Gene expression during development is often exclusively studied at the level of transcription. However, an additional and essential level of control occurs via post-transcriptional mRNA decay. Regulation of mRNA decay is particularly important during nervous system development, where the structure of neurons requires selective stabilization of mRNAs far from their site of synthesis and the generation of cellular diversity requires the programmed decay of mRNAs that regulate proliferation and differentiation. Defective mRNA decay has been implicated in many neurological birth defects, including fragile X-syndrome (the most common form of hereditary mental impairment) and spinal muscular atrophy (a leading genetic cause of infant mortality). The study of mRNA decay during embryonic development has previously been hindered by the lack of methods allowing in vivo, cell type-specific measurements of transcript stability. We have developed a technique (based on TU-tagging methods) that overcomes this technical challenge and allows neural-specific, genome-wide measurements of mRNA decay in intact Drosophila embryos. This technique provides the foundation for a systems-level approach that will allow us to construct a Neural Development mRNA Decay Network. This network will contain the following information: the decay rates of all mRNAs expressed in the embryonic nervous system, the cis-elements that target these mRNAs for decay, the trans-acting RNA-binding proteins and miRNAs that bind these cis-elements, and the spatial dynamics of mRNA - RNA-binding protein interactions. This information will be obtained using a systems-level approach that combines genome-wide analysis of mRNA decay rates in wildtype and RBP mutant embryos, computational identification of candidate linear and structural cis-elements, molecular genetic definition of cis element effects on transcript stability in vivo, biochemical analysis of RBP-mRNA interactions in vitro and in vivo, and imaging of fluorescent mRNA - RBP interactions within neurons. This work will generate a comprehensive and predictive network map of neural mRNA decay dynamics, thus filling a significant gap in current models of gene expression during neural development.

Public Health Relevance

Regulated decay of messenger RNAs (mRNAs) is an essential yet often overlooked mechanism that determines when and where genes are expressed. Precise control of mRNA decay is particularly important in nervous system development and mRNA decay defects contribute to multiple human neural development disorders. We aim to construct a comprehensive Neural Development mRNA Decay Network which will define protein-RNA interactions and pathways that are essential for neural development.

National Institute of Health (NIH)
Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD)
Research Project (R01)
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Special Emphasis Panel (ZRG1-CB-J (59))
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Coulombe, James N
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University of California Merced
Schools of Earth Sciences/Natur
United States
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Cleary, Michael D (2018) Uncovering cell type-specific complexities of gene expression and RNA metabolism by TU-tagging and EC-tagging. Wiley Interdiscip Rev Dev Biol 7:e315
Burow, Dana A; Martin, Sophie; Quail, Jade F et al. (2018) Attenuated Codon Optimality Contributes to Neural-Specific mRNA Decay in Drosophila. Cell Rep 24:1704-1712
Burow, Dana A; Umeh-Garcia, Maxine C; True, Marie B et al. (2015) Dynamic regulation of mRNA decay during neural development. Neural Dev 10:11