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Genome Research Papers on Brain Cortex Transcriptome Compartments, Drosophila Metabolomes, More

Researchers at the Lieber Institute for Brain Development, Johns Hopkins School of Medicine, and the Bloomberg School of Public Health share results from a transcriptomic study of human brain development that distinguished between transcripts in the nucleus and cytoplasm in post-mortem prenatal and adult cortex brain samples. The team's RNA sequencing analyses, which relied on Ribo-Zero and poly(A)+ library prep protocols, highlighted genes with expression, splicing, and other features that varied by cellular compartment and over time during brain development. It also pointed to an apparent enrichment for psychiatric disease-related gene transcripts in the nuclear compartment. "These results suggest that although gene-level expression is globally comparable between fractions, nuclear retention of transcripts may play an under-appreciated role in developmental regulation of gene expression in brain," they say, "particularly in genes whose dysregulation is related to neuropsychiatric disorders."

A team from the US and China presents a systems-based metabolomic analysis of fruit flies from the Drosophila melanogaster Genetic Reference Panel (DGRP). After identifying more than 450 metabolites in flies from 40 DGRP lines using liquid chromatography-tandem mass spec, the researchers quantified metabolite variation, bringing in gene expression and genetic variant data to put together sex-specific metabolite modules. From there, they came up with networks for focusing in on the genetic factors and metabolic features behind fruit fly traits and behavior and, conversely, attempted to predict Drosophila traits from metabolites and genetic variants. "[O]ur observations constitute a 'proof-of-concept' that metabolites can be good predictors of phenotypes," the authors say, "and that even with a small training set phenotypic prediction based on variation of the metabolome can yield greater accuracy than predictions based on genetic variants alone."

Investigators at the University of Cologne, Cleveland Clinic, and elsewhere take a look at pathogenic variant-prone human sequences. Using thousands of sequence alignments, the team analyzed the burden of missense variants falling in almost 10,000 protein-coding genes, uncovering pathogenic variant enriched (PER) regions of the genome, genes, and gene families. These regions were enriched for variants in 6,753 individuals with neurodevelopment compared to more than 1,900 of their unaffected siblings, the authors note, while missense variants in the PERs tended to be pathogenic rather than benign in the ClinVar database.