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Genome Research Papers on Sperm Mutations, Trypanosoma Brucei Chromatin, Single-Worm Transcriptomics

Researchers at the University of Edinburgh's MRC Human Genetics Unit considers ties between chromatin structure and mutation in human sperm cells. "Using ATAC-seq, we profile the open chromatin landscape of human spermatogonia, the most proliferative cell type of the germline, identifying transcription factor binding sites (TFBSs) and PRDM9-binding sites, a subset of which will initiate meiotic recombination," they write. Among other findings, the team saw a rise in rare structural variants in and around TFBs or sites bound by PRDM9, for example, along with TFBS-related insertion events. "Increased mutation loads at germline TFBSs disproportionately affect neural enhancers with activity in spermatogonia," the authors report, "potentially altering neurodevelopmental regulatory architecture."

Another University of Edinburgh-led team looks at histone regulation in the Trypanosoma brucei parasite. Starting with sequences from the trypanosome genome database, the researchers tracked down dozens of suspected histone lysine acetylation or methylation regulators — a set that included histone acetyltransferase or histone methyltransferase enzymes and proteins involved in reading, adding, or removing post-translational modifications that were subsequently analyzed with chromatin immunoprecipitation sequencing, proteomics, protein interaction networking, and other approaches. "The systematic approach employed provides detail of the composition and organization of the chromatin regulatory machinery in Trypanosoma brucei," they write, "and establishes a route to explore divergence from eukaryotic norms in an evolutionarily ancient but experimentally accessible eukaryote."

Finally, a Max Planck Institute for Developmental Biology team shares findings from a transcriptomic study focused on individual Pristionchus pacificus nematode worms tracked over time during development. By sequencing the model organism with single-worm transcriptomic approaches across more than three dozen developmental time points, the investigators identified expression fluctuations for some 10 percent of the genes considered. "Gene age analysis revealed an over-representation of ancient gene classes among oscillating genes," they note, including genes with clear orthologs in other worm model organisms species such as Caenorhabditis elegans.