NapRNAdb: a multispecies repository and analytical platform for napRNA discovery and functional annotation

Nucleic Acids Res. 2025 Nov 3:gkaf1100. doi: 10.1093/nar/gkaf1100. Online ahead of print.

ABSTRACT

Over 75% of the human genome transcribes noncapped RNAs (napRNAs), which typically function as noncoding RNAs in gene expression regulation. While short napRNAs (e.g. small RNAs) have well-defined transcriptomic roles, long napRNAs with diverse terminal modifications remain poorly characterized. To advance research, we developed NapRNAdb (https://bioinformaticsscience.cn/naprnadb), the first database dedicated to NAP-seq-derived napRNAs, enabling cross-species napRNA transcriptome profiling (40 species). This resource integrates 30 708 napRNAs derived from human and mouse NAP-seq with their expression profiles in multiple biological models, comprising 1016 ACA-napRNAs, 297 CD-napRNAs, 2302 Pol3-napRNAs, 157 polyA-pocket-ACA-napRNAs, 1536 stably expressed linear intron RNAs, 57 small nucleolar RNAs (snoRNAs)-intron napRNAs, 55 microRNA spacer-embedded RNAs, and 25 288 others. Leveraging evolutionary conservation analysis, NapRNAdb cost-effectively identifies 197 345 napRNAs spanning 8 categories in 38 species, with secondary structure and cross-species conservation for each molecule. Critically, NapRNAdb delivers the "PreTool" module for efficiently evaluating target sequence potential for napRNA processing via sequence similarity analysis. It also supports gene queries to verify participation in napRNA formation. Additionally, it systematically deciphers interaction networks linking napRNAs to RNA modifications, RNA-binding proteins, and disease-associated single nucleotide variants. Overall, NapRNAdb provides interactive interfaces to explore transcriptional, structural, expressional, and functional landscapes for napRNAs, facilitating comprehensive dissection of their biology while accelerating mechanistic insights into this field.

PMID:41182820 | DOI:10.1093/nar/gkaf1100