One protein in particular is critical for brain development. It is a master regulator of gene expression and is abundantly present in neurons. Its dysfunction is the cause of Rett syndrome, a neurological disorder that can lead to severe cognitive, motor and communication problems in girls.
Yet scientists know little about how this essential protein does its crucial job at the molecular level. “People have been studying this protein for decades without a clear consensus on what it does, where it binds to the genome, and what its functions are,” says Rockefeller’s Shixin Liu. Now, a new study from Liu’s lab sheds light on how the protein, MeCP2, interacts with DNA and chromatin.
The findings, published in Molecular and structural biology of natureprovide insight into this master regulator and could open new avenues for Rett syndrome therapies.
A single molecule approach
MeCP2 is a puzzling protein. Although it has been implicated in regulating thousands of genes and is thought to be critical to neurological development, its effects on the genome are difficult to determine. Too little wild-type MeCP2 causes Rett syndrome, but too much of the protein causes an equally debilitating neurological disorder known as MeCP2 duplication syndrome.
Liu and his colleagues took advantage of the lab’s area of expertise — observing and manipulating single molecules — to better understand how MeCP2 interacts with DNA. The team clamped a single piece of DNA between plastic microspheres, each held in place by a laser, and then incubated the DNA with fluorescently labeled MeCP2 proteins. This setup allowed them to closely monitor the dynamic behavior of the mysterious protein.
MeCP2 is generally thought to perform its functions exclusively on DNA modified with methylated cytosines, but a satisfactory explanation for such specificity has not been found, as the protein readily binds to both methylated and unmethylated DNA. The team found that MeCP2 moves dynamically on DNA, but in a much slower manner with regard to the methylated form compared to the unmethylated one. Furthermore, they showed that these different dynamics allow MeCP2 to recruit another regulatory protein more efficiently to methylated DNA sites, which may help direct MeCP2’s gene regulatory functions to specific locations within the genome. “We found that MeCP2 slides along unmethylated DNA faster, and this difference in movement may explain how the protein differentiates between the two,” says Gabriella Chua, a graduate fellow in Liu’s lab and first author on the paper.
“That’s something we could only have discovered using a single-molecule technique.”
Liu and Chua also found that the protein shows a marked preference for binding to nucleosomes — protein coils that contain our genetic material — rather than naked DNA. This interaction stabilizes nucleosomes in a way that can suppress gene transcription, indicating how MeCP2 itself regulates gene expression.
New insights into nucleosomes
The observation that a master regulator of gene expression most frequently interacts with this tightly coiled form of DNA helps reinforce a growing notion that nucleosomes are much more than inert “storage spools” of DNA, and that scientists need to begin thinking about MeCP2’s function more in the context of nucleosomes.
“Our data are one of the most compelling examples of this phenomenon to date,” Liu says. “It is clear that MeCP2 prefers to bind to nucleosomes.” In this way, MeCP2 functions as a chromatin-binding protein, in contrast to the conventional view that sees it primarily as a methyl-DNA binding protein. In this study, the team has also focused on the part of the protein that is responsible for its nucleosome-binding activity.
“Naked DNA is a minority: nucleosomes are present in all our genomes,” says Chua. “Several recent studies have shown that nucleosomes are not simply passive barriers to transcription, but active sites for genetic regulation.” A particularly striking example of this functionality of nucleosomes is the interaction of MeCP2 with them.
In future work, the team plans to expand the current in vitro study to examine MeCP2 in vivo, where interactions between the protein and the nucleosome are expected to be more complex. They also aim to use the techniques described in this paper to better study the numerous MeCP2 mutations that cause diseases such as Rett syndrome. The hope is that a more complete understanding of the protein at the heart of this devastating disease may one day lead to therapies. “There is no cure for Rett syndrome, but the research community studying it is determined and energized. Many found our data intriguing when we shared it with them,” Chua says. “Our findings highlight how basic research can help the clinical community better understand a disease.”