Flanking sequence preference modulates de novo DNA methylation in the mouse genome

Abstract

Mammalian de novo DNA methyltransferases (DNMT) are responsible for the establishment of cell-type-specific DNA methylation in healthy and diseased tissues. Through genome-wide analysis of de novo methylation activity in murine stem cells we uncover that DNMT3A prefers to methylate CpGs followed by cytosines or thymines, while DNMT3B predominantly methylates CpGs followed by guanines or adenines. These signatures are further observed at non-CpG sites, resembling methylation context observed in specialised cell types, including neurons and oocytes. We further show that these preferences result from structural differences in the catalytic domains of the two de novo DNMTs and are not a consequence of differential recruitment to the genome. Molecular dynamics simulations suggest that, in case of human DNMT3A, the preference is due to favourable polar interactions between the flexible Arg836 side chain and the guanine that base-pairs with the cytosine following the CpG. By exchanging arginine to a lysine, the corresponding side chain in DNMT3B, the sequence preference is reversed, confirming the requirement for arginine at this position. This context-dependent enzymatic activity provides additional insights into the complex regulation of DNA methylation patterns.

Local CpG density affects the trajectory and variance of age-associated DNA methylation changes

“…A computational analysis of DNA re-methylation dynamics suggests these processes are required to explain the observed rates of DNA re-methylation following replication [ 62 ]. The efficiency of DNMTs is also influenced by bases surrounding CpGs in vitro [ 63 , 64 ] and in vivo [ 65 ]. These preferences could affect the efficiency by which some CpGs are methylated and could explain the effect of some of the SNPs we have uncovered that do not directly affect CpGs.…”

The interplay between DNA and histone methylation: molecular mechanisms and disease implications

“…Its function, however, can be partially compensated by catalytically inactive isoforms of DNMT3B such as DNMT3B3 (Weisenberger et al, 2004;Duymich et al, 2016;Zeng et al, 2020). DNMT3A and DNMT3B have distinct mechanisms of DNA substrate engagement and show differential preference for the flanking sequence of target CpG (Handa & Jeltsch, 2005;Dukatz et al, 2020;Gao et al, 2020;Mallona et al, 2021), and we point readers to the excellent reviews of the molecular and structural basis for the catalysis of de novo methylation by DNMT3 (Jurkowska & Jeltsch, 2016;Ren et al, 2018). Furthermore, DNMT3A/B as well as DNMT3L can interact with histone tails through shared regulatory domains.…”

Mediating and maintaining methylation while minimizing mutation: Recent advances on mammalian DNA methyltransferases

“…DNMT1 strongly disfavors a C at −2 ( Figure 4f ) [ 54 ], while it is accepted there by DNMT3A and 3B ( Figure 4e ) [ 55 ]. On the 3 ′ side, DNMT3A prefers CpGs followed by C/T +at 1, while DNMT3B predominantly methylates CpGs followed by G/A at +1 [ 56 ], fitting structural observations [ 55 ]. DNMT1 has no (or limited) preference at the +1 position, which allows the maintenance enzyme to propagate without bias (on the 3 ′ side) the methylation generated by either DNMT3A or DNMT3B.…”