9% NaCl solution.