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1. Using targeted genome methylation for crop improvement

   https://doi.org/10.1093/jxb/eraf131  

   Wang, Zhibo; Bart, Rebecca_S; Lechon, ed., Tamara (March 2025, Journal of Experimental Botany)

   Abstract Genome editing allows scientists to specifically change the DNA sequence of an organism. This powerful technology now fuels basic biology discovery and tangible crop improvement efforts. There is a less well understood layer of information encoded in genomes, known collectively as ‘epigenetics’, that impacts gene expression, without changing the DNA sequence. Epigenetic processes allow organisms to rapidly respond to environmental fluctuation. Like genome editing, recent advances have demonstrated that it is possible to edit the epigenome of a plant and cause heritable phenotypic changes. In this review, we aim to specifically consider the unique advantages that targeted epigenome editing might provide over existing biotechnology tools. This review is aimed at a broad audience. We begin with a high-level overview of the tools currently available for crop improvement. Next, we present a more detailed overview of the key discoveries that have been made in recent years, primarily using the model system Arabidopsis, new efforts to extend targeted methylation to crop plants, the current status of the technology, and the challenges that remain to realize the full potential of targeted epigenome editing. We end with a forward-looking commentary on how epi-alleles might interface with breeding programs across a variety of crops. 

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2. DNA methylation of methylation complex genes in relation to stress and genome-wide methylation in mother-newborn dyads

   Clukay CJ, Hughes DA (January 2017, American journal of physical anthropology)
3. DNA methylation of methylation complex genes in relation to stress and genome-wide methylation in mother-newborn dyads

   https://doi.org/10.1002/ajpa.23341  

   Clukay, Christopher J.; Hughes, David A.; Rodney, Nicole C.; Kertes, Darlene A.; Mulligan, Connie J. (January 2018, American Journal of Physical Anthropology)
4. An enzymatic activation of formaldehyde for nucleotide methylation

   https://doi.org/10.1038/s41467-021-24756-8  

   Bou-Nader, Charles; Stull, Frederick W.; Pecqueur, Ludovic; Simon, Philippe; Guérineau, Vincent; Royant, Antoine; Fontecave, Marc; Lombard, Murielle; Palfey, Bruce A.; Hamdane, Djemel (December 2021, Nature Communications)

   Abstract Folate enzyme cofactors and their derivatives have the unique ability to provide a single carbon unit at different oxidation levels for the de novo synthesis of amino-acids, purines, or thymidylate, an essential DNA nucleotide. How these cofactors mediate methylene transfer is not fully settled yet, particularly with regard to how the methylene is transferred to the methylene acceptor. Here, we uncovered that the bacterial thymidylate synthase ThyX, which relies on both folate and flavin for activity, can also use a formaldehyde-shunt to directly synthesize thymidylate. Combining biochemical, spectroscopic and anaerobic crystallographic analyses, we showed that formaldehyde reacts with the reduced flavin coenzyme to form a carbinolamine intermediate used by ThyX for dUMP methylation. The crystallographic structure of this intermediate reveals how ThyX activates formaldehyde and uses it, with the assistance of active site residues, to methylate dUMP. Our results reveal that carbinolamine species promote methylene transfer and suggest that the use of a CH 2 O-shunt may be relevant in several other important folate-dependent reactions. 

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5. DNA Methylation in Ctenophores

   https://doi.org/10.1007/978-1-0716-3642-8_18  

   Dabe, Emily C; Kohn, Andrea B; Moroz, Leonid L (January 2024, Springer US)