Comparison of the Genome-Wide DNA Methylation Profiles between Fast-Growing and Slow-Growing Broilers

Abstract

IntroductionGrowth traits are important in poultry production, however, little is known for its regulatory mechanism at epigenetic level. Therefore, in this study, we aim to compare DNA methylation profiles between fast- and slow-growing broilers in order to identify candidate genes for chicken growth. Methylated DNA immunoprecipitation-sequencing (MeDIP-seq) was used to investigate the genome-wide DNA methylation pattern in high and low tails of Recessive White Rock (WRRh; WRRl) and that of Xinhua Chickens (XHh; XHl) at 7 weeks of age. The results showed that the average methylation density was the lowest in CGIs followed by promoters. Within the gene body, the methylation density of introns was higher than that of UTRs and exons. Moreover, different methylation levels were observed in different repeat types with the highest in LINE/CR1. Methylated CGIs were prominently distributed in the intergenic regions and were enriched in the size ranging 200–300 bp. In total 13,294 methylated genes were found in four samples, including 4,085 differentially methylated genes of WRRh Vs. WRRl, 5,599 of XHh Vs. XHl, 4,204 of WRRh Vs. XHh, as well as 7,301 of WRRl Vs. XHl. Moreover, 132 differentially methylated genes related to growth and metabolism were observed in both inner contrasts (WRRh Vs. WRRl and XHh Vs. XHl), whereas 129 differentially methylated genes related to growth and metabolism were found in both across-breed contrasts (WRRh Vs. XHh and WRRl Vs. XHl). Further analysis showed that overall 75 genes exhibited altered DNA methylation in all four contrasts, which included some well-known growth factors of IGF1R, FGF12, FGF14, FGF18, FGFR2, and FGFR3. In addition, we validate the MeDIP-seq results by bisulfite sequencing in some regions.ConclusionsThis study revealed the global DNA methylation pattern of chicken muscle, and identified candidate genes that potentially regulate muscle development at 7 weeks of age at methylation level.

Genome-Wide Epigenetic Studies in Chicken: A Review

“…They observed a decrease of DNA methylation level in the promoter region, especially at the transcription start site (TSS), and an increase in the gene body regions [74]. This is consistent with the observation that average methylation patterns were the lowest in CpG islands that are localized in the promoters [75]. Slight methylation variations were observed along the gene body [74].…”

Genome-wide analysis of CpG islands in some livestock genomes and their relationship with genomic features

“…A genome-wide profile of DNA methylation in CGIs has been reported for many organisms (Du et al 2012;Kwak et al 2014), which confirms the obtained results in the cur- doi: 10.17221/78/2015-CJAS rent study. The CGIs in the gene body (CDS plus introns) are relatively highly methylated, whereas CGIs in the promoter (around TSSs) remain hypomethylated, a finding that is consistent with human (Du et al 2012) and chicken (Hu et al 2013). …”

“…The results of Hu et al (2013) have shown that the average methylation density was the lowest in CGIs followed by promoters and within the gene body, however, the methylation density of introns was high in comparison with the regions. Also, methylated CGIs were prominently distributed in the intergenic regions.…”

Epigenetics and developmental programming of welfare and production traits in farm animals

“…DNA binding of MyoD and induction of muscle-determining genes is also regulated by epigenetic changes to binding sites in the promoters of its target genes (Fong et al 2012). Dynamic changes in DNA modification regulate myogenic commitment and differentiation (Tsumagari et al 2013), and global changes in DNA methylation patterns have been mapped in fast-and slow-growing strains of chicken, evidence for a direct epigenetic effect on muscle growth (Hu et al 2013b). It is also apparent that long non-coding RNAs play an important role in regulating muscle growth, at least in part by controlling muscle-specific promoter activity (Mousavi et al 2013).…”