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MeDIP based methylome analysis of muscle from two pig breeds with varying muscularity

ABSTRACT: We report the application of methylated DNA immunopreciptation (MeDIP)-next generation sequencing for examining methylome in two different breeds of pigs. Two muscle samples from each animal/breed processed to isolated DNA. DNA was isolated from two muscle samples (one per breed) was used for methylated DNA immunoprecipitation (MeDIP). 5 methyl cytosine regions were immunoprecipitated and processed for next generation sequencing in Hiseq 2500 (Illumina). The pre-processed reads were mapped to the Sus scrofa genome v11.1 downloaded from UCSC (http://genome.ucsc.edu/) with Burrows–Wheeler alignment (BWA) (version 0.7.17). The MeDIP data generated was used for identification of differentially methylated regions (DMRs) across the chromosome between the breeds using Burrrows Eheeler Alignment (BWA version 0.7.17. Uniquely mapped reads were processed further with MEDIPS. A total of 1545 and 25 DMRs (P<0.1) were identified across the pig chromosome and mitochondrial DNA respectively.

ORGANISM(S): Sus scrofa

PROVIDER: GSE184969 | GEO | 2023/09/29

REPOSITORIES: GEO

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Project description:Chicken growth traits are important in poultry production, however, little is known for its regulatory mechanism at epigenetic level. Therefore, this study aims to compare DNA methylation profiles between fast- and slow-growing broilers in order to identify candidate genes underlying 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). The results showed that the average of methylation density was the lowest in CGIs followed by promoters. Within the gene body, the methylation density of introns was higher than 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 range of 200-300 bp. In total 13,294 methylated genes were found in four samples, including 4,085 differentially methylated genes between WRRh and WRRl, 5,599 between XHh and XHl, 4,204 between WRRh and XHh, as well as 7,301 between WRRl and 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 further validate the MeDIP-seq results by bisulfite sequencing in some regions. 12 Breast muscle samples were collected from two breeds of different growth rate, Recessive White Rock (WRR) and Xinhua Chickens (XH). Each breed included low and high-weight groups and 3 samples from each group were pooled equally for methylated DNA immunoprecipitation-sequencing (MeDIP-seq).

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MeDIP based methylome analysis of muscle from two pig breeds with varying muscularity

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