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Random Forest model reveals the interaction between N6-methyladenosine modifications and RNA-binding proteins
RNA-binding proteins (RBPs) have critical roles in N6-methyladenosine (m6A) modification process. We designed a Random Forest (RF) model to systematically analyze the interaction among RBPs and m6A modifications by integrating the binding signals from hundreds of RBPs. Accurate prediction of m6A sit...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10009289/ https://www.ncbi.nlm.nih.gov/pubmed/36922995 http://dx.doi.org/10.1016/j.isci.2023.106250 |
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author | Hong, Wei Zhao, Yanding Weng, Yi-Lan Cheng, Chao |
author_facet | Hong, Wei Zhao, Yanding Weng, Yi-Lan Cheng, Chao |
author_sort | Hong, Wei |
collection | PubMed |
description | RNA-binding proteins (RBPs) have critical roles in N6-methyladenosine (m6A) modification process. We designed a Random Forest (RF) model to systematically analyze the interaction among RBPs and m6A modifications by integrating the binding signals from hundreds of RBPs. Accurate prediction of m6A sites demonstrated significant connections between RBP bindings and m6A modifications. The relative importance of different RBPs from the model provided a quantitative metric to evaluate their interactions with m6A modifications. Redundancy analysis showed that several RBPs may have similar binding patterns with m6A sites. The RF model exhibited fairly high prediction accuracy across cell lines, suggesting a conservative RBP interaction network regulates m6A occupancy. Specific RBPs can engage to the corresponding regional m6A sites and deploy distinct regulatory processes, such as cleavage site selection of the alternative polyadenylation (APA). We also integrated histone modifications into our RF model, which demonstrated H3K36me3 and H3K27me3 as determining features for m6A distribution. |
format | Online Article Text |
id | pubmed-10009289 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-100092892023-03-14 Random Forest model reveals the interaction between N6-methyladenosine modifications and RNA-binding proteins Hong, Wei Zhao, Yanding Weng, Yi-Lan Cheng, Chao iScience Article RNA-binding proteins (RBPs) have critical roles in N6-methyladenosine (m6A) modification process. We designed a Random Forest (RF) model to systematically analyze the interaction among RBPs and m6A modifications by integrating the binding signals from hundreds of RBPs. Accurate prediction of m6A sites demonstrated significant connections between RBP bindings and m6A modifications. The relative importance of different RBPs from the model provided a quantitative metric to evaluate their interactions with m6A modifications. Redundancy analysis showed that several RBPs may have similar binding patterns with m6A sites. The RF model exhibited fairly high prediction accuracy across cell lines, suggesting a conservative RBP interaction network regulates m6A occupancy. Specific RBPs can engage to the corresponding regional m6A sites and deploy distinct regulatory processes, such as cleavage site selection of the alternative polyadenylation (APA). We also integrated histone modifications into our RF model, which demonstrated H3K36me3 and H3K27me3 as determining features for m6A distribution. Elsevier 2023-02-20 /pmc/articles/PMC10009289/ /pubmed/36922995 http://dx.doi.org/10.1016/j.isci.2023.106250 Text en © 2023 The Author(s) https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Article Hong, Wei Zhao, Yanding Weng, Yi-Lan Cheng, Chao Random Forest model reveals the interaction between N6-methyladenosine modifications and RNA-binding proteins |
title | Random Forest model reveals the interaction between N6-methyladenosine modifications and RNA-binding proteins |
title_full | Random Forest model reveals the interaction between N6-methyladenosine modifications and RNA-binding proteins |
title_fullStr | Random Forest model reveals the interaction between N6-methyladenosine modifications and RNA-binding proteins |
title_full_unstemmed | Random Forest model reveals the interaction between N6-methyladenosine modifications and RNA-binding proteins |
title_short | Random Forest model reveals the interaction between N6-methyladenosine modifications and RNA-binding proteins |
title_sort | random forest model reveals the interaction between n6-methyladenosine modifications and rna-binding proteins |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10009289/ https://www.ncbi.nlm.nih.gov/pubmed/36922995 http://dx.doi.org/10.1016/j.isci.2023.106250 |
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