Integration of ATAC-seq and RNA-seq analysis identifies key genes affecting intramuscular fat content in pigs

Abstract

Meat quality is one of the most important economic traits in pig breeding and production, and intramuscular fat (IMF) content is the major factor in improving meat quality. The IMF deposition in pigs is influenced by transcriptional regulation, which is dependent on chromatin accessibility. However, how chromatin accessibility plays a regulatory role in IMF deposition in pigs has not been reported. Xidu black is a composite pig breed with excellent meat quality, which is an ideal research object of this study. In this study, we used the assay for transposase-accessible chromatin using sequencing (ATAC-seq) and RNA sequencing (RNA-seq) analysis to identify the accessible chromatin regions and key genes affecting IMF content in Xidu black pig breed with extremely high and low IMF content. First, we identified 21,960 differential accessible chromatin peaks and 297 differentially expressed genes. The motif analysis of differential peaks revealed several potential cis-regulatory elements containing binding sites for transcription factors with potential roles in fat deposition, including Mef2c, CEBP, Fra1, and AP-1. Then, by integrating the ATAC-seq and RNA-seq analysis results, we found 47 genes in the extremely high IMF (IMF_H) group compared with the extremely low IMF (IMF_L) group. For these genes, we observed a significant positive correlation between the differential gene expression and differential ATAC-seq signal (r2 = 0.42). This suggests a causative relationship between chromatin remodeling and the resulting gene expression. We identified several candidate genes (PVALB, THRSP, HOXA9, EEPD1, HOXA10, and PDE4B) that might be associated with fat deposition. Through the PPI analysis, we found that PVALB gene was the top hub gene. In addition, some pathways that might regulate fat cell differentiation and lipid metabolism, such as the PI3K-Akt signaling pathway, MAPK signaling pathway, and calcium signaling pathway, were significantly enriched in the ATAC-seq and RNA-seq analysis. To the best of our knowledge, our study is the first to use ATAC-seq and RNA-seq to examine the mechanism of IMF deposition from a new perspective. Our results provide valuable information for understanding the regulation mechanism of IMF deposition and an important foundation for improving the quality of pork.

Single-nucleus and bulk RNA sequencing reveal cellular and transcriptional mechanisms underlying lipid dynamics in high marbled pork

“…For signalling pathways, we found that DEGs were enriched in glycerophospholipid metabolism, the cGMP-PKG signalling pathway, the calcium signalling pathway, and the Notch signalling pathway. Consistent with our findings, Xu et al found that the MAPK signalling pathway and calcium signalling pathway were significantly associated with IMF deposition 44 . Notch signalling plays an important role in regulating metabolic disorders and participates in beige adipocyte formation, adipocyte dedifferentiation and function 49 , 50 .…”

“…Marbling formation is a complex process, and the regulatory mechanism of IMF deposition involves genes related to lipid metabolism signaling pathways 44 . In our study, we found that the expression of FABP4 , FABP5 , LIPE , ELOVL1 , and CPT1A was positively associated with IMF deposition, but LPL expression was negatively associated with IMF deposition.…”

A Biophysical Model for ATAC-seq Data Analysis

“…data collected from different cells from the same sample, include joint analysis of differentially accessible regions (DARs) (9) and differential gene expression. Such methods have been used to compare gene regulation across tissues between healthy and pathological conditions (10)(11)(12)(13)(14)(15), and across tissue types (16), as well as to identify new gene-regulatory pathways (17,18). Combined use of scRNA-seq and scATAC-seq data can also help to distinguish cell-types (19,20) and scATAC data can be used to impute scRNA data (21).…”

HOXA9 gene inhibits proliferation and differentiation and promotes apoptosis of bovine preadipocytes

“…Existing reports show that HOXA 9 differentially expressed in female abdominal and gluteal subcutaneous adipose tissue, which regulated the deposition of fat in different parts of body [ 23 ]. Sadkowski et al also showed that HOXA 9 was a key candidate gene for regulating IMF development in pigs and cattle through joint analysis of ATAC-seq and RNA-seq [ 24 , 25 ], but the specific function and mechanism are not clear. Gain-of-function and lose-of-function are the main way to verify gene function in the field of life science [ 26 ].…”