Genetic regulation of gene expression is highly dynamic during cellular differentiation, with hundreds of expression quantitative trait loci (eQTLs) changing over time, according to a new study in Science this week. Scientists from Johns Hopkins and the University of Chicago generated time-series RNA sequencing data in 19 human cells lines, capturing 16 timepoints during the differentiation of induced pluripotent stem cells to cardiomyocytes. They find hundreds of dynamic eQTLs that change over time, with enrichment in enhancers of relevant cell types, as well as nonlinear dynamic eQTLs that affect only intermediate stages of differentiation and cannot be found by using data from mature tissues. "These fleeting genetic associations with gene regulation," the team writes, "may explain some of the components of complex traits and disease." GenomeWeb has more on this, here.
A new analysis of ancient DNA appearing in Science Advances this week shows that European Neanderthals were more closely related to relatives who lived tens of thousands of years later in the same region than a Neanderthal from Russia who lived around the same time. A team of European investigators examined nuclear genomic sequences from Western European Neandertals who lived about 120,000 years ago — one from the Scladina Cave in Belgium and the other from the Hohlenstein-Stadel Cave in Germany — and find that they were both related to all future Neanderthal groups, but not a contemporaneous group known as Altai Neanderthals that lived in Siberia. The finding suggests that the population to which the Scladina and Hohlenstein-Stadel individuals belonged migrated east from Europe, eventually replacing Altai Neanderthals. GenomeWeb also covers this study, here.
Also in Science Advances, US and Japanese collaborators present a high-quality draft sequence and gene annotations of the common goldfish — a close relative of the common carp that shares a genome duplication that occurred about 14 million years ago in a common ancestor — providing a new resource for comparative genomics and understanding the causes of goldfish variants. Using long-read sequencing, the scientists identify 70,324 coding genes and more than 11,000 non-coding transcripts in the goldfish genome. Notably, they find that the two subgenomes in goldfish retained extensive synteny and collinearity between goldfish and the widely used model organism zebrafish. However, "genes were lost quickly after the carp whole-genome duplication, and the expression of 30 percent of the retained duplicated gene diverged substantially" across sampled tissues, they write. "Loss of sequence identity and/or exons determined the divergence of the expression levels across all tissues, while loss of conserved noncoding elements determined expression variance between different tissues."