Comparison of Epigenetic Differences in Genomes of Cloned Cattle from Different Donor Cell Sources

The aim of this study was to investigate the epigenetic differences between cattle cloned using fetal fibroblasts (FFBs) and fetal oviduct epithelial cells (FOVs) as donor nuclei. We employed assay for transposase-accessible chromatin sequencing (ATAC-seq), RNA sequencing (RNA-seq), and whole-genome 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC) methylation sequencing to analyze these differences. Our findings revealed that cloned cattle derived from FOV donor nuclei exhibited higher chromatin accessibility and increased expression of genes associated with blastocyst development compared to those derived from FFBs. Specific gene motifs and corresponding transcription factors potentially involved in blastocyst development were identified. Notably, live cloned cattle derived from FFBs showed a 5hmC content exceeding 4‰, whereas this value was below 2‰ in deceased clones. Compared to naturally fertilized embryos, somatic cell nuclear transfer (SCNT) zygotes exhibited incomplete epigenetic reprogramming. Epigenetic modifications in live cloned cattle varied based on donor cell type, with these differences primarily localized in intergenic and intronic regions, rather than gene expression regulatory regions. Our study highlights distinct patterns of chromatin accessibility and gene expression in cattle cloned from FOV donor nuclei, characterized by more open chromatin and higher transcriptional activity. Additionally, the original 5mC differences in donor cells were retained in cloned embryos during development, while developmentally failed embryos showed abnormally low 5hmC levels. Supplementary Material File (manuscript.docx) - Download - 2.39 MB Information & Authors Information Version history Peer review timeline Published Theriogenology Version of Record1 Oct 2025Published Copyright This work is licensed under a Non Exclusive No Reuse License.

Authors Metrics & Citations Metrics Article Usage 209views 109downloads Citations Download citation Mingxuan Sheng, Dongdong Bo, Haoqiang Ma, et al. Comparison of Epigenetic Differences in Genomes of Cloned Cattle from Different Donor Cell Sources. Authorea. 16 January 2025. DOI: https://doi.org/10.22541/au.173701380.09722792/v1 DOI: https://doi.org/10.22541/au.173701380.09722792/v1 If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download. For more information or tips please see 'Downloading to a citation manager' in the Help menu.