NaRaDa: A comprehensive nascent RNA database

Zhibiao Mai; Duo Li; Peng Tang; Chuanman Zhou; Yongbing Zhao; Jiekai Chen; Xichen Bao

doi:10.59717/j.xinn-life.2025.100143

The Innovation Life > 2025 Vol. 3 > No. 3 > 100143

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NaRaDa: A comprehensive nascent RNA database

1.
Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine; Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
2.
Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Chinese Academy of Sciences, Hong Kong SAR, China
3.
University of Chinese Academy of Sciences, Beijing 101408, China
4.
State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
5.
China-New Zealand Joint Laboratory on Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
6.
These authors contributed equally

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Corresponding author: bao_xichen@gibh.ac.cn
Received Date: November 25, 2024

Accepted Date: June 06, 2025

Published Online: June 12, 2025

The Innovation Life 3(3), https://doi.org/10.59717/j.xinn-life.2025.100143 | Cite this article

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PUBLIC SUMMARY

PUBLIC SUMMARY
1. NaRaDa compiles and organizes 3,664 nascent RNA-seq datasets from 415 studies across 22 species.
  
  558,574 transcriptional regulatory elements (TREs) across different species have been identified for browsing.
  
  NaRaDa also provides in-depth analysis of biological processes or events to study the transcriptional regulation.

ABSTRACT

ABSTRACT

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 Nascent RNA database (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.

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Mai Z., Li D., Tang P., et al. (2025). NaRaDa: A comprehensive nascent RNA database. The Innovation Life 3:100143. https://doi.org/10.59717/j.xinn-life.2025.100143

Mai Z., Li D., Tang P., et al. (2025). NaRaDa: A comprehensive nascent RNA database. The Innovation Life 3:100143. https://doi.org/10.59717/j.xinn-life.2025.100143

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NaRaDa: A comprehensive nascent RNA database

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