Tübingen, 29 October 2018. Up to one third of genes in an animal genome have never been seen in any other organism, raising the fundamental questions of how new genes are born, and how they are integrated into the biological networks of their hosts.
Two new papers from the Department for Integrative Evolutionary Biology to be published in the November issue of Genome Research used the model nematode system Pristionchus pacificus to address these questions. First, PhD student Neel Prabh and colleagues sequenced the genomes of eight different species with increasing divergence from the focal organism. Based on the distribution of genes within these genomes, they could estimate the relative age of a given gene and contrast the evolutionary dynamics of young and old genes. This showed that nematode chromosomes have rather stable chromosome centers that are comprised of old genes, whereas novel genes arise at the chromosome arms, evolve rapidly and have a high chance of being lost again. This is consistent with a model where new genes are born at a constant rate, but are soon lost and replaced by other genes because they fail to be integrated into cellular networks, or because of a change in environmental conditions that favor their existence. In the future, Prabh and colleagues plan to use their data set to study in detail the molecular mechanisms by which new genes are born.
In the second paper, lead author Dr. Michael Werner performed a series of molecular fishing experiments to capture regulatory regions of ‘new’ vs. ‘old’ genes. Consistent with previous results in field, they found a unique signature of new genes being shorter and having less expression. But for the first time, they traced this result to new genes being present in highly compacted DNA-protein complexes called ‘heterochromatin’ at the edge of chromosome arms. Surprisingly however, they found a small percentage of young genes that were highly expressed – indicative of potential function. But instead of the classic regulatory architecture present at old genes (called ‘promoters’), these new genes seemed to be expressed by a different type of regulatory element called ‘enhancers’. This startling finding led them to hypothesize a model whereby new genes get expressed by enhancers, but if they provide a useful function for the organism, evolution will eventually convert the enhancer to a classical promoter.
Originally thought to be very different, enhancers and promoters have recently been shown to have several molecular features in common. If the model proposed by Werner and colleagues turns out to be true, it would complete the circle of evidence that these two types of regulatory elements are connected. Collectively, these two papers from the Sommer Lab have shed light on the question of how new genes “find their way” into the complex network of genetic pathways.
- Young genes have distinct gene structure, epigenetic profiles, and transcriptional regulation: 10.1101/gr.234872.118
- Deep taxon sampling reveals the evolutionary dynamics of novel gene families in Pristionchus nematodes: 10.1101/gr.234971.118