Heuristic definition of Body methylated (BM) genes

Range genes that methylate >90% of their CG sites and <5% of their CHG and CHH sites unitless
Organism Eukaryotes
Reference Vidalis A, Živković D, Wardenaar R, Roquis D, Tellier A, Johannes F. Methylome evolution in plants. Genome Biol. 2016 Dec 20 17(1):264. doi: 10.1186/s13059-016-1127-5. p.5 left column 2nd paragraphPubMed ID27998290
Primary Source [105] Takuno S, Gaut BS. Body-methylated genes in Arabidopsis thaliana are functionally important and evolve slowly. Mol Biol Evol. 2012 29: 219–27. DOI: 10.1093/molbev/msr188PubMed ID21813466
Comments P.5 left column 2nd paragraph: "Gene-body methylation (gbM) as a neutral byproduct of transcription: Arguably one of the most enigmatic features of plant methylomes is the methylation of gene bodies. Body methylated (BM) genes have been heuristically defined as genes that methylate more than 90% of their CG sites and less than 5% of their CHG and CHH sites [primary source]. The latter requirement filters out genes that feature TE [transposable element]-like methylation patterns, perhaps because they were originally derived from TEs or contain intact or degenerate TE copies. In A. thaliana, about 18% of genes are BM whereas about 65% are unmethylated (UM). Unlike its repressive role in TEs and repeats, methylation in gene bodies tends to occur in moderate to highly expressed genes [refs 62, 97]. The molecular mechanisms by which gene-body methylation (gbM) contributes to transcription, if at all, and its evolutionary significance are not fully understood." P.1 left column bottom paragraph: "In the model plant Arabidopsis thaliana, cytosine methylation occurs in symmetrical CG and CHG contexts, as well as in asymmetrical CHH sequence contexts (where H = A, T, C) [ref 56]."
Entered by Uri M
ID 113097