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   Clukay, Christopher J.; Hughes, David A.; Rodney, Nicole C.; Kertes, Darlene A.; Mulligan, Connie J. (January 2018, American Journal of Physical Anthropology)
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   Dabe, Emily C; Kohn, Andrea B; Moroz, Leonid L (January 2024, Springer US)
4. Methylation Data Analysis and Interpretation

   https://doi.org/10.1146/annurev-biodatasci-120924-091033  

   Zhu, Yuehua; Mao, Weiguang; Hosseini, Rezwan; Chikina, Maria (August 2025, Annual Review of Biomedical Data Science)

   DNA methylation, a covalent modification, fundamentally shapes mammalian gene regulation and cellular identity. This review examines methylation's biochemical underpinnings, genomic distribution patterns, and analytical approaches. We highlight three distinctive aspects that separate methylation from other epigenetic marks: its remarkable stability as a silencing mechanism, its capacity to maintain distinct states independently of DNA sequence, and its effectiveness as a quantitative trait linking genotype to disease risk. We also explore the phenomenon of methylation clocks and their biological significance. The review addresses technical considerations across major assay types—both array-based technologies and sequencing approaches—with emphasis on data normalization, quality control, cell proportion inference, and the specialized statistical models required for next-generation sequencing analysis. 

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5. RNA-directed DNA methylation mutants reduce histone methylation at the paramutated maize booster1 enhancer

   https://doi.org/10.1093/plphys/kiae072  

   Hövel, Iris; Bader, Rechien; Louwers, Marieke; Haring, Max; Peek, Kevin; Gent, Jonathan I; Stam, Maike (February 2024, Plant Physiology)

   Paramutation is the transfer of mitotically and meiotically heritable silencing information between two alleles. With paramutation at the maize (Zea mays) booster1 (b1) locus, the low-expressed B′ epiallele heritably changes the high-expressed B-I epiallele into B′ with 100% frequency. This requires specific tandem repeats and multiple components of the RNA-directed DNA methylation pathway, including the RNA-dependent RNA polymerase (encoded by mediator of paramutation1, mop1), the second-largest subunit of RNA polymerase IV and V (NRP(D/E)2a, encoded by mop2), and the largest subunit of RNA Polymerase IV (NRPD1, encoded by mop3). Mutations in mop genes prevent paramutation and release silencing at the B′ epiallele. In this study, we investigated the effect of mutations in mop1, mop2, and mop3 on chromatin structure and DNA methylation at the B′ epiallele, and especially the regulatory hepta-repeat 100 kb upstream of the b1 gene. Mutations in mop1 and mop3 resulted in decreased repressive histone modifications H3K9me2 and H3K27me2 at the hepta-repeat. Associated with this decrease were partial activation of the hepta-repeat enhancer function, formation of a multi-loop structure, and elevated b1 expression. In mop2 mutants, which do not show elevated b1 expression, H3K9me2, H3K27me2 and a single-loop structure like in wild-type B′ were retained. Surprisingly, high CG and CHG methylation levels at the B′ hepta-repeat remained in all three mutants, and CHH methylation was low in both wild type and mutants. Our results raise the possibility of MOP factors mediating RNA-directed histone methylation rather than RNA-directed DNA methylation at the b1 locus. 

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