# Single-molecule Investigation of the Interaction Between MeCP2 and Chromatin

> **NIH NIH F31** · ROCKEFELLER UNIVERSITY · 2024 · $48,974

## Abstract

PROJECT SUMMARY/ABSTRACT
The methyl-CpG binding protein 2 (MeCP2) is a highly abundant chromatin-binding protein that recognizes
methylated DNA to coordinate the expression of thousands of genes essential for neuronal function. Mutations
in MeCP2 cause Rett syndrome, a severe neurological disorder affecting one in every 10,000 females and
characterized by psychiatric and motor regression at 6-18 months. Although several treatments are available for
improving some isolated features of Rett syndrome, there are currently no approved therapies that directly
address the underlying defects of MeCP2 loss of function. One primary reason for the lack of MeCP2-targeted
interventions is an inadequate understanding of how MeCP2 reads methylated DNA within hierarchically
organized chromosomes. MeCP2 is known to bind to methylated DNA with a higher affinity than unmethylated
DNA, but how it navigates the main structural form of packaged DNA in the nucleus, nucleosomes, to reach its
canonical methyl-DNA substrate remains unclear. Over 80% of the MeCP2 protein is structurally disordered,
resulting in extensive conformational heterogeneity and binding plasticity that could underlie the regulatory
capacity of the protein, but simultaneously hamper detailed mechanistic characterization of the protein’s
chromatin-binding behavior. To this end, I used a single-molecule platform combining fluorescence microscopy
with optical trapping to directly observe the real-time trajectory and dynamics of individual MeCP2 on DNA and
nucleosomes. This approach enabled the visualization of how MeCP2 navigates the chromatin landscape
harboring methylated CpG sites. I discovered that MeCP2 exhibits long-range, diffusive behavior on bare DNA,
whereas methylation drastically suppresses such motions. Unexpectedly, I also found that MeCP2 preferentially
and stably binds nucleosomes irrespective of methylation status, suggesting that nucleosomes may serve to
regulate the availability of MeCP2 for its canonical methyl-reader activity. Based on my preliminary data, I
hypothesize that nucleosomes regulate the availability of MeCP2 for methyl-DNA recognition and biophysically
modify MeCP2 dynamics and binding configurations on DNA. To test this hypothesis, I will 1) characterize the
dynamics of MeCP2 on DNA with and without methylation, 2) examine the binding and biophysical interaction of
MeCP2 with nucleosomes wrapped with methylated or unmethylated DNA and investigate how Rett mutations
impact this interaction, and 3) determine the structural basis of the MeCP2-nuclesome interaction. Successful
completion of the proposed aims will provide novel insights into how MeCP2 biophysically navigates through a
complex chromatin environment to reach its canonical methyl-DNA substrate at unprecedented spatial and
temporal resolution. My report will establish an experimental framework for systematic interrogation of Rett
syndrome mutations and their impact on fundamental MeCP2-nucleosome and DNA inter...

## Key facts

- **NIH application ID:** 10913516
- **Project number:** 5F31MH132306-03
- **Recipient organization:** ROCKEFELLER UNIVERSITY
- **Principal Investigator:** Gabriella N. L. Chua
- **Activity code:** F31 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $48,974
- **Award type:** 5
- **Project period:** 2022-09-01 → 2025-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10913516

## Citation

> US National Institutes of Health, RePORTER application 10913516, Single-molecule Investigation of the Interaction Between MeCP2 and Chromatin (5F31MH132306-03). Retrieved via AI Analytics 2026-05-27 from https://api.ai-analytics.org/grant/nih/10913516. Licensed CC0.

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