{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T02:59:24Z","timestamp":1774407564687,"version":"3.50.1"},"reference-count":52,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,4,16]],"date-time":"2024-04-16T00:00:00Z","timestamp":1713225600000},"content-version":"vor","delay-in-days":20,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"National Cancer Institute Informatics Technology for Cancer Research","award":["U01CA279618"],"award-info":[{"award-number":["U01CA279618"]}]},{"name":"National Institute of Health","award":["1SC3GM136594-02"],"award-info":[{"award-number":["1SC3GM136594-02"]}]},{"name":"National Institute of Health","award":["HG013359"],"award-info":[{"award-number":["HG013359"]}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["CA124332"],"award-info":[{"award-number":["CA124332"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["CA096512"],"award-info":[{"award-number":["CA096512"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>N6-methyladenosine (m6A) is the most abundant mRNA modification within mammalian cells, holding pivotal significance in the regulation of mRNA stability, translation and splicing. Furthermore, it plays a critical role in the regulation of RNA degradation by primarily recruiting the YTHDF2 reader protein. However, the selective regulation of mRNA decay of the m6A-methylated mRNA through YTHDF2 binding is poorly understood. To improve our understanding, we developed m6A-BERT-Deg, a BERT model adapted for predicting YTHDF2-mediated degradation of m6A-methylated mRNAs. We meticulously assembled a high-quality training dataset by integrating multiple data sources for the HeLa cell line. To overcome the limitation of small training samples, we employed a pre-training-fine-tuning strategy by first performing a self-supervised pre-training of the model on 427\u00a0760 unlabeled m6A site sequences. The test results demonstrated the importance of this pre-training strategy in enabling m6A-BERT-Deg to outperform other benchmark models. We further conducted a comprehensive model interpretation and revealed a surprising finding that the presence of co-factors in proximity to m6A sites may disrupt YTHDF2-mediated mRNA degradation, subsequently enhancing mRNA stability. We also extended our analyses to the HEK293 cell line, shedding light on the context-dependent YTHDF2-mediated mRNA degradation.<\/jats:p>","DOI":"10.1093\/bib\/bbae170","type":"journal-article","created":{"date-parts":[[2024,4,16]],"date-time":"2024-04-16T01:51:01Z","timestamp":1713232261000},"source":"Crossref","is-referenced-by-count":7,"title":["Understanding YTHDF2-mediated mRNA degradation by m6A-BERT-Deg"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4595-6167","authenticated-orcid":false,"given":"Ting-He","family":"Zhang","sequence":"first","affiliation":[{"name":"Cancer Virology Program , UPMC Hillman Cancer Center, , Pittsburgh, PA 15232 , USA"},{"name":"University of Pittsburgh School of Medicine , UPMC Hillman Cancer Center, , Pittsburgh, PA 15232 , USA"},{"name":"Department of Medicine, University of Pittsburgh School of Medicine , Pittsburgh, PA,15261 , USA"}]},{"given":"Sumin","family":"Jo","sequence":"additional","affiliation":[{"name":"Cancer Virology Program , UPMC Hillman Cancer Center, , Pittsburgh, PA 15232 , USA"},{"name":"University of Pittsburgh School of Medicine , UPMC Hillman Cancer Center, , Pittsburgh, PA 15232 , USA"},{"name":"Department of Electrical and Computer Engineering , Swanson School of Engineering, , Pittsburgh, PA, 15261 , USA"},{"name":"University of Pittsburgh , Swanson School of Engineering, , Pittsburgh, PA, 15261 , USA"}]},{"given":"Michelle","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Electrical and Computer Engineering, The University of Texas at San Antonio , San Antonio, TX, 78249 , USA"}]},{"given":"Kai","family":"Wang","sequence":"additional","affiliation":[{"name":"Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children\u2019s Hospital of Philadelphia , Philadelphia, PA, 19104 , USA"},{"name":"Department of Pathology and Laboratory Medicine , Perelman School of Medicine, , Philadelphia, PA, 19104 , USA"},{"name":"University of Pennsylvania , Perelman School of Medicine, , Philadelphia, PA, 19104 , USA"}]},{"given":"Shou-Jiang","family":"Gao","sequence":"additional","affiliation":[{"name":"Cancer Virology Program , UPMC Hillman Cancer Center, , Pittsburgh, PA 15232 , USA"},{"name":"University of Pittsburgh School of Medicine , UPMC Hillman Cancer Center, , Pittsburgh, PA 15232 , USA"},{"name":"Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine , Pittsburgh, PA, 15219 , USA"}]},{"given":"Yufei","family":"Huang","sequence":"additional","affiliation":[{"name":"Cancer Virology Program , UPMC Hillman Cancer Center, , Pittsburgh, PA 15232 , USA"},{"name":"University of Pittsburgh School of Medicine , UPMC Hillman Cancer Center, , Pittsburgh, PA 15232 , USA"},{"name":"Department of Medicine, University of Pittsburgh School of Medicine , Pittsburgh, PA,15261 , USA"},{"name":"Department of Electrical and Computer Engineering , Swanson School of Engineering, , Pittsburgh, PA, 15261 , USA"},{"name":"University of Pittsburgh , Swanson School of Engineering, , Pittsburgh, PA, 15261 , USA"},{"name":"Department of Pharmaceutical Sciences, University of Pittsburgh School of Medicine , Pittsburgh, PA, 15261 , USA"}]}],"member":"286","published-online":{"date-parts":[[2024,4,15]]},"reference":[{"issue":"3","key":"2024041601505626200_ref1","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1038\/s12276-020-0407-z","article-title":"The emerging role of RNA modifications in the regulation of mRNA stability","volume":"52","author":"Boo","year":"2020","journal-title":"Exp Mol 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