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Our Science

We are interested in how cells in the nervous system make decisions to turn genes on or off, and how those decisions are remembered in processes such as development or plasticity, and in injury or disease.  The goal of the Meffert lab is to gain a mechanistic understanding of how selective gene programs are recruited and maintained.  Rather than focusing on single genes, we investigate the upstream processes that allow coordinate regulation of many genes to achieve biological impact.  We uncover dynamic molecular mechanisms for spatial control of gene programs at cellular and subcellular levels, with a focus on the roles played by non-coding RNA and RNA-binding proteins.  Understanding how genes can be co-regulated post-transcriptionally to produce concerted programs is a fundamental biological question that is also attractive to our laboratory because of its particular relevance for compartmentalized responses in the nervous system, such as in synaptic plasticity.  

We are highly collaborative and have pioneered multi-disciplinary approaches in molecular diagnostics, biochemistry, high resolution cellular imaging, mouse genetics and behavior, and computational analysis. Discovery-based sequencing strategies have been developed to reveal in vivo small RNA targets through the production of small RNA: target chimeric molecules. The Meffert lab leverages an understanding of basic gene control mechanisms to illuminate potential therapeutic targets in both nerve injury and the development of cognitive disabilities, including Autism Spectrum Disorders, such as Fragile X Syndrome, in which disrupted growth and function of synaptic connections is a central component. Ongoing studies use mouse models and human samples to test how translation, miRNA biogenesis and miRNA:target interactions, may be pathologically regulated to produce phenotypes associated with disease.

Our Approach

Multiple approaches are integrated to investigate gene regulation in the nervous system at both transcriptional and post-transcriptional levels. We combine techniques of molecular biology, cell biology, biochemistry, high resolution imaging, high-throughput expression analysis and computational strategies, with both mouse and human models of disease.  Discovery-based sequencing technologies have been developed to reveal in vivo small RNA targets through the production of small noncoding RNA:target RNA chimeric molecules.

Technological Innovations:

CIMERAseq: A method for unambiguously profiling sncRNA:target RNA interactions

Xinbei Li, William T. Mills IV, Daniel Jin, and Mollie K. Meffert. (2024), Genome-wide and cell-type selective profiling of in vivo small noncoding RNA:target RNA interactions by chimeric RNA sequencing. Cell Reports Meth, 4(8) 100836.

SCRAP: Bioinformatic pipeline for analysis of small chimeric RNA-sequencing data

Sreenivas Eadara, Xinbei Li, Emily A. Eiss, and Mollie K. Meffert. (2023) Computational Analysis Tutorial for Chimeric Small Noncoding RNA: Target RNA Sequencing Libraries. J Vis Exp, (2023).

William T. Mills IV, Sreenivas Eadara, Andrew E. Jaffe, and Mollie K. Meffert. (2022), SCRAP: a bioinformatic pipeline for the analysis of small chimeric RNA-seq data. RNA, 29 (1); 1-17.

RNAscope: A technique to amplify the signal of a single RNA for visualization under a microscope

Xinbei LiSreenivas EadaraSangmin JeonYan Liu, Gabriella MuwangaLintao QuMichael J. Caterina, and Mollie K. Meffert (2021), Combined single-molecule fluorescence in-situ hybridization and immunohistochemistry analysis in intact murine dorsal root ganglia and sciatic nerve. STAR Protocols, 2(2):100555.

Selected Publications

  • Xinbei Li, William T. Mills IV, Daniel Jin, and Mollie K.Meffert. (2024), Genome-wide and cell-type selective profiling of in vivo small noncoding RNA:target RNA interactions by chimeric RNA sequencing. Cell Reports Meth, 4(8) 100836.

  • Megha Subramanian, William T. Mills IV, Manish D Paranjpe, Uche Onuchukwu, Manasi Inamdar, Amanda R. Maytin, Xinbei Li, Joel L. Pomerantz, and Mollie K.Meffert. (2023), Growth suppressor microRNAs mediate synaptic overgrowth and behavioral deficits in Fragile X mental retardation protein deficiency. iScience, 27 (1) 108676.

  • William T. Mills IV, Sreenivas Eadara, Andrew E.  Jaffe, and Mollie K. Meffert. (2022), SCRAP: a bioinformatic pipeline for the analysis of small chimeric RNA-seq data. RNA, 29 (1); 1-17.

  • Alexandra M Amen, Claudia R. Ruiz, Jay Shi, Megha Subramanian, Daniel Pham, and Mollie K. Meffert, (2017) A rapid induction mechanism for Lin28a in trophic responses.  Molecular Cell, 65 (3); 490 - 503.

  • Erica C. Dresselhaus, Matthew C. Boersma, and Mollie K. Meffert, (2018), Targeting of NF-kB to dendritic spines is required for synaptic signaling and spine development. J.Neurosci., 8(17); 4093-4103.

  • Laurel M. Oldach, Kirill Gorshkov,William T. Mills, Jin Zhang*, and Mollie Meffert* (2018), A biosensor for MAPK-dependent Lin28 signaling. Molecular Biol of the Cell, 29(10), 1157-1167.  PMID29540527.

  • Yu-Wen A. Huang*, Claudia R. Ruiz*, E.C.H. Eyler*, Kathie Lin, and Mollie K. Meffert. “Dual regulation of miRNA biogenesis generates target specificity in neurotrophin-induced protein synthesis.” Cell, 148(5); 933-946. 2012.

Funding

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National Institute of Health
National Institute of Mental Health

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The Braude Foundation

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Distinguished Scientist Award: The Sontag Foundation

Eric C. Aker Endowment

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The Simons Foundation

HHMI Gilliam Fellows Program

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Johns Hopkins University
School of Medicine

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