• Title Director of Graduate Studies; Associate Professor of Biology; Member, Whitaker Cardiovascular Institute
  • Education PhD, Baylor College of Medicine
  • Phone 617-353-2469
  • Area of Interest Cardiac development and disease, muscle regeneration, muscular dystrophy, mouse developmental biology, gene regulation
  • CV

Current Research

Our lab focuses on gene regulation in muscle development and disease. Understanding this process in differentiation and homeostasis can yield insight into the mechanisms that drive pathological gene expression in cardiac and skeletal muscle diseases. We use a systems-level approach to investigate the complex gene regulatory networks and mechanisms in cardiac and skeletal muscle differentiation.

Our most recent research relates to the role of noncoding RNAs (ncRNAs) in muscle differentiation and regeneration. Small ncRNAs such as microRNAs (miRNAs) and small nucleolar RNAs (snoRNAs), and long noncoding RNAs (lncRNAs), are now recognized as key molecular components in gene regulatory networks. We previously identified a ncRNA locus (Dlk1-Dio3) – encoding the above classes of ncRNAs – and demonstrated its role in skeletal muscle differentiation and regeneration, and in cardiomyocyte proliferation. Recently, we have shown that Meg3, a lncRNA in the Dlk1-Dio3 locus, regulates myoblast plasticity and muscle regeneration through epithelial mesenchymal transition (EMT). In addition, we have shown that the entire Dlk1-Dio3 ncRNA cluster coordinates mitochondrial metabolism and chromatin structure to maintain proper myogenic cell state. We continue to investigate the multi-functional gene regulatory role of this imprinted ncRNA locus utilizing genome-wide transcriptomic and genomic approaches.

Selected Publications

  • Pinheiro A, Petty CA, Cabrera K, Tost EP, Gower AC, Marano M, Leviss EM, Boberg M, Mahendran J, Bock P, Stephens C, Fetterman J, Naya FJ. 2024. The Dlk1-Dio3 noncoding RNA cluster coordinately regulates mitochondrial respiration and chromatin structure to establish proper cell state for muscle differentiation. Development. 151(24):dev203127. doi: 10.1242/dev.203127. PMID: 39612212.
  • Dill TL, Carroll A, Pinheiro A, Gao J, Naya FJ (2021) The long noncoding RNA Meg3 regulates myoblast plasticity and muscle regeneration through epithelial mesenchymal transition. Development. 148(2):dev194027. doi: 10.1242/dev.194027. PMID: 33298462.
  • Pinheiro A and Naya FJ (2021) The Key lnc(RNA)s in Cardiac and Skeletal Muscle Development, Regeneration, and Disease. J Cardiovasc Dev Dis.
  • Dill TL, Naya FJ (2018) A Hearty Dose of Noncoding RNAs: The Imprinted DLK1-DIO3 Locus in Cardiac Development and Disease. J Cardiovasc Dev Dis. 5(3). pii: E37. doi: 10.3390/jcdd5030037.
  • Medrano JL, Naya FJ (2017) The transcription factor MEF2A fine-tunes gene expression in the atrial and ventricular chambers of the adult heart. J Biol Chem. 292(51): 20975-20988.
  • Desjardins CA, Naya FJ (2017) Antagonistic regulation of cell cycle and differentiation gene programs in neonatal cardiomyocytes by homologous MEF2 transcription factors. J Biol Chem. 292(25): 10613-10629.
  • Clark AL, Naya FJ (2015) MicroRNAs in the Myocyte Enhancer Factor 2 (MEF2)-regulated Gtl2-Dio3 Noncoding RNA Locus Promote Cardiomyocyte Proliferation by Targeting the Transcriptional Coactivator Cited2. J Biol Chem. 290(38): 23162-72.
  • Estrella NL, Desjardins CA, Nocco SE, Clark AL, Maksimenko Y, and Naya FJ (2015) MEF2 transcription factors regulate distinct gene programs in mammalian skeletal muscle differentiation. J Biol Chem. 290(2): 1256-68.

Courses Taught:

  • BI 213 Intensive Cell Biology
  • BI 553 Molecular Biology 2

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