Transcriptomic and epigenomic landscapes during cell fusion in BeWo trophoblast cells

Introduction: Syncytialization is a process essential to the genesis and vitality of the decisive maternal-fetal interface, the syncytiotrophoblast. While the role of specific genes important in syncytial fusion is appreciated, an integrated global analysis of syncytialization is absent. Methods: We leveraged a variety of approaches (RNA-seq, genome-scale DNA methylation and ChIP-seq) to assemble a genome-wide transcriptomic and epigenomic view of syncytialization in BeWo cells. Results: RNA-seq analysis of expression profiles revealed alterations in similar to 3000 genes over the 3 day time-course of forskolin, including identification of several previously unrecognized genes to be involved in syncytialization. These genes were enriched for cell differentiation, morphogenesis, blood vessel and placental labyrinth development and steroid hormone response. Genome-scale DNA methylation via reduced representation bisulfite sequencing (RRBS) showed altered methylation of a number of CpGs associated with cell differentiation and commitment. Finally, genome-wide localization of seven key histone marks encompassing permissive (H3K4me3, H3K9ac, H3K27ac), enhancer (H3K4me1), elongation (H3K36me3) and repressive (H3K27me3, H3K9me3) states was performed via ChiP-seq. These analyses clearly revealed that syncytialization was associated with a gain in transcriptionally permissive/active marks (H3K4me3, K9ac, K27ac and K36me3) among genes that are either constitutive or upregulated in syncytialization. Discussion: Overall, these results provide a novel resource to elucidate the underlying epigenetic mechanisms coordinating transcriptional changes associated with syncytialization in BeWo cells. (C) 2015 Elsevier Ltd. All rights reserved.