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Nature Papers Present Enhancer-Gene Maps, Bacterial Methylomes Detected from Nanopore Sequencing, More

Newly created genome-wide maps of more than 6 million enhancer-gene connections and their use in interpreting the functions of disease-related genetic variants are reported in Nature this week. In the paper, a team led by Broad Institute scientists use their activity-by-contact model, which predicts which enhancers regulate which genes, to create enhancer-gene maps in 131 human cell types and tissues, then apply the maps to analyze fine-mapped genetic variants associated with 72 diseases and complex traits. Among their findings are new genes and pathways related to inflammatory bowel disease, hundreds of genes that appear to control different traits through effects in different cell types, and a role for the mitochondrial metabolism-related gene PPIF in tuning mitochondrial function in macrophages. The work, the study's authors write, "highlights a path to creating a comprehensive map of enhancer regulation in the human genome."

A review of the reference genomes available for seed-free plants, as well as areas where such resources are lacking, is presented in Nature Plants this week. Researchers from the University of Zurich and Cornell University highlight the insights and advances that have results from the recent publication of high-quality genomes from Charophyte algae, bryophytes, lycophytes, and ferns. They also note, however, that gaps remain in seed-free lineages. In their review, the authors also discuss various unique features that have emerged from genomic studies of seed-free plants and their importance in comparison to seed plant genomes. Lastly, they touch on future research directions that will further understanding of plant genome evolution.

An approach for using nanopore sequencing to discover different types of DNA methylation from bacteria and the microbiome is described by a Mount Sinai-led team in this week's Nature Methods. The investigators note that existing methods for detecting DNA modification from nanopore sequencing data cannot effectively characterize unknown bacterial methylomes without previous knowledge. They also find that nanopore sequencing signals display complex heterogeneity across methylation events of the same type, which suggests that detection methods are best developed using a diverse collection of species. To enable nanopore sequencing for broad methylation discovery, they generated a training dataset from an assortment of bacterial species and develop a technique that combines the identification and fine mapping of the three forms of methylation into a multi-label classification framework. They applied their approach to individual bacteria and the mouse gut genome, as well as demonstrate a method for nanopore sequencing-based methylation binning of metagenomic contigs, associating mobile genetic elements with their host genomes, and identifying misassembled metagenomic contigs.