Evaluation of N6-methyldeoxyadenosine antibody-based genomic profiling in eukaryotes
- 1Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA;
- 2Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA;
- 3Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington 98195-7720, USA;
- 4Brotman Baty Institute for Precision Medicine, Seattle, Washington 98195, USA
Abstract
Low-level DNA N6-methyldeoxyadenosine (DNA-m6A) has recently been reported across various eukaryotes. Although anti-m6A antibody–based approaches are commonly used to measure DNA-m6A levels, this approach is known to be confounded by DNA secondary structures, RNA contamination, and bacterial contamination. To evaluate for these confounding features, we introduce an approach for systematically validating the selectivity of antibody-based DNA-m6A methods and use a highly selective anti-DNA-m6A antibody to reexamine patterns of DNA-m6A in C. reinhardtii, A. thaliana, and D. melanogaster. Our findings raise caution about the use of antibody-based methods for endogenous m6A quantification and mapping in eukaryotes.
Footnotes
-
[Supplemental material is available for this article.]
-
Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.276696.122.
- Received March 2, 2022.
- Accepted February 2, 2023.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see https://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
