Numerous various databases worldwide collate information on the growing number of long non-coding RNAs (lncRNAs) that have been extensively characterized in several species. In this Comment, we overview the types and features of lncRNA databases, and discuss their contribution to facing challenges and seizing opportunities in lncRNA research.
This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$189.00 per year
only $15.75 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
References
Frankish, A. et al. GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Res 51, D942–D949 (2023).
Hon, C. C. et al. An atlas of human long non-coding RNAs with accurate 5’ ends. Nature 543, 199–204 (2017).
Iyer, M. K. et al. The landscape of long noncoding RNAs in the human transcriptome. Nat. Genet. 47, 199–208 (2015).
Zhao, L. et al. NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants. Nucleic Acids Res. 49, D165–D171 (2021).
Li, Z. et al. LncBook 2.0: integrating human long non-coding RNAs with multi-omics annotations. Nucleic Acids Res. 51, D186–D191 (2023).
RNAcentral Consortium. RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. Nucleic Acids Res. 49, D212–D220 (2021).
Li, J. et al. TANRIC: an interactive open platform to explore the function of lncRNAs in cancer. Cancer Res. 75, 3728–3737 (2015).
Li, J. H., Liu, S., Zhou, H., Qu, L. H. & Yang, J. H. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 42, D92–D97 (2014).
Bao, Z. et al. LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases. Nucleic Acids Res. 47, D1034–D1037 (2019).
Liu, L. et al. LncRNAWiki 2.0: a knowledgebase of human long non-coding RNAs with enhanced curation model and database system. Nucleic Acids Res. 50, D190–D195 (2022).
Acknowledgements
We apologize to all those database authors whose publications are not cited here owing to limited space. This work was supported by Strategic Priority Research Program of the Chinese Academy of Sciences (XDB38030400); Youth Innovation Promotion Association of Chinese Academy of Sciences (2019104); the National Natural Science Foundation of China (32030021).
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Competing interests
The authors declare no competing interests.
Supplementary information
Rights and permissions
About this article
Cite this article
Ma, L., Zhang, Z. The contribution of databases towards understanding the universe of long non-coding RNAs. Nat Rev Mol Cell Biol 24, 601–602 (2023). https://doi.org/10.1038/s41580-023-00612-z
Published:
Issue Date:
DOI: https://doi.org/10.1038/s41580-023-00612-z
