Browsing by Author "Meyer, Kate D"

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    Epitranscriptomics in parasitic protists: Role of RNA chemical modifications in posttranscriptional gene regulation.
    (PLoS pathogens, 2022-12) Catacalos, Cassandra; Krohannon, Alexander; Somalraju, Sahiti; Meyer, Kate D; Janga, Sarath Chandra; Chakrabarti, Kausik
    "Epitranscriptomics" is the new RNA code that represents an ensemble of posttranscriptional RNA chemical modifications, which can precisely coordinate gene expression and biological processes. There are several RNA base modifications, such as N6-methyladenosine (m6A), 5-methylcytosine (m5C), and pseudouridine (Ψ), etc. that play pivotal roles in fine-tuning gene expression in almost all eukaryotes and emerging evidences suggest that parasitic protists are no exception. In this review, we primarily focus on m6A, which is the most abundant epitranscriptomic mark and regulates numerous cellular processes, ranging from nuclear export, mRNA splicing, polyadenylation, stability, and translation. We highlight the universal features of spatiotemporal m6A RNA modifications in eukaryotic phylogeny, their homologs, and unique processes in 3 unicellular parasites-Plasmodium sp., Toxoplasma sp., and Trypanosoma sp. and some technological advances in this rapidly developing research area that can significantly improve our understandings of gene expression regulation in parasites.
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    Exploring the brain epitranscriptome: perspectives from the NSAS summit.
    (Frontiers in neuroscience, 2023-01) Lee, Sung-Min; Koo, Bonsang; Carré, Clément; Fischer, André; He, Chuan; Kumar, Ajeet; Liu, Kathy; Meyer, Kate D; Ming, Guo-Li; Peng, Junmin; Roignant, Jean-Yves; Storkebaum, Erik; Sun, Shuying; De Pietri Tonelli, Davide; Wang, Yinsheng; Weng, Yi-Lan; Pulvirenti, Luigi; Shi, Yanhong; Yoon, Ki-Jun; Song, Hongjun
    Increasing evidence reinforces the essential function of RNA modifications in development and diseases, especially in the nervous system. RNA modifications impact various processes in the brain, including neurodevelopment, neurogenesis, neuroplasticity, learning and memory, neural regeneration, neurodegeneration, and brain tumorigenesis, leading to the emergence of a new field termed neuroepitranscriptomics. Deficiency in machineries modulating RNA modifications has been implicated in a range of brain disorders from microcephaly, intellectual disability, seizures, and psychiatric disorders to brain cancers such as glioblastoma. The inaugural NSAS Challenge Workshop on Brain Epitranscriptomics hosted in Crans-Montana, Switzerland in 2023 assembled a group of experts from the field, to discuss the current state of the field and provide novel translational perspectives. A summary of the discussions at the workshop is presented here to simulate broader engagement from the general neuroscience field.
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    Identification of Novel N6-methyladenosine (m6A) Reader Proteins and the Characterization of their Molecular and Physiological Functions
    (2022) Choi, Seung Ho

    N6-methyladenosine (m6A) is deposited co-transcriptionally on thousands of cellular mRNAs and plays important roles in mRNA processing and cellular function. m6A is particularly abundant within the brain and is critical for neurodevelopment. However, the mechanisms through which m6A contributes to brain development are inco¬¬mpletely understood. Here, we discover serine-/arginine-rich splicing factor 7 (SRSF7) and RNA-binding motif-containing protein 45 (RBM45) as m6A-binding proteins in transformed hippocampal neurons. We find that SRSF7 binds to exon-intron junctions in methylated pre-mRNA targets and regulates the gene expression of thousands of cellular mRNAs, including the m6A RNA methyltransferase, METTL3. We find that RBM45 binds to thousands of cellular RNAs, predominantly within intronic regions. Rbm45 depletion disrupts the constitutive splicing of a subset of target pre-mRNAs, leading to altered mRNA and protein levels through both m6A-dependent and m6A-independent mechanisms. Finally, we find that RBM45 is highly expressed during embryonic neurodevelopment, demonstrating that expression of RBM45 is necessary for neuroblastoma cell differentiation and that its depletion impacts the expression of genes involved in several neurodevelopmental signaling pathways. Altogether, our findings identify roles for SRSF7 and RBM45 in gene expression regulation, and highlight a previously unknown function for RBM45 in the control of pre-mRNA processing and neuronal differentiation, mediated in part by the recognition of methylated RNA.