Dynamic transcriptome and chromatin architecture in granulosa cells during chicken folliculogenesis

Ovarian follicle development is a complex and well-orchestrated biological process. Granulosa cells (GCs) are the most important somatic cells in the ovary, which play important roles in the growth of follicles. Three-dimensional (3D) chromatin architecture has emerged as an important regulator of transcription in eukaryote, but how these changes in granulosa cells during folliculogenesis of chicken are largely unexplored. Here, we performed an integrative analysis of transcriptomic and chromatin structural characterization for chicken follicular granulosa cells of 10 and 3 growth stages respectively. In this study, focusing on the special folliculogenesis process in chicken, we conducted bulk RNA-seq of GCs at ten follicle growth stages (SWF, LWF, SYF, LYF, F5, F4, F3, F2, F1, and POF) and single cell RNA-seq (scRNA-seq) of GCs at three representative stages (SWF, F1, and POF) to depict the transcriptome landscapes during the stepwise folliculogenesis. We also performed in situ high-throughput chromatin conformation capture (Hi-C) sequencing, ATAC-seq, and ChIP-seq analyses for GCs at the three representative stages to further investigate the chromatin architecture dynamics and their close associations with the temporal gene expression profiling during the development.