# Integrative Analysis of Whole-Genome Bisulfite Sequencing and RNA-Seq in Skeletal Muscle of Xin’anjiang Water Buffalo

## TL;DR

This study explores DNA methylation and gene expression in skeletal muscle of male and female Xin’anjiang water buffalo to understand how these factors relate to transcriptional differences.

## Contribution

The study provides novel insights into the methylation and gene expression patterns in skeletal muscle of Xin’anjiang water buffalo using integrative WGBS and RNA-seq analysis.

## Key findings

- 31,333 DMCs, 1,961 DMRs, and 230 DEGs were identified between male and female XAJB skeletal muscle.
- CG methylation showed a strong negative correlation with gene expression in the 2 kb upstream region.
- Ten DEGs were validated by qRT-PCR and linked to key biological pathways like ECM-receptor interaction and PPAR signaling.

## Abstract

Xin’anjiang water buffalo (XAJB), an indigenous swamp buffalo (Bubalus bubalis) in China, is mainly distributed in the Xin’anjiang River basin in Anhui Province. In this study, we used whole-genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) to explore the DNA methylation profiles and gene-expression patterns in skeletal muscle in the female (BF) and male (BM) groups of XAJB. The results showed that the most methylation changes occurred in CG context, and the distinct methylation landscapes were associated with the transcriptional signatures in the two cohorts. Due to the limited sample-size in this study, further research is needed to fully understand the association of methylation patterns with transcriptome profiles in the skeletal muscle of XAJB.

Xin’anjiang water buffalo (XAJB) is crucial for meat production and agricultural activities in Anhui Province of China. To generate hypotheses regarding how DNA methylation might correlate with transcriptional differences in skeletal muscle, WGBS and RNA-seq were performed on three BF and three BM adult XAJB. The results revealed 31,333 differentially methylated cytosines (DMCs), 1961 differentially methylated regions (DMRs), and 230 differentially expressed genes (DEGs) in skeletal muscle between the two groups. The qRT-PCR results of ten DEGs (COL1A1, THBS1, SLITRK4, VIPR2, IGFBP6, WIF1, MMP16, LMOD3, NPR3 and MYLK4) enriched in protein digestion and absorption pathway, PPAR signaling pathway, ECM-receptor interaction pathway or PI3K-Akt signaling pathway were consistent with the RNA-seq results. Most methylation changes occurred in CG context, and sixteen genes were predicted as dual differential genes in both methylation and transcriptome. Moreover, CG methylation showed a significant negative correlation with gene expression within the 2 kb upstream region (rho = −0.42, p < 0.001). Given the limited number of animals examined, additional investigations with expanded cohorts are essential to verify the association between the methylome and transcriptome signatures underlying skeletal muscle in XAJB.