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

长基因间非编码RNA(LincRNAs)是最近发现的一组没有蛋白质编码能力的转录本。尽管它们在复杂生物体的生物学中扮演着不同而重要的角色，但对它们的起源和进化几乎一无所知。该项目的目标是利用下一代RNA测序技术(RNA-Seq)和果蝇巨大的基因组资源来表征lincRNA序列和表达进化背后的力量。对纯物种中变异的分析不能解释lincRNA表达调控是如何进化的，但对杂交物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洞察。因此，本论文的具体目标是分析利用RNA-Seq对拟黑粉虱/拟黑粉虱杂交后代中lincRNA调控的进化。具体目标是(1)鉴定lincRNA表达的遗传方式，(2)鉴定lincRNA调控分化是通过顺式还是反式改变发生的，以及(3)鉴定lincRNAs是否可能导致杂交不亲和性。这项工作将是迄今为止对lincRNA进化最全面的分析，也是第一次通过杂交来研究密切相关物种的lincRNA调控进化。它将强调偏离生物学中心教条的一类未被研究的基因的重要性。这笔赠款将支持一名博士生和多名本科生的培训，并为当地高中生或马里兰大学少数民族学生管道的教师提供暑期研究体验。从这项工作中收集到的知识将在国家介绍和印刷中广泛传播。了解基因调控系统的进化为我们深入了解基因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.