@article{4b1c9f8c672541f4a44bd3271de286d0,
title = "Random Forest model reveals the interaction between N6-methyladenosine modifications and RNA-binding proteins",
abstract = "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.",
keywords = "Biochemistry, Biological sciences, Biophysics, Protein",
author = "Wei Hong and Yanding Zhao and Weng, {Yi Lan} and Chao Cheng",
note = "Funding Information: We acknowledge the ENCODE Consortium and the ENCODE production laboratories for generating RBP eCLIP and histone modification CHIP data of two cell lines. We also thank Tobie Lee for editorial assistance. This study is supported by the Cancer Prevention Research Institute of Texas (CPRIT) ( RR180061 to C.C.) and the National Cancer Institute of the National Institutes of Health ( 1R21CA227996 to C.C., R01ES031511 to Y.W.). C.C. is CPRIT Scholar in Cancer Research. Funding Information: We acknowledge the ENCODE Consortium and the ENCODE production laboratories for generating RBP eCLIP and histone modification CHIP data of two cell lines. We also thank Tobie Lee for editorial assistance. This study is supported by the Cancer Prevention Research Institute of Texas (CPRIT) (RR180061 to C.C.) and the National Cancer Institute of the National Institutes of Health (1R21CA227996 to C.C. R01ES031511 to Y.W.). C.C. is CPRIT Scholar in Cancer Research. W.H. and C.C. designed the study. W.H. Y.Z. and C.C. performed the computational analyses. W.H. Y.W. and C.C. prepared the manuscript. Y.W. and C.C. provided funding and study supervision. The authors declare no competing interests. We support inclusive, diverse, and equitable conduct of research. Publisher Copyright: {\textcopyright} 2023 The Author(s)",
year = "2023",
month = mar,
day = "17",
doi = "10.1016/j.isci.2023.106250",
language = "English (US)",
volume = "26",
pages = "106250",
journal = "iScience",
issn = "2589-0042",
publisher = "Elsevier",
number = "3",
}