Integrative analysis of somatic mutations in non-coding regions altering RNA secondary structures in cancer genomes
- Author(s)
- He, F; Wei, R; Zhou, Z; Huang, L; Wang, Y; Tang, J; Zou, Y; Shi, L; Gu, X; Davis, MJ; Su, Z;
- Details
- Publication Year 2019-06-03,Volume 9,Issue #1,Page 8205
- Journal Title
- Scientific Reports
- Publication Type
- Journal Article
- Abstract
- RNA secondary structure may influence many cellular processes, including RNA processing, stability, localization, and translation. Single-nucleotide variations (SNVs) that alter RNA secondary structure, referred to as riboSNitches, are potentially causative of human diseases, especially in untranslated regions (UTRs) and noncoding RNAs (ncRNAs). The functions of somatic mutations that act as riboSNitches in cancer development remain poorly understood. In this study, we developed a computational pipeline called SNIPER (riboSNitch-enriched or depleted elements in cancer genomes), which employs MeanDiff and EucDiff to detect riboSNitches and then identifies riboSNitch-enriched or riboSNitch-depleted non-coding elements across tumors. SNIPER is available at github: https://github.com/suzhixi/SNIPER/ . We found that riboSNitches were more likely to be pathogenic. Moreover, we predicted several UTRs and lncRNAs (long non-coding RNA) that significantly enriched or depleted riboSNitches in cancer genomes, indicative of potential cancer driver or essential noncoding elements. Our study highlights the possibly neglected importance of RNA secondary structure in cancer genomes and provides a new strategy to identify new cancer-associated genes.
- Publisher
- Springer Nature
- Research Division(s)
- Bioinformatics
- PubMed ID
- 31160636
- Publisher's Version
- https://doi.org/10.1038/s41598-019-44489-5
- Open Access at Publisher's Site
https://doi.org/10.1038/s41598-019-44489-5- Terms of Use/Rights Notice
- Refer to copyright notice on published article.
Creation Date: 2019-06-14 09:36:57
Last Modified: 2019-06-14 11:04:42