Comprehensive Pan-Cancer Mutation Density Patterns in Enhancer RNA
Significant advances have been achieved in understanding the critical role of enhancer RNAs (eRNAs) in the complex field of gene regulation. However, notable uncertainty remains concerning the biology of eRNAs, highlighting the need for continued research to uncover their exact functions in cellular...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-12-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/25/1/534 |
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| author | Troy Zhang Hui Yu Limin Jiang Yongsheng Bai Xiaoyi Liu Yan Guo |
| author_facet | Troy Zhang Hui Yu Limin Jiang Yongsheng Bai Xiaoyi Liu Yan Guo |
| author_sort | Troy Zhang |
| collection | DOAJ |
| description | Significant advances have been achieved in understanding the critical role of enhancer RNAs (eRNAs) in the complex field of gene regulation. However, notable uncertainty remains concerning the biology of eRNAs, highlighting the need for continued research to uncover their exact functions in cellular processes and diseases. We present a comprehensive study to scrutinize mutation density patterns, mutation strand bias, and mutation burden in eRNAs across multiple cancer types. Our findings reveal that eRNAs exhibit mutation strand bias akin to that observed in protein-coding RNAs. We also identified a novel pattern, in which mutation density is notably diminished around the central region of the eRNA, but conspicuously elevated towards both the beginning and end. This pattern can be potentially explained by a mechanism involving heightened transcriptional activity and the activation of transcription-coupled repair. The central regions of the eRNAs appear to be more conserved, hinting at a potential mechanism preserving their structural and functional integrity, while the extremities may be more susceptible to mutations due to increased exposure. The evolutionary trajectory of this mutational pattern suggests a nuanced adaptation in eRNAs, where stability at their core coexists with flexibility at their extremities, potentially facilitating their diverse interactions with other genetic entities. |
| first_indexed | 2024-03-08T15:04:48Z |
| format | Article |
| id | doaj.art-bb64c37349804ad9948d70d7404cb757 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-08T15:04:48Z |
| publishDate | 2023-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-bb64c37349804ad9948d70d7404cb7572024-01-10T14:59:52ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-12-0125153410.3390/ijms25010534Comprehensive Pan-Cancer Mutation Density Patterns in Enhancer RNATroy Zhang0Hui Yu1Limin Jiang2Yongsheng Bai3Xiaoyi Liu4Yan Guo5Department of Public Health and Sciences, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, USADepartment of Public Health and Sciences, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, USADepartment of Public Health and Sciences, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, USADepartment of Biology, Eastern Michigan University, Ypsilanti, MI 48197, USADepartment of Computer Science, University of South Carolina, Columbia, SC 29208, USADepartment of Public Health and Sciences, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, USASignificant advances have been achieved in understanding the critical role of enhancer RNAs (eRNAs) in the complex field of gene regulation. However, notable uncertainty remains concerning the biology of eRNAs, highlighting the need for continued research to uncover their exact functions in cellular processes and diseases. We present a comprehensive study to scrutinize mutation density patterns, mutation strand bias, and mutation burden in eRNAs across multiple cancer types. Our findings reveal that eRNAs exhibit mutation strand bias akin to that observed in protein-coding RNAs. We also identified a novel pattern, in which mutation density is notably diminished around the central region of the eRNA, but conspicuously elevated towards both the beginning and end. This pattern can be potentially explained by a mechanism involving heightened transcriptional activity and the activation of transcription-coupled repair. The central regions of the eRNAs appear to be more conserved, hinting at a potential mechanism preserving their structural and functional integrity, while the extremities may be more susceptible to mutations due to increased exposure. The evolutionary trajectory of this mutational pattern suggests a nuanced adaptation in eRNAs, where stability at their core coexists with flexibility at their extremities, potentially facilitating their diverse interactions with other genetic entities.https://www.mdpi.com/1422-0067/25/1/534enhancer RNAmutationmutation density |
| spellingShingle | Troy Zhang Hui Yu Limin Jiang Yongsheng Bai Xiaoyi Liu Yan Guo Comprehensive Pan-Cancer Mutation Density Patterns in Enhancer RNA International Journal of Molecular Sciences enhancer RNA mutation mutation density |
| title | Comprehensive Pan-Cancer Mutation Density Patterns in Enhancer RNA |
| title_full | Comprehensive Pan-Cancer Mutation Density Patterns in Enhancer RNA |
| title_fullStr | Comprehensive Pan-Cancer Mutation Density Patterns in Enhancer RNA |
| title_full_unstemmed | Comprehensive Pan-Cancer Mutation Density Patterns in Enhancer RNA |
| title_short | Comprehensive Pan-Cancer Mutation Density Patterns in Enhancer RNA |
| title_sort | comprehensive pan cancer mutation density patterns in enhancer rna |
| topic | enhancer RNA mutation mutation density |
| url | https://www.mdpi.com/1422-0067/25/1/534 |
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