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. 2023 Jun 5;13(11):1875.
doi: 10.3390/ani13111875.

Characterization of Chromatin Accessibility in Fetal Bovine Chondrocytes

Qi Zhang  1 , Qian Li  1 , Yahui Wang  1 , Yapeng Zhang  1 , Ruiqi Peng  1 , Zezhao Wang  1 , Bo Zhu  1 , Lingyang Xu  1 , Xue Gao  1 , Yan Chen  1 , Huijiang Gao  1 , Junwei Hu  2 , Cong Qian  2 , Minghao Ma  2 , Rui Duan  2 , Junya Li  1 , Lupei Zhang  1   2
Affiliations

Characterization of Chromatin Accessibility in Fetal Bovine Chondrocytes

Qi Zhang et al. Animals (Basel). .

Abstract

Despite significant advances of the bovine epigenome investigation, new evidence for the epigenetic basis of fetal cartilage development remains lacking. In this study, the chondrocytes were isolated from long bone tissues of bovine fetuses at 90 days. The Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) and transcriptome sequencing (RNA-seq) were used to characterize gene expression and chromatin accessibility profile in bovine chondrocytes. A total of 9686 open chromatin regions in bovine fetal chondrocytes were identified and 45% of the peaks were enriched in the promoter regions. Then, all peaks were annotated to the nearest gene for Gene Ontology (GO) and Kyoto Encylopaedia of Genes and Genomes (KEGG) analysis. Growth and development-related processes such as amide biosynthesis process (GO: 0043604) and translation regulation (GO: 006417) were enriched in the GO analysis. The KEGG analysis enriched endoplasmic reticulum protein processing signal pathway, TGF-β signaling pathway and cell cycle pathway, which are closely related to protein synthesis and processing during cell proliferation. Active transcription factors (TFs) were enriched by ATAC-seq, and were fully verified with gene expression levels obtained by RNA-seq. Among the top50 TFs from footprint analysis, known or potential cartilage development-related transcription factors FOS, FOSL2 and NFY were found. Overall, our data provide a theoretical basis for further determining the regulatory mechanism of cartilage development in bovine.

Keywords: ATAC-seq; bovine fetal chondrocytes; transcription factors.

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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
Venn diagram of calling peaks by MACS2 and IGV visualization. (a) A total of 9860 peaks are identified by grouping overlap call peaks for every two samples; (b) The location on the genome and peak map of genes SOX9 and RUNX2. The dashed box shows the enriched signals of genes.
Figure 2
Figure 2
The annotation of ATAC-seq peak regions on the bovine genome.
Figure 3
Figure 3
The results of GO and KEGG enrichment analysis. The horizontal axis shows the gene ratio. The vertical axis shows the biological process in GO or KEGG. (a) GO functional enrichment; (b) KEGG pathway enrichment.
Figure 4
Figure 4
Motif enrichment and footprint analysis integrating ATAC-seq and RNA-seq data. (a) Enriched motifs and predicted TFs NF-Y, ATF3, FOSL2, ATF2 and FOS, p-value and mRNA expression; (b) The horizontal axis shows the distance from motif center. The vertical axis shows the number of reads (n = 765, 388, 577, 73, 238, and 2, respectively).
Figure 4
Figure 4
Motif enrichment and footprint analysis integrating ATAC-seq and RNA-seq data. (a) Enriched motifs and predicted TFs NF-Y, ATF3, FOSL2, ATF2 and FOS, p-value and mRNA expression; (b) The horizontal axis shows the distance from motif center. The vertical axis shows the number of reads (n = 765, 388, 577, 73, 238, and 2, respectively).
Figure 4
Figure 4
Motif enrichment and footprint analysis integrating ATAC-seq and RNA-seq data. (a) Enriched motifs and predicted TFs NF-Y, ATF3, FOSL2, ATF2 and FOS, p-value and mRNA expression; (b) The horizontal axis shows the distance from motif center. The vertical axis shows the number of reads (n = 765, 388, 577, 73, 238, and 2, respectively).
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