Detection of DNA methylation signatures through the lens of genomic imprinting

• Published in: Scientific reports Vol. 14; no. 1; p. 1694
• Main Authors: Hubert, Jean-Noël, Iannuccelli, Nathalie, Cabau, Cédric, Jacomet, Eva, Billon, Yvon, Serre, Rémy-Félix, Vandecasteele, Céline, Donnadieu, Cécile, Demars, Julie
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 19-01-2024; Nature Publishing Group; Nature Portfolio
• Subjects: 631/208/1348; 631/61/212/177; Animal biology; Animal genetics; Animals; Biochemistry, Molecular Biology; Biotechnology; Bisulfite; Cytosine; Design; DNA Methylation; Epigenesis, Genetic; Epigenetics; Gene Expression; Genes; Genetics; Genome; Genomes; Genomic Imprinting; Genomics; Hogs; Humanities and Social Sciences; Life Sciences; Mammals - genetics; multidisciplinary; Science; Science (multidisciplinary); Sperm; Swine; Veterinary medicine and animal Health
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-024-52114-3

Genomic imprinting represents an original model of epigenetic regulation resulting in a parent-of-origin expression. Despite the critical role of imprinted genes in mammalian growth, metabolism and neuronal function, there is no molecular tool specifically targeting them for a systematic evaluation. We show here that enzymatic methyl-seq consistently outperforms the bisulfite-based standard in capturing 165 candidate regions for genomic imprinting in the pig. This highlights the potential for a turnkey, fully customizable and reliable capture tool of genomic regions regulated by cytosine methylation in any population of interest. For the field of genomic imprinting, it opens up the possibility of detecting multilocus imprinting variations across the genome, with implications for basic research, agrigenomics and clinical practice.