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Genome Research Papers on Microbes' Effects on Host Transfer RNA, Honeybee Evolution, Single-Cell Histones

Researchers in China and the US report on findings from a mouse model study looking at the ways that microbes may influence transfer RNA patterns in specific host tissues. Using tRNA-seq and demethylase tRNA-seq methods, the team characterized tRNAs profiles and modifications in two dozen intestine, brain, liver, and kidney tissue samples from mice missing microbes altogether or from mice without specific pathogens. "Our analyses reveal that cytosolic and mitochondrial tRNA expression and tRNA modifications in the host are reprogrammed in a tissue-specific and microbiome-dependent manner," the authors write, noting that results so far suggest "intestines and brains are more sensitive to the influence of the microbiome than the livers and kidneys."

A team from the University of North Carolina-Greensboro, University of California, Davis, and elsewhere explores evolutionary relationships between three honeybee species with different levels of eusocial behavior. With new and available genome sequences from dwarf, giant, and cavity-nesting Western honeybees in the Apis florea, A. dorsata, and A. mellifera species, respectively, the researchers conducted comparative genomic, phylogenomic, selection, and other analyses, comparing the Apis species sequences to one another and to those from Bombus bees. "We find that evolution of increased eusocial complexity in Apis proceeds via increases in the complexity of gene regulation," the authors write, adding that Apis diversification "is accompanied by positive selection in several genes whose putative functions present candidate mechanisms for lineage-specific adaptations, such as migration, immunity, and nesting behavior."

Finally, investigators at the National Heart, Lung, and Blood Institute outline an "indexing single-cell immunocleavage sequencing" (iscChIC-seq) method for assessing histone marks in individual cells. The strategy brings single-cell ChIC-seq together with terminal transferase- and DNA ligase enzyme-based multiplexing and barcoding steps — an approach the team used to identify T cell, B cell, natural killer cell, monocytes and other clusters based on histone H3K4me3 and H3K27me3 marks in more than 10,000 individual white blood cells. Based on these and other results, the authors suggest that iscChIC-seq "is a reliable technique for profiling histone modifications in a large number of single cells, which may find broad applications in studying cellular heterogeneity and differentiation status in complex developmental and disease systems."

The Scan

Guidelines for Ancient DNA Work

More than two dozen researchers have developed new ethical guidelines for conducting ancient DNA research, which they present in Nature.

And Cleared

A UK regulator has cleared former UK Prime Minister David Cameron in concerns he should have registered as a consultant-lobbyist for his work with Illumina, according to the Financial Times.

Suit Over Allegations

The Boston Globe reports that David Sabatini, who was placed on leave from MIT after allegations of sexual harassment, is suing his accuser, the Whitehead Institute, and the institute's director.

Nature Papers on Esophageal Cancer, Origin of Modern Horses, Exome Sequencing of UK Biobank Participants

In Nature this week: genetic and environmental influences of esophageal cancer, domestic horse origin traced to Western Eurasian steppes, and more.