Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China.
Department of Epidemiology and Biostatistics and Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P.R. China.
Nucleic Acids Res. 2022 Jan 7;50(D1):D46-D53. doi: 10.1093/nar/gkab832.
Enhancer RNAs (eRNAs) are a class of non-coding RNAs transcribed from enhancers. As the markers of active enhancers, eRNAs play important roles in gene regulation and are associated with various complex traits and characteristics. With increasing attention to eRNAs, numerous eRNAs have been identified in different human tissues. However, the expression landscape, regulatory network and potential functions of eRNAs in animals have not been fully elucidated. Here, we systematically characterized 185 177 eRNAs from 5085 samples across 10 species by mapping the RNA sequencing data to the regions of known enhancers. To explore their potential functions based on evolutionary conservation, we investigated the sequence similarity of eRNAs among multiple species. In addition, we identified the possible associations between eRNAs and transcription factors (TFs) or nearby genes to decipher their possible regulators and target genes, as well as characterized trait-related eRNAs to explore their potential functions in biological processes. Based on these findings, we further developed Animal-eRNAdb (http://gong_lab.hzau.edu.cn/Animal-eRNAdb/), a user-friendly database for data searching, browsing and downloading. With the comprehensive characterization of eRNAs in various tissues of different species, Animal-eRNAdb may greatly facilitate the exploration of functions and mechanisms of eRNAs.
增强子 RNA（eRNAs）是一类从增强子转录而来的非编码 RNA。作为活性增强子的标记物，eRNAs 在基因调控中发挥着重要作用，并与多种复杂的性状和特征相关。随着对 eRNAs 的关注度不断提高，在不同的人类组织中已经鉴定出了大量的 eRNAs。然而，eRNAs 在动物中的表达谱、调控网络和潜在功能尚未得到充分阐明。在这里，我们通过将 RNA 测序数据映射到已知增强子区域，系统地描述了 10 个物种的 5085 个样本中的 185177 个 eRNAs。为了基于进化保守性探索它们的潜在功能，我们研究了多个物种之间 eRNAs 的序列相似性。此外，我们确定了 eRNAs 与转录因子（TFs）或附近基因之间可能的关联，以破译它们可能的调控因子和靶基因，并对与性状相关的 eRNAs 进行了特征描述，以探索它们在生物学过程中的潜在功能。基于这些发现，我们进一步开发了一个用户友好的数据库 Animal-eRNAdb（http://gong_lab.hzau.edu.cn/Animal-eRNAdb/），用于数据搜索、浏览和下载。通过对不同物种不同组织中的 eRNAs 进行全面描述，Animal-eRNAdb 可能极大地促进了对 eRNAs 功能和机制的探索。
