In PLOS Genetics, a team from Canada and the US reports on results from a study that involving tracking DNA methylation levels at hundreds of thousands of sites in the genome in post-mortem brain samples from 738 individuals. By incorporating information on the individuals' times of death, the researchers were able to look at the rhythmicity in DNA methylation patterns at different points in a 24 hour cycle and in relation to changes in RNA expression, as gauged by RNA sequencing. Results of the analyses support the notion that methylation levels vary with time, particularly in parts of the genome falling near the transcription start sites of genes with rhythmic expression.
A PLOS Neglected Tropical Diseases study describes findings from a genome sequencing study of Treponema pallidum subspecies endemicum, a bacteria known for causing a non-venereally transmitted form of syphilis spread via direct contact or contaminated utensils. Researchers from the Czech Republic, the US, and the Netherlands used a combination of sequencing technologies to tackle the genome of a T. pallidum subsp. endemicum strain first isolated in Bosnia in the 1950s, producing a genome that was slightly smaller than previously describes sequences for T. pallidum subspecies that cause syphilis and yaws. Through comparisons with other T. pallidum subspecies, the team saw signs of both gene synteny and horizontal gene transfer events involving the treponemes, though T. pallidum subsp. endemicum clustered more closely with the yaws-causing agent than with the sexually transmitted pallidum subspecies.
Korean researchers performed RNA sequencing on leaf, root, stem, and tuber tissues collected at different stages of development in the Jerusalem artichoke (Helianthus tuberosus) — a plant known for producing a compound called inulin that's been touted as a potential diabetes and obesity treatment. After putting together a de novo assembly of the Jerusalem artichoke transcriptome, the team used data from gene, protein, and pathway databases to characterize these transcripts and their tissue-specific expression profiles, in some cases. "The sequence resources developed in this study will enable the analysis of thousands of transcripts," authors of the PLOS One study say, "and will thus accelerate marker-assisted breeding studies and studies of inulin biosynthesis in Jerusalem artichoke."