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RNA structure through multidimensional chemical mapping

机译：RNA结构通过多维化学映射

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The discoveries of myriad non-coding RNA molecules, each transiting through multiple flexible states in cells or virions, present major challenges for structure determination. Advances in high-throughput chemical mapping give new routes for characterizing entire transcriptomes in vivo, but the resulting one-dimensional data generally remain too information-poor to allow accurate de novo structure determination. Multidimensional chemical mapping (MCM) methods seek to address this challenge. Mutate-and-map (M-2), RNA interaction groups by mutational profiling (RING-MaP and MaP-2D analysis) and multiplexed center dot OH cleavage analysis (MOHCA) measure how the chemical reactivities of every nucleotide in an RNA molecule change in response to modifications at every other nucleotide. A growing body of in vitro blind tests and compensatory mutation/ rescue experiments indicate that MCM methods give consistently accurate secondary structures and global tertiary structures for ribozymes, ribosomal domains and ligand-bound riboswitch aptamers up to 200 nucleotides in length. Importantly, MCM analyses provide detailed information on structurally heterogeneous RNA states, such as ligand-free riboswitches that are functionally important but difficult to resolve with other approaches. The sequencing requirements of currently available MCM protocols scale at least quadratically with RNA length, precluding general application to transcriptomes or viral genomes at present. We propose a modify-cross-link-map (MXM) expansion to overcome this and other current limitations to resolving the in vivo 'RNA structurome'.
机译：发现无数的非编码RNA分子，每种柔性状态在细胞或病毒中的多种柔性状态，对结构测定具有主要挑战。高通量化学映射的进步提供了新的路线，用于在体内表征整个转录om，但是由此产生的一维数据通常保持过于信息差，以允许准确的De Novo结构确定。多维化学映射（MCM）方法寻求解决这一挑战。通过突变分析（环形图和MAP-2D分析）和地图（M-2），RNA相互作用基团和多路复用中心点OH切割分析（MOHCA）测量RNA分子变化中每个核苷酸的化学反垃圾响应于每种核苷酸的修饰。越来越多的体外盲试验和补偿突变/救援实验表明MCM方法赋予核酶，核糖酶，核糖体结构域和配体结合的核糖纤维活动，其长度高达200个核苷酸的全局二次结构和全球三级结构。重要的是，MCM分析提供有关结构性异质RNA状态的详细信息，例如无功能重要的核糖织物，其功能重要但难以与其他方法分辨。目前可用的MCM协议的测序要求至少与RNA长度相等，预先施加到目前的转录om或病毒基因组。我们提出了一个修改 - 交叉链接地图（MXM）扩展，以克服解决方案“RNA结构核心”的解决方案和其他当前限制。

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