DISSERTATION RESEARCH: Divergence of long intergenic noncoding RNAs in Drosophila pseudoobscura, Drosophila persimilis, and their hybrids

长基因间非编码RNA（lincRNA）是最近发现的一类没有蛋白质编码能力的转录本。虽然它们在复杂生物体的生物学中发挥着不同而重要的作用，但对它们的起源和进化几乎一无所知。该项目的目标是使用下一代RNA测序技术（RNA-Seq）和果蝇的大量基因组资源来表征lincRNA序列和表达进化的基础力量。纯物种中的变异分析不能解释lincRNA表达的调控是如何演变的，但对杂交种中错误表达的分析提供了对不同进化过程如何塑造调控过程的深入了解。因此，本论文改进基金的具体目标是利用RNA-Seq分析D. pseudobscura/拟暗纹叶蝉D. Persimilis杂种。具体目标是（1）确定lincRNA表达的遗传模式，（2）确定lincRNA调控分歧是否通过顺式或反式变化发生，（3）确定lincRNA是否可能导致杂种不亲和性。这项工作将是迄今为止对lincRNA进化的最全面的分析，也是第一个通过杂种研究近缘物种中lincRNA调控进化的工作。它将强调偏离生物学中心法则的一类未被充分研究的基因的重要性。该补助金将支持博士生和多名本科生的培训，并为马里兰州少数民族学生管道大学的当地高中学生或教师提供夏季研究经验。从这项工作中获得的知识将以国家介绍和印刷品的形式广泛传播。了解基因调控系统的进化为基因型和表型之间的关系提供了重要的见解，这最终奠定了我们对疾病和农作物改良的理解。

Long intergenic non-coding RNAs (lincRNAs) are a recently discovered group of transcripts that have no protein-coding capacity. Although they play diverse and important roles in the biology of complex organisms, almost nothing is known of their origin and evolution. The goal of this project is to use next generation RNA sequencing technology (RNA-Seq) and the vast genomic resources of the fruit fly Drosophila to characterize the forces that underlie lincRNA sequence and expression evolution. Analyses of variation in pure species cannot explain how the regulation of lincRNA expression evolves, but analyses of misexpression in hybrids provides insight into how diverse evolutionary processes shape the regulatory process. Thus, the specific goal of this dissertation improvement grant is to analyze the evolution of lincRNA regulation using RNA-Seq in D. pseudoobscura/D. persimilis hybrids. Specific aims are (1) to identify the mode of inheritance of lincRNA expression, (2) identify whether lincRNA regulatory divergence occurs through cis or trans changes, and (3) identify whether lincRNAs may underlie hybrid incompatibilities.This work will be the most comprehensive analysis of lincRNA evolution to date and the first to examine lincRNA regulatory evolution in closely related species via hybrids. It will underscore the importance of an understudied class of genes that deviates from the central dogma of biology. This grant will support the training of both a doctoral student and multiple undergraduates as well as provide a summer research experience for a local high school student or teacher from the University of Maryland's Minority Student Pipeline. The knowledge gleaned from this work will be disseminated widely, both in national presentations and in print. Understanding the evolution of gene regulatory systems provides important insights into the relationship between genotype and phenotype, which ultimately underlies our understanding of disease and the improvement of agricultural crops.