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

论文研究：假暗果蝇、Persimilis 果蝇及其杂交种中长基因间非编码 RNA 的分化

• 批准号: 1405103
• 负责人: Carlos Machado
• 金额: $ 1.96万
• 依托单位: University of Maryland, College Park
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-06-01 至 2016-05-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1405103&HistoricalAwards=false
• 关键词: DISSERTATION; RESEARCH; Divergence; long; intergenic

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.

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发挥着多种多样的重要作用，但对它们的起源和进化几乎一无所知。该项目的目标是利用下一代RNA测序技术（RNA- seq）和果蝇的大量基因组资源来表征lincRNA序列和表达进化背后的力量。对纯物种变异的分析无法解释lincRNA表达调控是如何进化的，但对杂交物种错误表达的分析可以让我们深入了解不同的进化过程如何影响调控过程。因此，本论文改进资助的具体目标是利用RNA-Seq分析D. pseudobscura /D中lincRNA调控的演变。persimilis混合动力车。具体目的是：(1)确定lincRNA表达的遗传模式，(2)确定lincRNA调控差异是通过顺式还是反式变化发生的，以及(3)确定lincRNA是否可能是杂交不相容的基础。这项工作将是迄今为止对lincRNA进化最全面的分析，也是第一个通过杂交研究密切相关物种中lincRNA调控进化的研究。它将强调一类未被充分研究的基因的重要性，这些基因偏离了生物学的中心教条。这项资助将支持一名博士生和多名本科生的培训，并为马里兰大学少数族裔学生管道中的一名当地高中生或教师提供暑期研究经验。从这项工作中收集到的知识将在国家简报和印刷品中广泛传播。了解基因调控系统的进化为了解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。