MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
Nucleic Acids Res. 2021 Jan 8;49(D1):D183-D191. doi: 10.1093/nar/gkaa880.
RNA molecules fold into complex structures that are important across many biological processes. Recent technological developments have enabled transcriptome-wide probing of RNA secondary structure using nucleases and chemical modifiers. These approaches have been widely applied to capture RNA secondary structure in many studies, but gathering and presenting such data from very different technologies in a comprehensive and accessible way has been challenging. Existing RNA structure probing databases usually focus on low-throughput or very specific datasets. Here, we present a comprehensive RNA structure probing database called RASP (RNA Atlas of Structure Probing) by collecting 161 deduplicated transcriptome-wide RNA secondary structure probing datasets from 38 papers. RASP covers 18 species across animals, plants, bacteria, fungi, and also viruses, and categorizes 18 experimental methods including DMS-seq, SHAPE-Seq, SHAPE-MaP, and icSHAPE, etc. Specially, RASP curates the up-to-date datasets of several RNA secondary structure probing studies for the RNA genome of SARS-CoV-2, the RNA virus that caused the on-going COVID-19 pandemic. RASP also provides a user-friendly interface to query, browse, and visualize RNA structure profiles, offering a shortcut to accessing RNA secondary structures grounded in experimental data. The database is freely available at http://rasp.zhanglab.net.
RNA 分子折叠成复杂的结构，这些结构在许多生物过程中都很重要。最近的技术发展使使用核酸酶和化学修饰剂对转录组范围内的 RNA 二级结构进行探测成为可能。这些方法已广泛应用于许多研究中以捕获 RNA 二级结构，但以综合且易于访问的方式从非常不同的技术中收集和呈现此类数据一直具有挑战性。现有的 RNA 结构探测数据库通常侧重于低通量或非常特定的数据集。在这里，我们通过收集 38 篇论文中的 161 个去重的转录组范围的 RNA 二级结构探测数据集，创建了一个名为 RASP（RNA 结构探测图谱）的综合 RNA 结构探测数据库。RASP 涵盖了 18 个跨越动物、植物、细菌、真菌和病毒的物种，并对 18 种实验方法进行了分类，包括 DMS-seq、SHAPE-Seq、SHAPE-MaP 和 icSHAPE 等。特别地，RASP 为导致当前 COVID-19 大流行的 RNA 病毒 SARS-CoV-2 的 RNA 基因组的几个 RNA 二级结构探测研究整理了最新的数据集。RASP 还提供了一个用户友好的界面，用于查询、浏览和可视化 RNA 结构谱，为访问基于实验数据的 RNA 二级结构提供了捷径。该数据库可在 http://rasp.zhanglab.net 免费获取。
