Characterization of the Small RNA Transcriptome of the Marine Coccolithophorid, Emiliania huxleyi.
Characterization of the Small RNA Transcriptome of the Marine Coccolithophorid, Emiliania huxleyi.
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DOI：
10.1371/journal.pone.0154279
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发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Read BA
中科院分区：
文献类型：
--
作者：
Zhang X;Gamarra J;Castro S;Carrasco E;Hernandez A;Mock T;Hadaegh AR;Read BA
小rna （smrna）通过在转录或转录后水平沉默靶基因来控制多种细胞过程。虽然在植物中进行了广泛的研究，但对海洋浮游植物（如Emiliania huxleyi）中的smrna及其靶点知之甚少。在批量培养中，赫胥黎细胞从对数生长阶段过渡到固定生长阶段，对不同时间点提取的smrna进行深度测序。计算分析预测了18个E. huxleyi特异性mirna。这18个候选miRNA及其前体在长度（分别为18 - 24nt和71 - 252nt）、基因组拷贝数（3 - 1459）和靶向基因数（2-107）方面存在差异。茎环实时逆转录酶（RT） PCR用于验证miRNA表达，当生长减慢和细胞进入固定期时，miRNA表达变化近三个数量级。茎环RT PCR还用于检测钙化和非钙化培养物中miRNA的表达谱，发现当营养变得有限和钙化增强时，一小部分miRNA的表达存在差异。除了miRNAs，内源性小rna如ra- sirna、ta- sirna、nat- sirna和piwiRNAs也被预测与si- rna的生物发生和加工机制一起。本研究首次对赫胥黎氏杆菌的smRNAs通路进行全基因组研究。研究结果为smrna在调节海洋浮游植物生理生长和适应方面的重要性提供了新的见解，并进一步挑战了smrna随多细胞进化的概念，扩展了我们对这些古老调控途径的看法。
Small RNAs (smRNAs) control a variety of cellular processes by silencing target genes at the transcriptional or post-transcription level. While extensively studied in plants, relatively little is known about smRNAs and their targets in marine phytoplankton, such as Emiliania huxleyi (E. huxleyi). Deep sequencing was performed of smRNAs extracted at different time points as E. huxleyi cells transition from logarithmic to stationary phase growth in batch culture. Computational analyses predicted 18 E. huxleyi specific miRNAs. The 18 miRNA candidates and their precursors vary in length (18–24 nt and 71–252 nt, respectively), genome copy number (3–1,459), and the number of genes targeted (2–107). Stem-loop real time reverse transcriptase (RT) PCR was used to validate miRNA expression which varied by nearly three orders of magnitude when growth slows and cells enter stationary phase. Stem-loop RT PCR was also used to examine the expression profiles of miRNA in calcifying and non-calcifying cultures, and a small subset was found to be differentially expressed when nutrients become limiting and calcification is enhanced. In addition to miRNAs, endogenous small RNAs such as ra-siRNAs, ta-siRNAs, nat-siRNAs, and piwiRNAs were predicted along with the machinery for the biogenesis and processing of si-RNAs. This study is the first genome-wide investigation smRNAs pathways in E. huxleyi. Results provide new insights into the importance of smRNAs in regulating aspects of physiological growth and adaptation in marine phytoplankton and further challenge the notion that smRNAs evolved with multicellularity, expanding our perspective of these ancient regulatory pathways.