Multi-omics integration strategies for animal epigenetic studies-A review

Genome-wide studies have provided considerable insights into the genetic basis of inheritance; however, they could only partially explain the heritability of complex traits [1]. Complex traits in livestock can be attributed to genetic factors; however, the final phenotypic outcome is highly dependent on the farm environment, ecotypes, and individual genetic backgrounds. This missing heritability in complex traits can be attributed to the contribution of epigenetic variability, arising from the interactions with environmental factors. Transcription, translation, and the subsequent protein modification constitute the transfer of genetic information from an archived copy of DNA to mRNA with subsequent protein production. Every cell in an organism essentially has the same DNA sequences, but the qualitative and quantitative differences in gene expression determine the cell types and functions. Regulation of gene expression is the key to differentiation and development. Epigenetics can be defined as the inheritable changes that modify DNA or related proteins without altering the DNA sequence [2]. Epigenetic information is encoded in the gene sequence and is regulated through DNA methylation, histone modification, and RNA interference (RNAi) [3]. Various epigenetic mechanisms regulate Genome-wide studies provide considerable insights into the genetic background of animals; however, the inheritance of several heritable factors cannot be elucidated. Epigenetics explains these heritabilities, including those of genes influenced by environmental factors. Knowledge of the mechanisms underlying epigenetics enables understanding the processes of gene regulation through interactions with the environment. Recently developed next-generation sequencing (NGS) technologies help understand the interactional changes in epigenetic mechanisms. There are large sets of NGS data available; however, the integrative data analysis approaches still have limitations with regard to reliably interpreting the epigenetic changes. This review focuses on the epigenetic mechanisms and profiling methods and multi-omics integration methods that can provide comprehensive biological insights in animal genetic studies.

Automated summary

Genome-wide studies provide insights into genetic background, but fail to completely explain heritability of complex traits; livestock traits are influenced by genetic factors, farm environment, and individual genetic backgrounds; epigenetics explains missing heritability and mechanisms of gene regulation in response to environmental factors.