Molecular Switch Inactivates X Chromosome, May Provide Insight Into Rett

To better understand X-linked disorders such as Rett syndrome, researchers discovered an enzyme called DCP1A that acts as a molecular switch to inactivate only one X chromosome, a process essential for normal  development in females.

The results were reported in the study, “Decapping enzyme 1A breaks X-chromosome symmetry by controlling Tsix elongation and RNA turnover,” published in the journal Nature Cell Biology. 

Females inherit two X chromosomes, one from each parent, but only one is active during development. Allowing both X chromosomes to be active, or inactive, would be toxic to the cell. 

The process of selecting one X chromosome to be active while the other remains silent — called X chromosome inactivation (XCI) — is essential for healthy development and underlies Rett syndrome and other X-linked developmental diseases.

Studies have identified an RNA molecule that initiates XCI; it is called Xist. A second such RNA molecule known as Tsix binds to Xist, which prevents XCI. While both chromosomes bind Tsix and are active in the early stages of development, over time Tsix is silenced in only one X chromosome, which induces Xist-dependent inactivation.

However, understanding how Xist is silenced in one chromosome but not the other is complicated by the very low levels of these unique RNAs, or other interacting proteins, which are difficult to measure accurately. 

To overcome this problem, researchers at Massachusetts General Hospital (MGH), associated with Harvard Medical School, developed methods to amplify these RNA molecules. In doing so, they uncovered the mechanism underlying the inactivation of just one X chromosome. 

The team previously discovered that for XCI to occur, both X chromosomes must interact directly with each other, in a process called X–X pairing. 

“But until now, no one knew what one X chromosome was saying to the other to make the decision,” Jeannie Lee, MD, PhD, the study’s senior author, said in a press release. 

When they applied a method called BioRBP in mouse embryonic stem cells, investigators found that an enzyme known as DCP1A interacts with Tsix. DCP1A is an RNA “decapping” enzyme as it cuts a segment (or cap) of RNA, allowing it to be degraded. 

Depleting DCP1A in cells led to a marked increase in X–X pairing and also prevented the switch that shuts off Tsix production in the chromosome. In turn, forcing Tsix degradation resolved the accumulation of X–X pairing and led to an increase in Xist in just one X chromosome.

“DCP1A allows the two X chromosomes to have a fateful ‘conversation’,” said Lee. “DCP1A flips the switch that starts the entire cascade of X chromosome inactivation.”

Further experiments found that Tsix recruits a protein called CTCF, which acts as a “glue” holding X chromosomes together during X–X pairing. When DCP1A cleaves Tsix in one X chromosome, CTCF binds the unstable Tsix to shut the chromosome down permanently. 

The team found that physically connecting (tethering) DCP1A to Tsix, which forced the interaction, caused the inactivation of one X chromosome, while the other remained active. 

“Combined with the cooperative binding of CTCF, DCP1A could drive ‘winner-takes-all’ scenario and thereby flip a … switch for XCI,” the investigators wrote.

“This discovery will help scientists understand how other molecular conversations take place in the cell,” Lee said.