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This Week in Genome Research: Oct 10, 2018

German researchers report on novel gene families detected in nematodes from the Pristionchus genus. Using a phylogenomic strategy, the researchers discerned between orthologous and novel gene families with genome sequences for the P. pacificus nematode, half a dozen other Pristionchus species, and two outgroup representatives, retracing evolutionary dynamics and potential gene formation mechanisms. "In the future," they say, "we would like to exploit our phylogenomic framework to further investigate the mechanisms that drive the formation of novel genes and to quantify what fraction of orphan genes can be explained by them." 

Some members of the same team explore gene structure, epigenetics, and transcriptional regulators that mark novel, young genes. The researchers used RNA sequencing, chromatin immunoprecipitation sequencing, ATAC-seq, and long read Iso-seq to dig into the young gene families found phylogenetically in the P. pacificus nematode. Their results suggest young genes are shorter and more exon-poor, for example, and typically show more muted expression and chromatin states that differ from conserved genes. The authors say these and other findings line up with a "model whereby a new gene that originates near an enhancer and is adaptive, will eventually acquire more sophisticated regulatory architecture — thereby transitioning the enhancer into a promoter." 

A University of Montpellier-led team describes a sequencing method for characterizing nuclear bodies and other large ribonucleoprotein (RNP) complexes, which appear to coincide with active chromosomal compartments in its mouse embryonic stem cell experiments. The researchers found that they could successfully isolate and assess salt-insoluble RNPs with a "high salt recovered" sequencing strategy, HRS-seq. And in the mouse embryonic stem cell system, they found that these RNP complexes "essentially correspond to the most highly expressed genes, and to cis-regulatory sequences like super-enhancers that belong to the active A chromosomal compartment."