Transcriptomic and epigenomic analysis of bovine embryonic stem cells derived from in vitro fertilized and somatic cell nuclear transfer embryos

NAVARRO M; HALSTEAD, MICHELLE MARGARET; MUTTO AA; ROSS PJ

Bologna

Congreso; Nineteenth International Congress on Animal Reproduction; 2022

International Congress on Animal Reproduction (ICAR)

Bovine embryonic stem cells ESC (bESCs) can be derived from in vitro fertilized (IVF) and somatic cell nuclear transfer embryos (SCNT). Given that SCNT embryos often present epigenetic dysregulation that can lead to abnormal development, we set out to assess the transcriptomic and epigenomic status of SCNT-derived ESCs.bESCs were derived from day-7 SCNT or IVF blastocysts in N2B27 base media containing BSA, FGF2 and IWR1. For each ESC group, genome-wide transcriptome and histone profiles (H3K4me3, H3K9me3, H3K27me3) were generated for three independent cell lines using 3?-Tag-Seq and Cut&Tag techniques, respectively, and compared to bovine fetal fibroblasts (FIB).After 4 weeks in culture, well-defined colonies appeared in both groups with an equivalent efficiency (30%). All ESC exhibited pluripotency features: alkaline phosphatase activity, pluripotency marker expression and euploidy. Principal component analysis of gene expression as well as histone profiles of H3K4me3, H3K9me3 and H3K27me3 showed that IVF-ESC and SCNT-ESC clustered together but separate from FIB, suggesting that transcriptomes and epigenomes of both ESC sources were similar, but distinct from FIB. Specifically, 2,378 differently expressed genes (DEG, p2) were found in bESC compared to FIB and only 46 DEG were found between SCNT-bESC and IVF-bESC. Additionally, we identified 439 H3K27me3 peaks, 214 H3K4me3 peaks, and 1,041 H3K9me3 peaks that differed between both bESC sources. However, those modifications were spread out over all chromosomes without a predominance in regions surrounding DEG, promoters or body genes.Finally, categorization of chromatin states genome wide showed that both ESCs shared the same epigenetic pattern in promoters. Minor differences found between both ESC could be stochastic in nature, possibly related to genotype variability or the techniques themselves.These results suggest that SCNT-ESC resemble IVF-ESC transcriptionally and epigenetically, enabling the generation of pluripotent stem cells from adult individuals, thus, allowing the expansion of agricultural and economically important production traits.