Rett mutations may disrupt early development through DNA remodeling
Study findings provide potential foundation for future therapeutic strategies
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Mutations in the MECP2 gene — the main cause of Rett syndrome — may disrupt early development by altering how DNA is three-dimensionally organized within chromatin, the complex of DNA and proteins that packages genetic material inside cells, according to a study in China.
“This work provides a new three-dimensional genomic perspective for understanding Rett syndrome pathogenesis [disease processes] and offers a theoretical foundation for future therapeutic strategies aimed at restoring chromatin structure,” researchers wrote.
The study, “MECP2 mutations disrupt pluripotent stem cell fate through remodeling of the three-dimensional genome,” was published in Cell Death & Disease.
Mutations in MECP2 gene disrupt function or reduce levels of key protein
Rett syndrome is mainly caused by mutations in the MECP2 gene that either disrupt the function or reduce levels of MeCP2, a protein that helps determine which genes are turned on and off inside cells. These changes impair communication between nerve cells and brain development, ultimately leading to Rett symptoms.
MeCP2 has emerged as a regulator of chromatin. How genetic material is organized within chromatin influences which genes are active and how they are regulated. Genes in tightly packed chromatin are generally harder to access and less active, while those in more open chromatin are easier to reach and more likely to be active. DNA folding also shapes how genes interact with regulatory DNA elements that control their activity.
Most studies exploring these chromatin-related roles have focused on mature nerve cells, where MeCP2 is known to be essential for normal function. Much less is understood about whether the protein also helps shape chromatin architecture during earlier stages of development.
To investigate that question, a team of researchers in China examined how MECP2 mutations affect the three-dimensional organization of DNA in human induced pluripotent stem cells (iPSCs) — adult cells reprogrammed into a stem-cell-like state that can model early human development in the lab.
Mutant cells showed signs of impaired growth
The team created three iPSC models carrying different loss-of-function MECP2 mutations affecting major functional regions of the protein. These mutant cells showed signs of impaired growth, with those carrying mutations that caused greater shortening of the MeCP2 protein showing the most pronounced defects.
When used to create embryoid bodies, clusters of stem cells that mimic some of the earliest stages of embryonic development, the mutant cells also developed abnormally. Compared with embryoid bodies formed from cells carrying normal MECP2, they developed fewer internal cavities, hollow structures that normally appear as cells organize into early embryo-like structures.
The mutant cells also showed an earlier decline in OCT4, a protein that helps stem cells maintain their immature state before developing into specialized cell types. Together with the abnormal cavity formation, these findings suggested that MECP2 mutations disrupted the normal development and organization of these early embryo-like structures.
To understand why this happened, the team turned to a series of analyses examining how DNA is packaged inside cells.
They found that MECP2 mutations extensively remodeled the three-dimensional architecture of the genome. In the mutant cells, large regions of DNA switched between more open and more compact chromatin. Boundaries that help organize interactions between different DNA regions, including those between genes and regulatory DNA elements, were also frequently rearranged.
These changes affected more than DNA structure alone. As chromatin organization shifted, so did gene activity. Genes linked to cell growth and cell-cycle regulation showed altered activity, while others involved in nervous system development became less active.
CTCF protein identified as possible key player in changes
The team also found that some DNA regions became more easily accessible while others became harder to reach. Many of these altered DNA regions contained sequences recognized by proteins involved in maintaining stem cells, including OCT4, as well as proteins that help organize chromatin structure, particularly CTCF.
Further experiments pointed to CTCF as a key player in these changes.
Although overall CTCF levels remained unchanged, MECP2 mutations caused CTCF to bind more strongly to certain DNA regions that normally interact with the MeCP2 protein. This increased binding was associated with altered chromatin looping and changes in how genes interacted with regulatory DNA elements, ultimately affecting nearby gene activity.
Restoring levels of functioning MeCP2 in one mutant stem-cell model partially reversed the abnormal CTCF binding and some altered DNA interactions, supporting a direct link between MeCP2 loss and genome remodeling.
“Together, these findings establish a novel mechanistic framework in which MECP2 functions as a global regulator of the three-dimensional genome in pluripotent stem cells,” the researchers wrote.
