Pronounced sequence specificity of the TET enzyme catalytic domain guides its cellular function

Abstract

TET (ten-eleven translocation) enzymes catalyze the oxidation of 5-methylcytosine bases in DNA, thus driving active and passive DNA demethylation. Here, we report that the catalytic cores of mammalian TET enzymes favor CpGs embedded within bHLH and bZIP transcription factor binding sites, with 250-fold preference in vitro. Crystal structures and molecular dynamics calculations show that sequence preference is caused by intra-substrate interactions and CpG flanking sequence indirectly affecting enzyme conformation. TET sequence preferences are physiologically relevant as they explain the rates of DNA demethylation in TET-rescue experiments in culture and in vivo within the zygote and germline. Most and least favorable TET motifs represent DNA sites that are bound by methylation-sensitive immediate-early transcription factors and OCT4, respectively, illuminating TET function in transcriptional responses and pluripotency support. One-Sentence Summary: The catalytic domains of the enzymes that facilitate passive and drive active DNA demethylation have intrinsic sequence preferences that target DNA demethylation to bHLH and bZIP transcription factor binding sites.

5-methylcytosine turnover: Mechanisms and therapeutic implications in cancer

“…As for DNMTs, the recognition of a target locus by TET enzymes is also impacted by surrounding DNA bases. Although this idea has been somewhat controversial, recent studies demonstrated that the catalytic domain of TETs has a sequence specificity with a higher preference for some motifs in the genome ( Hu et al, 2015 ; Ravichandran et al, 2021 ). TET1 and TET3 have been shown to rapidly oxidize methylated CpG sites (mCpGs) with an A or a T at the -1 and +1 positions respectively.…”