MeCP2 protein more dynamic than known, new study into Rett finds
Disease mutations seen to impair complex MeCP2 interactions with DNA
The behavior of MeCP2, the protein missing or defective in most people with Rett syndrome, is far more dynamic than was known, according to a study by U.S. researchers that provides new insights into the mechanisms underlying the rare condition.
MeCP2 was previously believed to exert its regulatory functions by exclusively binding to specific regions of the DNA. The new findings unveil a dynamic interplay with bare DNA, as well as complex DNA-protein subunits called nucleosomes, which are found in the nucleus of cells.
Rett-associated mutations disrupt the MeCP2 interactions with the genome — an individual’s complete set of DNA — at different levels, the researchers found. These findings may “potentially inform targeted intervention strategies to restore the normal activities of MeCP2,” according to the distinct mutation types, the team wrote.
The study, “Differential dynamics specify MeCP2 function at nucleosomes and methylated DNA,” was published in the journal Nature Structural & Molecular Biology.
Investigating the mechanisms related to the MeCP2 protein
Most Rett cases stem from mutations in the MECP2 gene, which lead to the lack of a functional version of MeCP2 protein. This protein is highly abundant in mature nerve cells and influences brain development and function.
The MeCP2 protein is believed to regulate the activity, or expression, of thousands of genes, but the molecular mechanisms regarding how it interacts with the genome are far from clear.
“People have been studying this protein for decades without a clear consensus on what it is doing, where it binds to the genome, and what its functions are,” Shixin Liu, PhD, an associate professor at Rockefeller University in New York and the study’s lead author, said in a university news story.
MeCP2 has been thought to suppress gene activity by exclusively targeting methylated-rich DNA regions. Methylation is a process by which specific chemical tags, called methyl groups, sit on top of a particular region of DNA.
However, increasing evidence supports a more complex mode of action as the MeCP2 protein also is able to bind DNA regions without methylation. How MeCP2 is able to distinguish between the two regions and whether it behaves differently is unknown.
To shed light on the MeCP2 complex interactions with the genome, the researchers leveraged the Liu lab’s expertise in single-molecule visualizations to track the interactions of MeCP2 with DNA in real time.
In such experiments, a single piece of DNA is restricted between two tiny plastic beads, each held by a laser trap. The researchers then added MeCP2 proteins that had a fluorescent tag attached and followed their interaction with a microscope.
The team found that the MeCP2 protein dynamically moves on DNA — but it moved much more slowly in the methylated regions compared with the unmethylated ones. This slow pace offers extra time for the MeCP2 protein to recruit additional proteins into the methylated DNA regions, which allows it to exert its silencing effects.
“We found that MeCP2 slides along unmethylated DNA faster, and this difference in motion may explain how the protein differentiates between the two,” said Gabriella Chua, a graduate fellow in Liu’s lab and the study’s first author.
“That’s something we could only have discovered using a single-molecule technique,” Chua added.
Researchers hope findings will lead to tailored therapies
The scientists first used bare DNA strands, but DNA does not exist bare inside the nucleus of cells; it instead is tightly packed with other proteins in spools called nucleosomes.
“Bare DNA is in the minority — nucleosomes are pervasive in our genomes,” Chua said.
To that end, the researchers reconstituted the nucleosomes, and then observed that MeCP2 had a very strong preference for these structures, helping to stabilize them.
According to Liu, these data are “one of the most definitive examples of this phenomenon to date.” Liu added that “it’s clear that MeCP2 prefers binding to nucleosomes.”
Because nucleosomes serve as strong barriers against gene activity, these findings support yet another mechanism related to how MeCP2 regulates gene expression. Contrasting to the initial narrow view of a protein limited to methylated DNA, these findings support the role of MeCP2 as a master regulator of gene activity via its strong interaction with nucleosomes.
There’s no cure for Rett, but the community of researchers studying it are determined and energized. Many found our data intriguing. … Our findings highlight how basic research can help the clinical community better understand a disease.
Finally, the researchers assessed the impact of several distinct mutations associated with Rett. They found that the mutations altered distinct aspects of MeCP2 dynamics. For example, certain mutations seem to impair the MeCP2 binding capacity to methylated DNA regions, but had no effect on its binding to nucleosomes. One Rett-associated mutation caused the MeCP2 protein to lose its ability to distinguish methylated from unmethylated DNA, while another caused marked problems in gene activity.
According to the researchers, these findings may help develop more informed and tailored therapeutic interventions to restore the activity of MeCP2 in agreement with the type of mutation.
“There’s no cure for Rett, but the community of researchers studying it are determined and energized. Many found our data intriguing when we shared it with them,” Chua said. “Our findings highlight how basic research can help the clinical community better understand a disease.”
In the future, the researchers expect to study the MeCP2-genome interactions inside a living organism, where interactions are expected to be more complex, rather than in a lab dish.
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