Methyl-CpG-binding domain as a protein interaction partner in promoter regulation and neurodevelopment through evolutionary expanded entanglement

Authors

• Stephanie M. Bilinovich, Michigan State University
• Surya B. Chhetri, HudsonAlpha Institute for Biotechnology
• Jackson T. Mitchell, Michigan State University
• Gage O. Leighton, University of North Carolina at Chapel Hill
• Vladislav Jdanov, Michigan State University
• Jacob K. Zieba, Michigan State University
• Taylor W. Cook, Michigan State University
• Krysta L. Engel, HudsonAlpha Institute for Biotechnology
• Robert M. Vaughan, Michigan State University
• Humza Bhatti, Michigan State University
• Sadie L. Heeringa, Calvin College
• Amy M. Wilstermann, Calvin College
• Sophie Vanderweele, Michigan State University
• Akansha S. Das, Michigan State University
• Emily C. Sherry, Michigan State University
• Stephen A. Duncan, Medical University of South Carolina
• Katie L. Uhl, Michigan State University
• David C. Hinds, Johns Hopkins University
• Mark Mackiewicz, Johns Hopkins University
• Sarah K. Meadows, Johns Hopkins University
• Kimberly M. Newberry, Johns Hopkins University
• E. Christopher Partridge, Johns Hopkins University
• Sara G. Cline, Athens State University
• C. Joy Shepard, Athens State University
• D. Casey Smith, Athens State University
• Antonio Bradley, Athens State University
• Daniel Vogt, Michigan State University
• Daniel B. Campbell, Michigan State University
• Lucas Pozzo-Miller, Michigan State University
• Caleb P. Bupp, Michigan State University
• Austin J. Goodyke, Corewell Health
• Surender Rajasekaran, Michigan State University
• Rebecca C. Knickmeyer, Michigan State University
• Benjie Blair, Jacksonville State University

Department

Biology

Document Type

Article

Publication Date

2025

Abstract

There is increasing evidence that the methyl-binding domain (MBD) is a protein-protein interaction motif that can function independently of methylated DNA binding. The MBD proteins found throughout plants and invertebrates duplicated into multiple vertebrate DNA and non-DNA-binding members (MBD1, MBD2, MBD3, MBD4, MBD5, MBD6, MECP2, BAZ2A, BAZ2B, SETDB1, andSETDB2). Although many invertebrate species possess MBD proteins that can bind and recognize DNA methylation, the DNA-binding function has been independently lost multiple times, with only minor alterations to the protein interaction residues. The nucleosome remodeling and deacetylase (NuRD) complex, which interacts with MBD2/3 and is colocalized with MBD1/4 ChIP-Seq, is maintained in species where MBD2/3 cannot bind to DNA. NuRD ChIP-seq data from HepG2 cell line, human induced pluripotent stem cells (iPSCs), and human iPSC-derived liver cells suggest that the NuRD complex is highly localized to nonmethylated CpG-rich housekeeping gene promoter elements, which are essential in organogenesis and maintained within theDrosophila melanogaster MBD2/3 non-DNA-binding system. Integration of MBD interaction proteins and NuRD gene expression from >115 million cells of single-cell RNA-seq, along with thousands of bulk tissue profiles, highlights a critical role of MBD3,MECP2, and GATAD2B in brain development and intellectual disability syndromes that is maintained throughout invertebrate neural development and likely involves evolutionary expanded entanglement as the vertebrate MBD proteins expanded. This work suggests that MBD has a largely unexplored role as a critical protein interaction motif that is evolutionarily conserved for regulating enhancers and promoters.

Publication/Presentation Information

Cell Physiology, 329(3), 2025, C848–C867. 

Recommended Citation

Bilinovich, S. M., Chhetri, S. B., Mitchell, J. T., Leighton, G. O., Jdanov, V., Zieba, J. K., Cook, T. W., Engel, K. L., Vaughan, R. M., Bhatti, H., Heeringa, S. L., Wilstermann, A. M., Vanderweele, S., Das, A. S., Sherry, E. C., Duncan, S. A., Uhl, K. L., Hinds, D. C., Mackiewicz, M., … Prokop, J. W. (2025). Methyl-CpG-binding domain as a protein interaction partner in promoter regulation and neurodevelopment through evolutionary expanded entanglement. American Journal of Physiology. Cell Physiology, 329(3), C848–C867. https://doi.org/10.1152/ajpcell.00749.2024