RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes [RNA-seq]

Chicken erythrocytes are nucleated cells often referred to as transcriptionally inactive, although the epigenetic changes and chromatin remodeling that mediate transcriptional repression and the extent of gene silencing during avian terminal erythroid differentiation are not fully understood. Here we characterized the changes in gene expression, chromatin accessibility, genome organization, and chromatin nuclear disposition during the terminal stages of erythropoiesis in chicken and found a complex chromatin reorganization at different genomic scales. We identified a robust decrease in transcription in erythrocytes. Nevertheless, a set of genes maintains their expression in erythrocytes, including genes involved in RNA pol II promoter-proximal pausing. Erythrocytes exhibit an inverted nuclear architecture and reposition euchromatin towards the nuclear periphery together with the paused RNA polymerase. In erythrocytes, chromatin domains are partially lost genome-wide except at mini domains retained around paused promoters. Our results suggest that promoter-proximal pausing of the RNA pol II participates in the transcriptional regulation of the erythroid genome and highlight the role of RNA polymerase in the maintenance of local chromatin organization. Total stranded RNAseq on chicken primary fibroblasts, HD3 Erythroblasts cell line, primary embryonic (Embryonic day 10; eRBC) and adult red blood cells (aRBC). Three replicates per cell types are included.