Paper: Interaction of methyl-CpG-binding protein2 (MeCP2) with distinct enhancers in the mouse cortex 

What happens when epigenetic gene regulation goes wrong in the brain? 

Rett syndrome is a neurodevelopmental condition that leads to the loss of motor and communication skills, along with intellectual disability. It’s particularly striking because it is X-linked, meaning it primarily affects girls, and the fact that to this day, we have no cure. 

The key player in Rett syndrome is a protein called Methyl-CpG Binding Protein 2 (MeCP2), which is mutated in individuals with the disorder. As you may have learned in Biology, DNA methylation is one of the main ways that factors outside the DNA sequence - ie. epigenetic factors - can regulate gene expression. These are reversible chemical changes that don't alter the DNA bases themselves. You can think of methylation as placing little flags on certain DNA bases, typically cytosines (C) , which signal specific proteins like MeCP2 to bind to those regions and influence gene activity. This usually triggers a cascade of additional proteins to be recruited, resulting in either gene activation or repression. Because this process unfolds as a chain of events, it also creates opportunities for amplification: a small change can be magnified at each step as more proteins are recruited, ultimately having a profound effect on gene expression. Different methyl-binding proteins recognize different DNA sequences, giving us specificity in gene regulation, even though we only have 64 codons to work with. Traditionally, MeCP2 is thought to bind to mCG sites - methylated cytosine followed by guanine. But in neurons, MeCP2 also binds strongly to mCA sequences - which are methylated cytosines followed by adenine. This suggests a specialized function for MeCP2 in neural tissue, which makes sense considering how different neurons are from other cell types. 

In this paper, the authors dig into how MeCP2 regulates genes in neurons, typing to uncover the molecular mechanisms behind its powerful effect on brain development. They find that MeCP2 doesn’t just bind to methylated DNA, but also binds to methyl-binding hubs (MBHs), which are genomic regions that paradoxically have fewer methylated cytosines than the surrounding areas. These MBHs are often located at enhancer regions - non-coding DNA sequences that serve as remote controllers of gene activation - ie. they affect genes that are not geographically next to them. Enhancers can loop through space, folding the DNA so distant regulatory proteins bound to enhance can physically reach and influence a gene’s promoter. 

The presence of MBHs at these distal enhancer sites, and the fact that they still bind MeCP2 despite low methylation suggest two things: 

1. MeCP2 might play an important role in neural gene expression through these MBHs and 

2. This gene expression control may occur in ways that are independent of methylation patterns. 

The authors propose that MeCP2 bound to MBHs might repress genes that are otherwise being activated at these enhancer regions - acting as a kind of counterbalance to fine tune gene activity. Interestingly, while one MBH site can only modestly repress a gene, multiple MBHs can work together to cause strong, cumulative repression. 

How did they figure this out? 

The main technique used is called CUT&RUN, a powerful, precise method for mapping protein-DNA interactions. It works by using antibodies to target specific proteins (like MeCP2) and enzymes to precisely cut the DNA at those binding sites. The resulting DNA fragments can then be sequenced to identify exactly where the protein was bound. More on this at the journal club!

What does this mean? 

The fact that MeCP2 can regulate genes independently of methylation suggests it may play a more diverse role in the genome than previously thought. Proteins like MeCP2 may not just be readers of epigenetic marks, but also act as multi-purpose regulators that perform different tasks depending on where they bind. The genes affected by these MBH bound enhancer regions are involved in building the architecture of neurons - forming axons, synapses and the machinery neurons use to send and receive signals. Disruption of this system could help explain the symptoms of Rett syndrome, but may also shed light on other neurological conditions where axonal transport and neural connectivity are disrupted, such as ALS, Parkinson’s or Alzheimer’s. 

This week’s journal club: 

We will explore exciting topics related to gene regulation in the brain, and how single proteins like MeCP2 can act as regulators with multiple functions. We will discuss how epigenetics shapes both gene expression and inheritance patterns, and how this understanding helps us make sense of neurodevelopmental diseases like Rett syndrome. We will also learn about modern molecular biology techniques like CUT&RUN, and how researchers  discover more about the genome through DNA-protein interactions.