POSTAR3: an updated platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins.
POSTAR3: an updated platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins.
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POSTAR3：用于探索 RNA 结合蛋白协调的转录后调控的更新平台
DOI：
10.1093/nar/gkab702
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发表时间：
2022-01-07
影响因子：
14.9
通讯作者：
Lu ZJ
中科院分区：
文献类型：
--
作者：
Zhao W;Zhang S;Zhu Y;Xi X;Bao P;Ma Z;Kapral TH;Chen S;Zagrovic B;Yang YT;Lu ZJ
摘要RNA结合蛋白（RBP）在转录后调控中起着重要作用。准确鉴定RBP结合位点在多个细胞系和不同物种的组织类型是一个基本的奋进，了解RBP的调节机制，在生理和病理条件下。我们的POSTAR注释过程利用公开可用的大规模CLIP-seq数据集和外部功能基因组注释来生成RBP结合位点及其与其他调节事件以及功能变体的关联的全面地图。在这里，我们介绍了POSTAR 3，一个更新的数据库，在数据收集，注释基础设施和分析方面进行了改进，支持多个物种中转录后调控的注释，包括：我们对CLIP-seq和Ribo-seq数据集进行了全面更新，涵盖了更多的生物条件，技术和物种;我们增加了RBP结合位点的RNA二级结构分析;我们提供了通过degradome-seq验证的miRNA介导的降解事件;我们在circRNA连接区域包括RBP结合位点;我们扩展了RBP结合位点的注释，特别是使用更新的基因组变体和与疾病相关的突变。POSTAR 3可在http://postar.ncrnalab.org上免费获得。
Abstract RNA-binding proteins (RBPs) play key roles in post-transcriptional regulation. Accurate identification of RBP binding sites in multiple cell lines and tissue types from diverse species is a fundamental endeavor towards understanding the regulatory mechanisms of RBPs under both physiological and pathological conditions. Our POSTAR annotation processes make use of publicly available large-scale CLIP-seq datasets and external functional genomic annotations to generate a comprehensive map of RBP binding sites and their association with other regulatory events as well as functional variants. Here, we present POSTAR3, an updated database with improvements in data collection, annotation infrastructure, and analysis that support the annotation of post-transcriptional regulation in multiple species including: we made a comprehensive update on the CLIP-seq and Ribo-seq datasets which cover more biological conditions, technologies, and species; we added RNA secondary structure profiling for RBP binding sites; we provided miRNA-mediated degradation events validated by degradome-seq; we included RBP binding sites at circRNA junction regions; we expanded the annotation of RBP binding sites, particularly using updated genomic variants and mutations associated with diseases. POSTAR3 is freely available at http://postar.ncrnalab.org.
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