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. 2024 May 30;25(11):6029.
doi: 10.3390/ijms25116029.

Integrative ATAC-seq and RNA-seq Analysis of the Longissimus Dorsi Muscle of Gannan Yak and Jeryak

Zhidong Zhao  1 , Dashan Guo  1 , Yali Wei  1 , Jingsheng Li  1 , Xue Jia  1 , Yanmei Niu  1 , Zhanxin Liu  1 , Yanbin Bai  1 , Zongchang Chen  1 , Bingang Shi  1 , Xiaolan Zhang  1 , Jiang Hu  1 , Jiqing Wang  1 , Xiu Liu  1 , Shaobin Li  1
Affiliations

Integrative ATAC-seq and RNA-seq Analysis of the Longissimus Dorsi Muscle of Gannan Yak and Jeryak

Zhidong Zhao et al. Int J Mol Sci. .

Abstract

Jeryak is the F1 generation of the cross between Gannan yak and Jersey cattle, which has the advantages of fast growth and high adaptability. The growth and development of skeletal muscle is closely linked to meat production and the quality of meat. However, the molecular regulatory mechanisms of muscle growth differences between Gannan yak and Jeryak analyzed from the perspective of chromatin opening have not been reported. In this study, ATAC-seq was used to analyze the difference of chromatin openness in longissimus muscle of Gannan yak and Jeryak. It was found that chromatin accessibility was more enriched in Jeryak compared to Gannan yak, especially in the range of the transcription start site (TSS) ± 2 kb. GO and KEGG enrichment analysis indicate that differential peak-associated genes are involved in the negative regulation of muscle adaptation and the Hippo signaling pathway. Integration analysis of ATAC-seq and RNA-seq revealed overlapping genes were significantly enriched during skeletal muscle cell differentiation and muscle organ morphogenesis. At the same time, we screened FOXO1, ZBED6, CRY2 and CFL2 for possible involvement in skeletal muscle development, constructed a genes and transcription factors network map, and found that some transcription factors (TFs), including YY1, KLF4, KLF5 and Bach1, were involved in skeletal muscle development. Overall, we have gained a comprehensive understanding of the key factors that impact skeletal muscle development in various breeds of cattle, providing new insights for future analysis of the molecular regulatory mechanisms involved in muscle growth and development.

Keywords: ATAC-seq; Jeryaks; RNA-seq; heterosis; longissimus muscle.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Quality control of ATAC-seq. (A) Distribution of insert sizes in groups M and P. (B) Enrichment of ATAC-seq signals is observed around the transcription start site (TSS). The x-axis represents the normalized length of gene or peaks, while the y-axis represents the degree of read enrichment. A higher value indicates a greater level of enrichment. TSS refers to transcription start site, and TES refers to transcription end site. The value −2.0 corresponds to 2 kb upstream of the TSS, and 2.0 corresponds to 2 kb downstream of the TES. (C) The heat map illustrates the results of Pearson correlation analysis.
Figure 2
Figure 2
Identification and analysis of peaks. (A) Venn diagram illustrates peak overlap between M and P groups. (B) Chromosomal distribution of all peaks. (C) Distribution ratio of peaks in gene functional elements. Genomic functional regions comprise promoter, intergenic, exon, intron, 5’UTR and 3’UTR. (D) ATAC-seq signals were found to be enriched around the TSS in groups M and P. The above figure shows the enrichment map surrounding the TSS. The heat map illustrates the enrichment near the TSS, with ±2.0 representing regions upstream and downstream of the TSS.
Figure 3
Figure 3
Functional enrichment analysis and motif analysis of differential peak-associated genes. (A) Volcano plot of differential peaks (FDR < 0.05, |Fold| > 0). The red dot represents the up-regulated difference peak and the blue dot represents the down-regulated difference peak. (B) GO enrichment analysis of differential peak-associated genes (p < 0.05). Red represents biological processes, green represents cellular components, and blue represents molecular functions. (C) KEGG enrichment analysis of differential peak-associated genes (p < 0.05). The dots range in color from 0 to 0.008. (D,E) The top 10 transcription factor binding motifs were enriched in significantly higher and significantly lower peak areas based on the p-values between the M and p groups, respectively.
Figure 4
Figure 4
Results of ATAC-seq and RNA-seq combined analysis. (A) Venn map of differentially expressed genes identified by ATAC-seq and RNA-seq. (B) GO enrichment analysis of overlapping differential genes. Red represents biological processes, green represents cellular components, and blue represents molecular functions. (C) KEGG enrichment analysis of overlapping differential genes. The dots range in color from 0 to 0.04. (D) Visual display of ATAC-seq and RNA-seq signals in FOXO1, CFL2, CRY2 and ZBED6 genes. (E) Map of the interaction network between genes and transcription factors (TFs). The green oval represents TFs. Diamonds represent genes, red represents up-regulated genes, while yellow represents down-regulated genes.
Figure 5
Figure 5
Validation of sequencing results was performed using qRT-PCR. The histogram depicts the expression levels of 9 genes by RNA-seq and qRT-PCR. The x-axis represents the 9 DEGs, while the y-axis represents the gene expression level.
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