# KDM5C and KDM5D influence DNA methylation in adult mouse liver

## TL;DR

This study investigates how KDM5C and KDM5D, enzymes linked to X and Y chromosomes, affect DNA methylation in mouse liver, finding they influence methylation but are not the main drivers of sex-based differences.

## Contribution

The study reveals that KDM5C and KDM5D influence DNA methylation at autosomal loci but are not primary mediators of sex-chromosome complement effects in mouse liver.

## Key findings

- Mutations in Kdm5c and Kdm5d induce significant changes in DNA methylation in adult mouse liver at autosomal loci.
- Loss of Kdm5c affects methylation at promoter and enhancer regions marked by H3K4me3 or H3K4me1 and H3K27ac.
- KDM5C and KDM5D are not the primary mediators of sex-chromosome complement effects on DNA methylation in adult mouse liver.

## Abstract

Several lines of evidence suggest that the sex-chromosome complement influences autosomal gene regulation and DNA methylation, however, the exact molecular mechanisms responsible for such effects remain elusive. X-linked epigenetic modifiers that escape X-chromosome inactivation, and hence have higher dosage in female cells, are the primary gene candidates for mediating the effects of X-dosage, whereas Y-linked paralogs may rescue such imbalance or have distinct effects on methylation.

Here, we tested the impacts of mutations in mouse histone lysine 4 demethylases Kdm5c (X-linked) and Kdm5d (Y-linked) on DNA methylation in mouse liver. KDM5C and KDM5D demethylate H3K4me2/3 thereby facilitating DNA methylation of their target DNA regions. Therefore, loss of either Kdm5c or Kdm5d is expected to reduce DNA methylation at such regions. We hypothesized that Kdm5c gene dosage was responsible for the X-dosage dependent DNA methylation in mouse liver and compared DNA methylation patterns in heterozygous mutant Kdm5c+/- and wild type females using whole genome bisulfite sequencing (WGBS) and DSS.

We examined the impacts of mutations in Kdm5c or Kdm5d on genome-wide DNA methylation and found that they had different targets but tended to map close to H3K4me1-enriched regions. We also compared the Kdm5c and Kdm5d sensitive regions to regions with sex-chromosome complement dependent DNA methylation and found no overlaps.

In summary, while Kdm5c and Kdm5d have multi-locus effects on DNA methylation in mouse liver, they are unlikely to be solely responsible for sex-chromosome complement effects on DNA methylation in adult mouse liver.

The online version contains supplementary material available at 10.1186/s13293-026-00844-6.

Several lines of evidence suggest that sex chromosomes influence gene regulation across the genome, however, the exact molecular mechanisms of such influence remain unknown. Certain genes on the X chromosome escape X-chromosome inactivation, and hence have higher dosage in female cells with two X chromosomes compared to male cells with one X and one Y. These are the primary gene candidates for mediating the effects of the different numbers of X chromosomes in males and females. Y-linked counterparts of such genes may rescue the imbalance or have separate effects on gene regulation. DNA methylation plays a critical role in gene regulation and is often used as a measure of gene activity. Here, we examined how mutations in mouse histone lysine 4 demethylases Kdm5c (X-linked) and Kdm5d (Y-linked) influenced DNA methylation in mouse liver and tested the hypothesis that higher Kdm5c gene dosage in females was responsible for the X-chromosome dosage dependent DNA methylation in mouse liver. We examined the impacts of mutations in Kdm5c or Kdm5d on genome-wide DNA methylation and found that they had different targets but tended to map close to regulatory regions with predominantly enhancer-type epigenetic features. We also compared the Kdm5c and Kdm5d sensitive regions to regions with sex-chromosome complement dependent DNA methylation and found no overlaps. In summary, while Kdm5c and Kdm5d have multi-locus effects on DNA methylation in mouse liver, they are unlikely to be solely responsible for sex-chromosome complement effects on DNA methylation in adult mouse liver.

The online version contains supplementary material available at 10.1186/s13293-026-00844-6.

We tested the impacts of mutations in sex-chromosome-linked genes encoding histone H3K4 demethylases, Kdm5c and Kdm5d, on sex-biased DNA methylation in adult mouse liver and determined that:

Mutations in Kdm5c and Kdm5d induce significant changes in DNA methylation in adult mouse liver, primarily at autosomal loci;Functional annotation indicates that loss of Kdm5c affects DNA methylation at promoter and enhancer regions enriched for histone H3K4me3 or H3K4me1 and H3K27ac marks, whereas loss of Kdm5d induces changes in methylation near enhancer regions;Overall, our data show that KDM5C and KDM5D are not the primary mediators of sex-chromosome complement effects on DNA methylation in the adult liver. However, interaction with other factors cannot be ruled out. These results are novel and add to the understanding of mechanisms responsible for sex-bias in the epigenome.

Mutations in Kdm5c and Kdm5d induce significant changes in DNA methylation in adult mouse liver, primarily at autosomal loci;

Functional annotation indicates that loss of Kdm5c affects DNA methylation at promoter and enhancer regions enriched for histone H3K4me3 or H3K4me1 and H3K27ac marks, whereas loss of Kdm5d induces changes in methylation near enhancer regions;

Overall, our data show that KDM5C and KDM5D are not the primary mediators of sex-chromosome complement effects on DNA methylation in the adult liver. However, interaction with other factors cannot be ruled out. These results are novel and add to the understanding of mechanisms responsible for sex-bias in the epigenome.

The online version contains supplementary material available at 10.1186/s13293-026-00844-6.