Transcriptomic effects of alginate hydrogel applied to the production of bovine embryos

<i>In vitro</i>-produced blastocysts are exposed to different stimuli when compared with <i>in vivo</i> ones. This includes the culture of <i>in vitro</i> embryos in a sturdy petri-dish, while <i>in vivo</i> embryos develop in a soft and dynamic structure. Here we hypothesized that a softer environment could differently modulate the <i>in vitro</i> produced embryos<i>.</i> To that aim, presumptive zygotes were produced by <i>in vitro</i> fertilization and divided into three groups: 1) Cultured in a regular Petri dish - Control (CON); 2) Cultured on top of an alginate hydrogel surface (TOP); 3) Encapsulated inside an alginate hydrogel sphere (ENC) and cultured. We observed a decrease in blastocyst rate in TOP and ENC compared with the CON. Profiling of 383 bovine miRNAs, we found 3 miRNAs involved in cell proliferation being differently modulated by the TOP and ENC groups (miR-1246; miR-1260b, and miR-541). Analyzing global levels of DNA methylation and hydroxymethylation, we observed increased levels of the two marks in the TOP group when compared with the CON and ENC systems. RNA sequencing (RNA-seq) analysis carried out using blastocysts showed alterations in several developmentally important genes among the three groups. In summary, our results indicate that <i>in vitro</i> embryo production was possible to achieve up to the blastocyst stage. However, with the experimental conditions used herein, the alginate hydrogels adversely affected the embryo development, which were paralleled by epigenetic and transcriptomic changes.