Single cell multiome analysis of the bovine placenta identifies gene regulatory networks in trophoblast differentiation

Abstract A central determinant of successful reproduction is pregnancy establishment and maintenance that relies on proper development of the conceptus (embryo/fetus and associated extraembryonic membranes including the placenta). Pregnancy loss in cattle can be caused by inadequate development and differentiation of the placenta. However, the cellular and molecular mechanisms regulating bovine placenta development and, particularly, trophoblast differentiation are not well understood. Recent single-cell RNA-seq analyses revealed dynamic changes in cell populations and gene expression patterns during bovine placental development. Here, the chromatin accessibility landscape across diverse cell populations was determined in the developing (day 40) and mature (day 170) bovine placenta using the 10X Genomics multiome (snRNA-seq and snATAC-seq) platform. Analyses revealed distinct trophoblast, mesenchyme, endothelial, immune, and epithelial cell populations characterized by unique gene expression and chromatin accessibility signatures. ATAC-seq peaks defined open chromatin regions, facilitating the identification of transcription factor binding sites and candidate gene regulatory networks (GRN) involved with trophoblast differentiation. Several transcription factors, known for their involvement in trophoblast differentiation in other mammalian species, were identified as candidate regulators of uninucleate (UNC) to binucleate (BNC) trophoblast differentiation. This study adds to our foundational understanding of gene regulation and expression in the placenta, offering insights into the mechanisms governing pregnancy loss in cattle.