Bifunctional Role of Fe(II)/2OG-Dependent TET Family 5-Methylcytosine Dioxygenases and ALKBH2,3 in Modified Cytosine Demethylation

Abstract

Three forms of methylated cytosines are present in the eukaryotic genome: 3-methylcytosine, 4-methylcytosine and 5-methylcytosine. 3-methylcytosines create methyl lesions, which impair local DNA function and flexibility, resulting in replication and transcription error. On the other hand, 5-methylcytosine is usually present at the gene promoter which blocks transcription and translation. Fe(II)/2OG-dependent nucleic acid-modifying enzymes are the class of enzymes responsible for the demethylation of these modified cytosines. ALKBH2 and 3 remove 3-methylcytosine via a one-step direct demethylation process. On the other hand, active demethylation of 5mC is initiated by Ten-Eleven Translocation (TET)-family dioxygenases. Via oxidative demethylation, TET1-3 converts 5mC into 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine. Remarkably, recent findings demonstrate that ALKBH2,3 possess oxidative demethylation properties, along with direct demethylation. On the other hand, the TET family of enzymes possess direct demethylation properties along with oxidative demethylation. Here we review the importance of methylated cytosines in human DNA, their origin, function and removal. In addition, we discuss the recent findings of extraordinary flexibility of Fe(II)/2OG-dependent nucleic acid-modifying enzymes ALKBH2,3 and TET family of enzymes in cytosine demethylation, as well as their impact on epigenetics.

Genome-wide Methylation Dynamics and Context-dependent Gene Expression Variability in Differentiating Preadipocytes

“…The present study focused on variations in the methylome across the entire genome at the single CG dinucleotide resolution of Pre-AD and adipocytes. However, some non-CpG changes have been observed [ 81 , 82 ]. Variable non-CpG methylation, ie, CHH and CHG, are observed.…”

WGBS of Differentiating Adipocytes Reveals Variations in DMRs and Context-Dependent Gene Expression

“…The present study focused on variations in the methylome across the entire genome at the single CG dinucleotide resolution of preadipocytes and adipocytes. However, some non-CpG changes have been observed [78] [79]. Variable non-CpG methylation, i.e., CHH and CHG, are observed.…”