Characterization of Small Silencing RNAs in Emiliania Huxleyi

描述（由申请人提供）：颗石藻是海洋植物，产生优雅雕刻的碳酸钙细胞覆盖物，称为颗石藻。Emiliania huxleyi（E. Huxleyi）是具有与骨形成和疾病相关的潜在生物医学应用的模式颗石藻。小分子沉默RNA（smRNA）在真核生物的转录后基因调控中起着重要作用，从单细胞到多细胞的植物和动物都有。小RNA参与了多种细胞过程，这些过程对基因组稳定性、发育和对环境压力的适应性反应至关重要。这些天然的smRNA沉默过程也称为RNA干扰，通过触发mRNA的酶促切割来抑制蛋白质表达。smRNA过程的特异性已被用于基因功能的系统分析和潜在的治疗目的。微小RNA（miRNAs）和小干扰RNA（siRNAs）是植物中已知的两大类smRNAs。目前对smRNAs及其在大肠杆菌中的调控作用知之甚少。huxleyi。这项研究的具体假设是E. huxleyi含有小RNA，如miRNA和siRNA，它们通过RNA沉默调节靶基因。最近发布的E. huxleyi基因组和E. huxleyi的结果，使得系统地表征smRNAs及其在E. huxleyi。初步的研究显示了在大肠杆菌中存在miRNAs的有力证据。huxleyi。我们在此建议，以表征小RNA在E。huxleyi利用计算方法，结合实验验证。具体而言，我们建议1）鉴定和表征大肠杆菌中的miRNA前体和成熟miRNA。huxleyi通过计算分析短RNA序列; 2）计算预测和表征E. huxleyi miRNAs，并通过实验验证预测结果; 3）鉴定和表征大肠杆菌中的siRNAs和其他类型的小RNA。huxleyi。据我们所知，这项研究将是第一个系统分析smRNAs在E。huxleyi，并因此将提供重要的见解转录后基因调控在这个microarray。

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.