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This Week in Genome Research: Nov 9, 2016

Using whole-genome sequence data for 133 unrelated rhesus macaque representatives, researchers from the Baylor College of Medicine and elsewhere examined population patterns and biological features found in the rhesus macaque. Based on sequences for 123 rhesus macaques originating in India, nine rhesus macaques from China, and re-sequencing data for the first sequenced rhesus macaque, the team looked at sequence diversity, variants resembling those linked to human disease, recombination patterns, and more. "Our results provide new insight into primate biology and open new avenues for research," the authors write, "both using rhesus macaques as models for the genetics of human disease and in studies of evolutionary and population genomics."

In an effort to untangle gene-by-environment interactions, investigators from Wayne State University and the University of Michigan tracked transcriptional patterns in five human cell lines exposed to 50 treatment types. Using RNA sequencing, the team profiled transcripts in three samples apiece in a lymphoblastoid cell line, peripheral blood mononuclear cells, human umbilical vein endothelial cells, human smooth muscle cells, and melanocytes — a search that uncovered almost 1,500 genes showing allele-specific expression, along with 215 genes suspected of showing gene-by-environment effects.

A Chinese Academy of Sciences-led team takes a look at the processes that drive movement of long terminal repeat retrotransposons in fruit flies, mosquitos, zebrafish, chickens, and mammals. Starting with sequences from 40 lines in the Drosophila melanogaster Genetic Reference Panel, the researchers focused in on candidate polymorphic retrocopies and scrutinized the sequences neighboring them before identifying similar sequences in other organisms. From their own results and past studies, the study's authors conclude that "LTR-mediated retroposition is highly conserved across a wide range of animal taxa and … represents an ancient and ongoing mechanism continuously shaping gene content evolution in eukaryotes." 

The Scan

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.

Family Genetic Risk Score Linked to Diagnostic Trajectory in Psychiatric Disorders

Researchers in JAMA Psychiatry find ties between high or low family genetic risk scores and diagnostic stability or change in four major psychiatric disorders over time.

Study Questions Existence of Fetal Microbiome

A study appearing in Nature this week suggests that the reported fetal microbiome might be the result of sample contamination.

Fruit Fly Study Explores Gut Microbiome Effects on Circadian Rhythm

With gut microbiome and gene expression experiments, researchers in PNAS see signs that the microbiome contributes to circadian rhythm synchronicity and stability in fruit flies.