RNA的质谱分析：连接基因组与蛋白质组
Mass spectrometry of RNA: linking the genome to the proteome.
作者信息
Meng Zhaojing, Limbach Patrick A
机构信息
Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA.
出版信息
Brief Funct Genomic Proteomic. 2006 Mar;5(1):87-95. doi: 10.1093/bfgp/ell012. Epub 2006 Feb 27.
Abstract
Ribonucleic acids (RNAs) are continuing to attract increased attention as they are found to play pivotal roles in biological systems. Just as genomics and proteomics have been enabled by the development of effective analytical techniques and instrumentation, the large-scale analysis of non-protein coding (nc)RNAs will benefit as new analytical methodologies, such as mass spectrometry (MS), are developed for their analysis. Mass spectrometry offers a number of advantages for RNA analysis arising from its ability to provide mass and sequence information starting with limited amounts of sample. This review will highlight recent developments in the field of MS that enable the characterization of RNA modification status, RNA tertiary structures, and ncRNA expression levels. These developments will also be placed in perspective of how MS of RNAs can help elucidate the link between the genome and proteome.
摘要
核糖核酸（RNAs）因其在生物系统中发挥关键作用而持续受到越来越多的关注。正如基因组学和蛋白质组学因有效分析技术和仪器的发展而得以实现一样，随着用于非蛋白质编码（nc）RNAs分析的新分析方法（如质谱（MS））的开发，对ncRNAs的大规模分析也将从中受益。质谱能够从有限量的样品开始提供质量和序列信息，这为RNA分析带来了诸多优势。本综述将重点介绍质谱领域的最新进展，这些进展能够实现对RNA修饰状态、RNA三级结构和ncRNA表达水平的表征。这些进展还将从RNA质谱如何有助于阐明基因组与蛋白质组之间的联系这一角度进行阐述。
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本文引用的文献
1
Indirect mass spectrometric methods for characterizing and sequencing oligonucleotides.间接质谱法用于寡核苷酸的特征分析和测序。
Mass Spectrom Rev. 1996;15(5):297-336. doi: 10.1002/(SICI)1098-2787(1996)15:5<297::AID-MAS2>3.0.CO;2-D.
2
Mass spectrometry of nucleic acids.核酸的质谱分析。
Mass Spectrom Rev. 1996;15(2):67-138. doi: 10.1002/(SICI)1098-2787(1996)15:2<67::AID-MAS1>3.0.CO;2-8.
3
Tandem mass spectrometry of small, multiply charged oligonucleotides.串联质谱法分析小的、多电荷寡核苷酸。
J Am Soc Mass Spectrom. 1992 Jan;3(1):60-70. doi: 10.1016/1044-0305(92)85019-G.
4
Detection of the common RNA nucleoside pseudouridine in mixtures of oligonucleotides by mass spectrometry.通过质谱法检测寡核苷酸混合物中常见的RNA核苷假尿苷。
Anal Chem. 2005 Aug 1;77(15):4687-97. doi: 10.1021/ac058023p.
5
Shotgun sequencing small oligonucleotides by nozzle-skimmer dissociation and electrospray ionization mass spectrometry.通过喷嘴-撇沫器解离和电喷雾电离质谱法对小寡核苷酸进行鸟枪法测序。
Eur J Mass Spectrom (Chichester). 2005;11(2):221-9. doi: 10.1255/ejms.736.
6
Non-coding RNAs: hope or hype?非编码RNA：希望还是炒作？
Trends Genet. 2005 May;21(5):289-97. doi: 10.1016/j.tig.2005.03.007.
7
Quantitation of ribonucleic acids using 18O labeling and mass spectrometry.使用18O标记和质谱法对核糖核酸进行定量分析。
Anal Chem. 2005 Mar 15;77(6):1891-5. doi: 10.1021/ac048801y.
8
Untying the FIV frameshifting pseudoknot structure by MS3D.通过MS3D解开猫免疫缺陷病毒移码假结结构
J Mol Biol. 2005 Jan 7;345(1):69-80. doi: 10.1016/j.jmb.2004.10.014.
9
Toward multiplexing the application of solvent accessibility probes for the investigation of RNA three-dimensional structures by electrospray ionization-Fourier transform mass spectrometry.迈向多重应用溶剂可及性探针，通过电喷雾电离-傅里叶变换质谱法研究RNA三维结构。
Anal Biochem. 2004 Nov 15;334(2):356-66. doi: 10.1016/j.ab.2004.07.034.
10
Regulation of nuclear receptor activity by a pseudouridine synthase through posttranscriptional modification of steroid receptor RNA activator.假尿苷合酶通过对类固醇受体RNA激活因子进行转录后修饰来调控核受体活性。
Mol Cell. 2004 Aug 27;15(4):549-58. doi: 10.1016/j.molcel.2004.06.044.
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