# H3K4me3 CUT&Tag and Transcriptome Analysis Reveal the Epigenetic Regulatory Landscape in Mammary Gland Tissues of Yili Horses at Different Lactation Stages

## TL;DR

This study explores how gene activity and epigenetic markers change in horse mammary glands during lactation, revealing genes linked to milk production and immune response.

## Contribution

The first comprehensive epigenomic profiling of H3K4me3 modifications in Yili horse mammary glands during lactation.

## Key findings

- 393 differentially expressed genes were identified between early and peak lactation stages.
- PTGES, COL1A1, PDGFRB, and RYR1 were consistently upregulated at both transcriptomic and chromatin levels.
- H3K4me3 regulates 72 differentially expressed genes involved in pathways like ECM–receptor interaction and calcium signaling.

## Abstract

Understanding how genes are turned on or off during lactation can help improve milk production and animal health. In this study, we examined the activity of specific genes in the mammary glands of Yili horses at two important time points: early lactation and peak lactation. We focused on a molecular marker called H3K4me3, which is found near genes that are actively being used by the cell. By combining two advanced techniques that measure both gene activity and molecular markers, we discovered several genes that are strongly linked to milk production and immune response. One gene, PTGES, was especially active during peak lactation. These changes suggest that the mammary gland shifts its focus from immune defense to stable energy use as lactation progresses. This research provides valuable knowledge about how milk production is controlled at the genetic level and offers new opportunities to improve breeding strategies, enhance milk yield, and support the health of dairy animals.

H3K4me3, a well-established histone modification associated with active promoters, plays a critical role in orchestrating gene expression programs that govern mammary gland development and lactation. In this study, we present the first comprehensive epigenomic profiling of H3K4me3 modifications during mammary gland development in Yili horses using Cleavage Under Targets and Tagmentation (CUT&Tag) and RNA sequencing. Mammary gland tissues were collected from two developmental stages—early lactation and peak lactation. A total of 393 differentially expressed genes (DEGs) were identified between two groups, among which 72 DEGs (54 upregulated H3K4me3 targets and 18 downregulated targets) were directly regulated by H3K4me3. KEGG enrichment analyses revealed that these DEGs were involved in ECM–receptor interaction, focal adhesion, the PI3K-Akt signaling pathway, and the calcium signaling pathway. In these pathways, five genes were identified as potential regulators of mammary gland development. Among these, PTGES, COL1A1, PDGFRB, and RYR1 exhibited consistent upregulation at both the transcriptomic and chromatin levels, whereas PRKAG3 showed significant downregulation. These findings offer novel insights into the epigenetic regulation of lactation in horses and lay a theoretical foundation for improving milk production traits through targeted molecular breeding strategies.