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This Week in Genome Research: Sep 12, 2018

A Queen Mary University of London-led team considers chromatin structure and its contributions to female caste phenotypes in the honey bee, Apis mellifera. The researchers used chromatin immunoprecipitation sequencing to map the distribution of H3K4me3, H3K27ac, and H3K36me3 histone marks across the genome in honey bee larvae heads at a stage where female bees are differentiating into sterile worker bees or queen bees. Together with RNA sequence data, the chromatin profiles uncovered intron regions with caste-specific H3K27ac marks that appeared to coincide with transcription features that distinguish female workers and queen bees. "We conclude that chromatin modifications play a crucial role in defining worker and queen honey bee castes by establishing and orchestrating caste-specific transcriptional networks," the authors write, adding that "the worker developmental pathway … is actively switched on from a default queen developmental program."

Researchers from the Chinese Academy of Sciences and elsewhere report on pluripotency patterns detected in pre-implantation rhesus monkey embryos profiled by single-cell RNA sequencing. The team sequenced dozens of individual cells isolated from the 16-cell to hatched blastocyst stage rhesus embryos, using the transcriptional clues to trace lineage segregation in the developing monkeys. "At the early- and middle-blastocyst stages, the epiblast cells have the transcriptome features of naïve pluripotency, whereas they display a continuum of primed pluripotency characteristics at the late- and hatched-blastocyst stages," they report, noting that the study "proposes an ideal time window for derivation of primate embryonic stem cells with naïve pluripotency."

Finally a team from the University of California, Berkeley, and Monmouth University maps quantitative trait loci and allele-specific expression in wild house mice adapted to five distinct latitudes along eastern North America. In an effort to identify cis-regulatory regions involved in environmental adaptations in the mice, the researchers did exome sequencing and liver RNA sequencing on 50 mice from five populations, uncovering 17 genes with expression levels and cis-eQTL activity that varied with latitudes. Two of the genes showed apparent ties to body mass, which tended to be greater in house mice from more northerly sites. From there, the authors used gene co-expression networking to dig further into the underpinnings of adaptive body size variability.