Inactivation of the X chromosome: same mechanism, different regulations depending on the species

The inactivation of the X chromosome is a process under natural selection t hat is already well documented. "In female mammals, which have two X chromosomes, one of the two is inactivated very early during the development of the embryo," explains Dr. Céline Morey, Inserm research fellow in the Sex Chromosomes, Development, and Diseases team (Labeled Research Team 'ERC' at Paris Cité University)  led by Dr. Claire Rougeulle, who is also director of the Institut Curie Research Center. "This makes it possible to balance the expression of genes with males, who have only one X chromosome. Without this mechanism, female embryos would not survive." 

This process is based on the expression of a non-coding RNA  called XIST, orchestrated at the level of an inactivation center which itself groups non-coding RNAs and regulatory sequences - enhancers. “For several years, we have been exploring the differences that exist in this fundamental process between mice, a model organism, and humans, with important implications for women's health. We then wanted to investigate whether the mechanisms involved could vary even between evolutionarily closely related species,” explains Dr. Claire Rougeulle.
 

Comparing closely related species to observe subtle variations

As part of the study, scientists chose to compare three extremely closely related species: humans, rhesus macaques, and marmosets. This genetic proximity, contrary to classical comparisons between distant species, makes it possible to observe fine modifications in the regulation of genes and thus to clearly understand their sequence during evolution.

"Each species represents a different stage in the evolution of primates, over a relatively short period of 55 million years," describes Céline Morey. In this study, the researchers used existing embryonic stem cell lines.

Regulatory mechanisms that diverge

Surprisingly, the study revealed that the regulatory circuits that control the non-coding XIST gene have diverged over the evolution of primates. In humans and marmosets, a regulatory non-coding RNA, JPX, plays a central role in controlling the expression levels of XIST.

In the macaque, the organization is different. The X chromosome inactivation center has integrated a sequence from a retrotransposon, a DNA fragment of viral origin capable of being inserted into the genome. This new exogenous element has modified the three-dimensional organization of the inactivation center. JPX is also present, but its role is diminished. It is an enhancer specific to the macaque—Enh5—which strengthens the expression of XIST.

"The result is the same for all three primates: the X chromosome is inactivated," notes Céline Morey. "But the pathway used is not the same, as if each species had used a regulatory mechanism specific to its evolutionary trajectory."

Under the influence of a neutral evolution

Another striking fact: contrary to what might be expected for sequences that participate in an essential biological function, they evolve neutrally, according to  natural genetic drift. "We find no detectable signs of selection, which challenges the classical view that functionality = conservation of the DNA sequence," continues the researcher. These results suggest that these non-coding sequences could constitute a mobilizable genetic reservoir, if living conditions change. They could then be recruited and retained in subsequent generations.

These discoveries provide key information. They reveal that genomes and biological mechanisms evolve dynamically, even over a short time scale. "The ability of genomes to recruit exogenous DNA sequences illustrates the formidable plasticity of regulations," summarizes Céline Morey. "More generally, our study invites us to use alternative approaches to the conservation of DNA sequences to identify the regulatory elements of the genome."