Differential DNA methylation analysis across the promoter regions using methylated DNA immunoprecipitation sequencing profiling of porcine loin muscle

Vet World Vol.13 June-2020 Article-14

Research Article

Veterinary World, 13(6): 1113-1125

https://doi.org/10.14202/vetworld.2020.1113-1125

Kaj Chokeshaiusaha¹, Denis Puthier², Thanida Sananmuang¹, Em-on Olanratmanee¹, Catherine Nguyen², and Roongtham Kedkovid^3,4

1. Department of Veterinary Science, Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-OK, Chon Buri, Thailand.
2. Aix-Marseille University, INSERM UMR 1090, TAGC, Marseille, France.
3. Department of Veterinary Medicine, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.
4. Swine Reproduction Research Unit, Chulalongkorn University, Bangkok, Thailand.

Background and Aim: Pork leanness and marbling are among the essential traits of consumer preference. To acquire knowledge about universal epigenetic regulations for improving breed selection, a meta-analysis of methylated DNA immunoprecipitation sequencing (MeDIP-seq) profiling data of mixed loin muscle types was performed in this study.

Materials and Methods: MeDIP-seq profiling datasets of longissimus dorsi muscle and psoas major muscles from male and female pigs of Landrace and Tibetan breeds were preprocessed and aligned to the porcine genome. Analysis of differential methylated DNA regions (DMRs) between the breeds was performed by focusing on transcription start sites (TSSs) of known genes (–20,000-3000 bases from TSS). All associated genes were further reviewed for their functions and predicted for transcription factors (TF) possibly associated with their TSSs.

Results: When the methylation levels of DMRs in TSS regions of Landrace breed were compared to those of Tibetan breed, 10 DMRs were hypomethylated (Landrace < Tibetan), and 19 DMRs were hypermethylated (Landrace > Tibetan), accordingly (p≤0.001). According to the reviews about gene functions, all associated genes were pieces of evidence for their roles in a variety of muscle and lipid metabolisms. Prediction of the binding TFs revealed the six most abundant binding TFs to such DMRs-associated TSS (p≤0.0001) as follows: ZNF384, Foxd3, IRF1, KLF9, EWSR1-FLI1, HES5, and TFAP2A.

Conclusion: Common DMRs-associated TSS between the lean-type and the marbled-type loin muscles were identified in this study. Interestingly, the genes associated with such regions were strongly evidenced for their possible roles on the muscle trait characteristics by which further novel research topics could be focused on them in the future. Keywords: differential DNA methylation, lean, loin muscle, marbled, methylated DNA immunoprecipitation sequencing, transcription start site.

Keywords: differential DNA methylation, lean, loin muscle, marbled, methylated DNA immunoprecipitation sequencing, transcription start site.

How to cite this article: Chokeshaiusaha K, Puthier D, Sananmuang T, Olanratmanee E, Nguyen C, Kedkovid R (2020) Differential DNA methylation analysis across the promoter regions using methylated DNA immunoprecipitation sequencing profiling of porcine loin muscle, Veterinary World, 13(6): 1113-1125.

Received: 13-01-2020 Accepted: 05-05-2020 Published online: 16-06-2020

Corresponding author: Roongtham Kedkovid E-mail: roongthamk@gmail.com

DOI: 10.14202/vetworld.2020.1113-1125

Copyright: Chokeshaiusaha, et al. This article is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http:// creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.