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Oxidation of 5hmC to 5fC\/5caC instead marks the committed step in replication-independent DNA demethylation, whereby 5fC\/5caC are actively excised and reverted to unmodified cytosine. Although prior work indicates that TET-mediated oxidation is influenced by bases neighboring 5mC, these studies have been unable to resolve more than two of the relevant species\u20145mC, 5hmC, and 5fC\/5caC\u2014at the same time. As 5hmC is the key fulcrum in DNA demethylation, we established a high-throughput enzymology approach to probe these three cytosine states at base resolution simultaneously across hundreds of sites. We reveal distinct context dependencies for 5hmC generation versus decay, with flanking bases differentially impacting 5hmC persistence. Notably, we demonstrate these predictable preferences in duplexed DNA are lost in single-stranded DNA, mechanistically linking these features to TET-mediated base-flipping. Furthermore, analysis of genomic 5hmC patterns uncovers evidence of sequence context bias in cellular 5hmC accumulation, suggesting a role for TET-intrinsic preferences in shaping cellular epigenetic landscapes.<\/jats:p>","DOI":"10.1093\/nar\/gkag956","type":"journal-article","created":{"date-parts":[[2026,10,10]],"date-time":"2026-10-10T11:49:48Z","timestamp":1791632988000},"source":"Crossref","is-referenced-by-count":0,"title":["Genomic\u00a0sequence context differentially impacts stepwise oxidation by TET enzymes to shape DNA hydroxymethylation landscapes"],"prefix":"10.1093","volume":"54","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4126-522X","authenticated-orcid":false,"given":"Noa","family":"Erlitzki","sequence":"first","affiliation":[{"name":"Graduate Group in Biochemistry, Biophysics, and Chemical Biology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA 19104 ,","place":["United States"]},{"name":"Department of Medicine, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA 19104 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christian E","family":"Loo","sequence":"additional","affiliation":[{"name":"Graduate Group in Biochemistry, Biophysics, and Chemical Biology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA 19104 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johanna M","family":"Fowler","sequence":"additional","affiliation":[{"name":"Department of Medicine, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA 19104 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9126-1932","authenticated-orcid":false,"given":"Wanding","family":"Zhou","sequence":"additional","affiliation":[{"name":"Center for Computational and Genomic Medicine, The Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104 ,","place":["United States"]},{"name":"Department of Pathology and Laboratory Medicine, University of Pennsylvania , Philadelphia, PA 19104 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7689-5678","authenticated-orcid":false,"given":"Rahul M","family":"Kohli","sequence":"additional","affiliation":[{"name":"Department of Medicine, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA 19104 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,10,13]]},"reference":[{"key":"2026101304473289300_B1","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1016\/j.jmb.2011.01.056","article-title":"The dinucleotide CG as a genomic signalling module","volume":"409","author":"Bird","year":"2011","journal-title":"J Mol 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