MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Fifth Affiliated Hospital, Sun Yat-sen University, Guangdong, Guangzhou 510275, P.R. China.
Nucleic Acids Res. 2022 Jan 7;50(D1):D279-D286. doi: 10.1093/nar/gkab1033.
RNA polymerase III (Pol III) transcribes hundreds of non-coding RNA genes (ncRNAs), which involve in a variety of cellular processes. However, the expression, functions, regulatory networks and evolution of these Pol III-transcribed ncRNAs are still largely unknown. In this study, we developed a novel resource, Pol3Base (http://rna.sysu.edu.cn/pol3base/), to decode the interactome, expression, evolution, epitranscriptome and disease variations of Pol III-transcribed ncRNAs. The current release of Pol3Base includes thousands of regulatory relationships between ∼79 000 ncRNAs and transcription factors by mining 56 ChIP-seq datasets. By integrating CLIP-seq datasets, we deciphered the interactions of these ncRNAs with >240 RNA binding proteins. Moreover, Pol3Base contains ∼9700 RNA modifications located within thousands of Pol III-transcribed ncRNAs. Importantly, we characterized expression profiles of ncRNAs in >70 tissues and 28 different tumor types. In addition, by comparing these ncRNAs from human and mouse, we revealed about 4000 evolutionary conserved ncRNAs. We also identified ∼11 403 tRNA-derived small RNAs (tsRNAs) in 32 different tumor types. Finally, by analyzing somatic mutation data, we investigated the mutation map of these ncRNAs to help uncover their potential roles in diverse diseases. This resource will help expand our understanding of potential functions and regulatory networks of Pol III-transcribed ncRNAs.
RNA 聚合酶 III（Pol III）转录了数百个非编码 RNA 基因（ncRNAs），这些基因参与了多种细胞过程。然而，这些 Pol III 转录的 ncRNAs 的表达、功能、调控网络和进化仍然在很大程度上未知。在这项研究中，我们开发了一个新的资源 Pol3Base（http://rna.sysu.edu.cn/pol3base/），以解码 Pol III 转录的 ncRNAs 的互作组、表达、进化、表观转录组和疾病变异。目前的 Pol3Base 版本包括通过挖掘 56 个 ChIP-seq 数据集，鉴定出约 79000 个 ncRNA 与转录因子之间的数千种调控关系。通过整合 CLIP-seq 数据集，我们解析了这些 ncRNA 与>240 种 RNA 结合蛋白的相互作用。此外，Pol3Base 还包含了位于数千个 Pol III 转录的 ncRNA 内的约 9700 个 RNA 修饰。重要的是，我们描绘了 ncRNAs 在>70 种组织和 28 种不同肿瘤类型中的表达谱。此外，通过比较人类和小鼠的这些 ncRNAs，我们揭示了约 4000 个进化保守的 ncRNAs。我们还在 32 种不同的肿瘤类型中鉴定到了约 11403 个 tRNA 衍生的小 RNA（tsRNAs）。最后，通过分析体细胞突变数据，我们研究了这些 ncRNAs 的突变图谱，以帮助揭示它们在多种疾病中的潜在作用。这个资源将有助于我们扩展对 Pol III 转录的 ncRNAs 的潜在功能和调控网络的理解。
