Characterization of Small Silencing RNAs in Emiliania Huxleyi

描述（由申请人提供）：球石藻是一种海洋浮游植物，可以产生优雅的雕刻碳酸钙细胞覆盖物，称为球石藻。huxleyi Emiliania huxleyi （E. huxleyi）是一种典型的球石属植物，在骨形成和疾病方面具有潜在的生物医学应用。已知小沉默rna （smrna）在许多真核生物（从单细胞到多细胞植物和动物）的转录后基因调控中起关键作用。小rna参与多种细胞过程，这些过程对基因组的稳定、发育和对环境胁迫的适应性反应至关重要。这些天然的smRNA沉默过程也被称为RNA干扰，通过触发mrna的酶切来抑制蛋白质表达。smRNA过程的特异性已被用于基因功能和潜在治疗目的的系统分析。MicroRNAs （miRNAs）和小干扰rna （sirna）是植物中已知的两大类smrna。目前对smrna及其在赫胥黎氏杆菌中的调控作用知之甚少。这项研究提出的具体假设是，赫胥黎肠杆菌含有小RNA，如mirna和sirna，它们通过RNA沉默来调节靶基因。最近，联合基因组研究所（JGI）发布了赫胥黎大肠杆菌基因组，并利用高通量Solexa测序生成了大量赫胥黎大肠杆菌小rna数据集，这使得系统表征赫胥黎大肠杆菌的smrna及其调控作用成为可能。初步研究有力地证明了huxleyi中存在microrna。在此，我们建议使用计算方法结合实验验证来表征赫胥黎氏杆菌的小rna。具体而言，我们建议1)通过计算分析短RNA序列来鉴定赫胥黎的miRNA前体和成熟miRNA；2)计算预测和表征赫胥黎E. mirna的靶点，并用实验证据验证预测；3)鉴定和表征赫胥黎氏杆菌的sirna和其他小rna。据我们所知，这项拟议的研究将是赫胥黎E. smRNAs的第一个系统分析，因此将为这种微藻的转录后基因调控提供重要的见解。

DESCRIPTION (provided by applicant): Coccolithophorids are marine phytoplanktons that produce elegantly sculptured calcium carbonate cell coverings known as coccoliths. Emiliania huxleyi (E. huxleyi) is a model coccolithophorid that has potential biomedical applications related to bone formation and diseases. Small silencing RNAs (smRNAs) are known to play a pivotal role in post transcriptional gene regulation in many eukaryotes, from unicellular to multicellular plants and animals. Small RNAs are involved in a variety of cellular processes that are essential to genome stability, development, and adaptive responses to environmental stress. These natural smRNA silencing processes otherwise known as RNA interference, suppress protein expression by triggering the enzymatic cleavage of mRNAs. The specificity of smRNA processes has been exploited for the systematic analysis of gene functions and potential therapeutic purposes. MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are two major classes of smRNAs known in plants. Very little is currently known about smRNAs and their regulatory roles in E. huxleyi. The specific hypothesis underlying this proposed research is that E. huxleyi contains small RNAs such as miRNAs and siRNAs, which regulate target genes through RNA silencing. The recent release of the E. huxleyi genome by the Joint Genome Institute (JGI) and a large dataset of small RNAs of E. huxleyi generated using high-throughput Solexa sequencing, make it feasible to systematically characterize smRNAs and their regulatory roles in E. huxleyi. Preliminary studies show strong evidence for the existence of miRNAs in E. huxleyi. We propose herein to characterize small RNAs in E. huxleyi using computational methods, combined with experimental validation. Specifically, we propose to 1) identify and characterize miRNA precursors and mature miRNAs in E. huxleyi by computationally analyzing the short RNA sequences; 2) computationally predict and characterize targets of E. huxleyi miRNAs and validate the predictions with experimental evidences; and 3) identify and characterize siRNAs and other classes of small RNAs in E. huxleyi. To our knowledge, this proposed research will be the first systemic analysis of smRNAs in E. huxleyi, and as such will provide important insights into post-transcriptional gene regulation in this microalga. PUBLIC HEALTH RELEVANCE: Coccolithophorids are presently being investigated by the biotechnology industry as a potential source for new pharmaceuticals, omega-3 fatty acids, biofuel, and polysaccharides. They also have important implications for human health in terms of understanding the process of calcification as it relates to bone disease, kidney stones, and heart disease. Insights into smRNA controlled gene regulation in E. huxleyi may lead to a better understanding of the fundamental biology of this important microcalcifier, which may offer new strategies to promote healthy biomineralization and mitigate calcification associated with disease states.