Mechanism of non-coding RNA regulation of DNMT3A

TL;DR

This paper explores how a specific non-coding RNA regulates DNMT3A, a key enzyme in DNA methylation, and shows that this regulation occurs independently of RNA/DNA structures.

Contribution

The study reveals a novel mechanism where Fos ecRNA modulates DNMT3A activity through direct protein binding rather than structural interactions.

Findings

Fos ecRNA and mRNA correlate strongly in primary cortical neurons at the single-cell level.

Fos-1 ecRNA binds to the DNMT3A tetramer interface, and DNMT3L restores inhibition disrupted by DNMT3A substitutions.

Regulatory RNAs dominate DNMT3A activity modulation in the presence of histone H3 tails or polynucleosomes.

Abstract

De novo DNA methylation by DNMT3A is a fundamental epigenetic modification for transcriptional regulation. Histone tails and regulatory proteins regulate DNMT3A, and the crosstalk between these epigenetic mechanisms ensures appropriate DNA methylation patterning. Based on findings showing that Fos ecRNA inhibits DNMT3A activity in neurons, we sought to characterize the contribution of this regulatory RNA in the modulation of DNMT3A in the presence of regulatory proteins and histone tails.

We show that Fos ecRNA and mRNA strongly correlate in primary cortical neurons on a single cell level and provide evidence that Fos ecRNA modulation of DNMT3A at these actively transcribed sites occurs in a sequence-independent manner. Further characterization of the Fos ecRNA-DNMT3A interaction showed that Fos-1 ecRNA binds the DNMT3A tetramer interface and clinically relevant DNMT3A substitutions that disrupt the inhibition of DNMT3A activity by Fos-1 ecRNA are restored by the formation of heterotetramers with DNMT3L. Lastly, using DNMT3L and Fos ecRNA in the presence of synthetic histone H3 tails or reconstituted polynucleosomes, we found that regulatory RNAs play dominant roles in the modulation of DNMT3A activity.

Our results are consistent with a model for RNA regulation of DNMT3A that involves localized production of short RNAs binding to a nonspecific site on the protein, rather than formation of localized RNA/DNA structures. We propose that regulatory RNAs play a dominant role in the regulation of DNMT3A catalytic activity at sites with increased production of regulatory RNAs.

The online version contains supplementary material available at 10.1186/s13072-025-00574-w.

Figures