Syndicate content

Allele-Specific RNA-Seq Used to Study Dynamics of Gene Silencing During Normal X-Inactivation

Each cell in a woman’s body (except egg cells) contains two X chromosomes. One of these chromosomes is switched off, in order to maintain appropriate gene dosage compensation with males who are XY. Dr. Hendrik Marks and Dr. Henk Stunnenberg, molecular biologists at Radboud University Nijmegen, Netherlands, together with the group of Dr. Joost Gribnau from Erasmus MC in Rotterdam, Netherlands, have shown the mechanism by which this inactivation is spread over the X chromosome, The scientific journal Genome Biology will publish the final results; and a provisional PDF was posted online on August 3, 2015. The article is titled “‘Dynamics of Gene Silencing During X Inactivation Using Allele-Specific RNA-Seq.” In terms of sex chromosomes, men have a single X chromosome, as well as a Y chromosome, whereas women have two copies of the X chromosome. A process called X inactivation makes sure that one of these X chromosomes becomes inactivated in females during early embryonic development. A random process determines which of the two is switched off. A nice example of X inactivation can be observed in the fur of female tortoiseshell and calico cats. The gene for fur coloration resides on the X chromosome, while each of the two X chromosomes codes for a different color: black or orange. In an orange “patch,” only the X chromosome encoding the orange color is active, while in the black “patches,” only the X chromosome encoding the black colour is active. During normal human embryo development, X inactivation in females takes place at a very early stage. Others had previously discovered that the molecule “Xist” is key during X inactivation. In order to further study this process, Dr. Marks and his colleagues used embryonic stem cells as a model system to study X inactivation.

With the latest technology, the scientists were able to keep the two X chromosomes apart and measure one of them – with its 166 million base pairs – in detail. Every day, they checked which parts of the chromosome had been switched off.

“The whole process took about eight days,” Dr. Marks explains “and the inactivation spreads out from the center of the X chromosome towards the ends. That doesn’t happen gradually, but moves jumpwise from domain to domain.”

“Domains are long pieces of DNA that cluster together in knots. As X inactivation jumps from domain to domain, we now know that these domains are co-regulated. It is very likely that diseases that are linked to incorrect inactivation of the X chromosome are due to improper spreading across domains.”

After one of the X chromosomes has been inactivated, it will stay inactive forever.

In the future, Dr. Marks hopes to discover why sometimes the one, while in other cases the other, X chromosome is inactivated during development. That could help in treating X-linked diseases – like Rett syndrome and fragile X syndrome.

“Reactivating (part of) the ‘right’ X chromosome could be a potential treatment for these diseases. So the next step is to figure out how to do that.”

[Press release] [Genome Biology abstract]