Multidimensional conservation analysis decodes the expression of conserved long noncoding RNAs

Qiuzhong Zhou, Yuxi Jiang, Chaoqun Cai, Wen Li, Melvin Khee Shing Leow, Yi Yang, Jin Liu, Dan Xu, Lei Sun

Research output: Contribution to journalArticlepeer-review


Although long noncoding RNAs (lncRNAs) experience weaker evolutionary constraints and exhibit lower sequence conservation than coding genes, they can still conserve their features in various aspects. Here, we used multiple approaches to systemically evaluate the conservation between human and mouse lncRNAs from various dimensions including sequences, promoter, global synteny, and local synteny, which led to the identification of 1,731 conserved lncRNAs with 427 high-confidence ones meeting multiple criteria. Conserved lncRNAs, compared with non-conserved ones, generally have longer gene bodies, more exons and transcripts, stronger connections with human diseases, and are more abundant and widespread across different tissues. Transcription factor (TF) profile analysis revealed a significant enrichment of TF types and numbers in the promoters of conserved lncRNAs. We further identified a set of TFs that preferentially bind to conserved lncRNAs and exert stronger regulation on conserved than non-conserved lncRNAs. Our study has reconciled some discrepant interpretations of lncRNA conservation and revealed a new set of transcriptional factors ruling the expression of conserved lncRNAs.

Original languageEnglish (US)
Article numbere202302002
JournalLife science alliance
Issue number6
StatePublished - Jun 2023
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2023 Zhou et al.


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