Defining the single base importance of human mRNAs and lncRNAs.

Abstract

As the fundamental unit of a gene and its transcripts, nucleotides have enormous impacts on the gene function and evolution, and thus on phenotypes and diseases. In order to identify the key nucleotides of one specific gene, it is quite crucial to quantitatively measure the importance of each base on the gene. However, there are still no sequence-based methods of doing that. Here, we proposed Base Importance Calculator (BIC), an algorithm to calculate the importance score of each single base based on sequence information of human mRNAs and long noncoding RNAs (lncRNAs). We then confirmed its power by applying BIC to three different tasks. Firstly, we revealed that BIC can effectively evaluate the pathogenicity of both genes and single bases through single nucleotide variations. Moreover, the BIC score in The Cancer Genome Atlas somatic mutations is able to predict the prognosis of some cancers. Finally, we show that BIC can also precisely predict the transmissibility of SARS-CoV-2. The above results indicate that BIC is a useful tool for evaluating the single base importance of human mRNAs and lncRNAs.

• Authors: Rui Fan, Xiangwen Ji, Jianwei Li, Qinghua Cui, Chunmei Cui
• Journal: Briefings in bioinformatics (Brief Bioinform) Vol. 24 Issue 5 (09 20 2023) ISSN: 1477-4054 [Electronic] England
• PMID: 37668090 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)
• Copyright: © The Author(s) 2023. Published by Oxford University Press. All rights reserved. For Permissions, please email: [email protected].

Chemical References

• RNA, Long Noncoding
• Nucleotides
• RNA, Messenger

Topics

• Humans
• COVID-19 (genetics)
• RNA, Long Noncoding (genetics)
• SARS-CoV-2 (genetics)
• Algorithms
• Nucleotides
• RNA, Messenger (genetics)