Burow Dana A, Umeh-Garcia Maxine C, True Marie B, Bakhaj Crystal D, Ardell David H, Cleary Michael D
Quantitative and Systems Biology Graduate Program, University of California, 5200 N. Lake Rd, Merced, CA, USA.
Neural Dev. 2015 Apr 21;10:11. doi: 10.1186/s13064-015-0038-6.
Gene expression patterns are determined by rates of mRNA transcription and decay. While transcription is known to regulate many developmental processes, the role of mRNA decay is less extensively defined. A critical step toward defining the role of mRNA decay in neural development is to measure genome-wide mRNA decay rates in neural tissue. Such information should reveal the degree to which mRNA decay contributes to differential gene expression and provide a foundation for identifying regulatory mechanisms that affect neural mRNA decay.
We developed a technique that allows genome-wide mRNA decay measurements in intact Drosophila embryos, across all tissues and specifically in the nervous system. Our approach revealed neural-specific decay kinetics, including stabilization of transcripts encoding regulators of axonogenesis and destabilization of transcripts encoding ribosomal proteins and histones. We also identified correlations between mRNA stability and physiologic properties of mRNAs; mRNAs that are predicted to be translated within axon growth cones or dendrites have long half-lives while mRNAs encoding transcription factors that regulate neurogenesis have short half-lives. A search for candidate cis-regulatory elements identified enrichment of the Pumilio recognition element (PRE) in mRNAs encoding regulators of neurogenesis. We found that decreased expression of the RNA-binding protein Pumilio stabilized predicted neural mRNA targets and that a PRE is necessary to trigger reporter-transcript decay in the nervous system.
We found that differential mRNA decay contributes to the relative abundance of transcripts involved in cell-fate decisions, axonogenesis, and other critical events during Drosophila neural development. Neural-specific decay kinetics and the functional specificity of mRNA decay suggest the existence of a dynamic neurodevelopmental mRNA decay network. We found that Pumilio is one component of this network, revealing a novel function for this RNA-binding protein.
基因表达模式由mRNA转录和降解速率决定。虽然已知转录可调节许多发育过程，但mRNA降解的作用尚未得到广泛定义。确定mRNA降解在神经发育中作用的关键一步是测量神经组织中全基因组的mRNA降解速率。此类信息应能揭示mRNA降解对基因表达差异的贡献程度，并为识别影响神经mRNA降解的调控机制提供基础。
我们开发了一种技术，可在完整的果蝇胚胎中、在所有组织中，特别是在神经系统中进行全基因组的mRNA降解测量。我们的方法揭示了神经特异性的降解动力学，包括轴突发生调节因子编码转录本的稳定以及核糖体蛋白和组蛋白编码转录本的不稳定。我们还确定了mRNA稳定性与mRNA生理特性之间的相关性；预计在轴突生长锥或树突内翻译的mRNA具有较长的半衰期，而编码调节神经发生的转录因子的mRNA具有较短的半衰期。对候选顺式调控元件的搜索确定了神经发生调节因子编码mRNA中Pumilio识别元件（PRE）的富集。我们发现RNA结合蛋白Pumilio的表达降低会稳定预测的神经mRNA靶标，并且PRE是触发神经系统中报告基因转录本降解所必需的。
我们发现差异mRNA降解有助于果蝇神经发育过程中参与细胞命运决定、轴突发生和其他关键事件的转录本的相对丰度。神经特异性的降解动力学和mRNA降解的功能特异性表明存在一个动态的神经发育mRNA降解网络。我们发现Pumilio是该网络的一个组成部分，揭示了这种RNA结合蛋白的新功能。
