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在体内对RNA二次结构的全基因组分析揭示了新的调节特征
Yiliang Ding1, Yin Tang2, Chun Kit Kwok3
11] Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA [2] Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA [3] Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA [4].
Nature
|November 26, 2013
概括
我们开发了structure-seq,这是一种新的方法,可以在全基因组范围内绘制活细胞中的RNA结构. 这揭示了RNA结构如何影响植物的基因表达,翻译和应激反应.
科学领域:
- 分子生物学分子生物学
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
背景情况:
- RNA结构在基因表达调节中起着至关重要的作用,包括翻译,多化和拼接.
- 有限的全基因组 in vivo RNA 结构数据阻碍了对活细胞中 RNA 的调节功能的理解.
研究的目的:
- 开发和应用一种高通量方法,用于全基因组的活体RNA结构映射.
- 为了生成第一个核酸分辨率在体内RNA结构图的Arabidopsis thaliana.
- 研究RNA结构和基因表达之间的关系,包括翻译效率,替代多基化,拼接和应激反应.
主要方法:
- 开发结构-seq,一种使用二甲基硫酸盐 (DMS) 甲基化的高通量方法,以在体内探测RNA结构.
- 下一代测序用于识别甲基基 (腺素和细胞素).
- 应用于Arabidopsis thaliana幼苗,以生成全基因组RNA结构图.
主要成果:
- 产生了任何生物体的核酸分辨率的第一个全基因组 in vivo RNA 结构图,覆盖了超过 10,000 个转录.
- 确定了编码区域中的三核酸周期重复和起始编码子上游的结构较差的区域,与翻译效率相关.
- 在替代多基化位点和5'拼接位点观察到不同的结构模式,与多基化和拼接事件相关.
- 发现压力反应mRNAs的体内RNA结构在silico中预测不佳,并表现出可能使形状变化的特征 (单链,更长的循环,更高的自由能量).
结论:
- 结构-seq提供了一种强大的工具,可以在全基因组范围内查询RNA结构和其生物功能.
- 在体内RNA结构显著影响关键的基因表达过程和细胞反应,特别是应激反应.
- 该方法在不同生物体中广泛适用于研究RNA结构和功能.
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