NaRaDa: A comprehensive nascent RNA database

<p>Nascent RNA-seq is pivotal for elucidating the dynamics and transcriptional regulation of enhancer RNA and protein-coding genes, and for revealing the regulatory linkages between enhancer-gene pairs in diverse physiological and pathological contexts. However, despite the rapid growth of nascent RNA-seq datasets, a comprehensive database for the collection and analysis of these datasets remains absent. Here, we developed the <i>Na</i>scent <i>R</i>N<i>A</i> <i>da</i>tabase (NaRaDa, http://www.narada.bio), which compiles and categorizes 3,664 global or precision run-on sequencing (GRO/PRO-seq) datasets from 415 studies across 22 species. NaRaDa provides a user-friendly interface for searching, visualizing, and assessing the quality of integrated GRO/PRO-seq datasets. Furthermore, NaRaDa identifies transcriptional regulatory elements (TREs) along with other annotation information from ENCODE, FANTOM5, and disease-associated risk SNPs, which are accessible by either “Gene-Centric” or “Project ID-Centric” modes. The database also furnishes researchers with web-based tools to identify differentially expressed genes, TREs, transcription pausing index changes, and more importantly, potential functional transcription factors, in response to specific treatments. These results can be readily downloaded for further independent analysis. NaRaDa serves as an invaluable resource for deepening our understanding of the regulatory mechanisms governing transcription and for identifying previously unrecognized correlations between genomic loci and diseases.</p>