Chromatin states contribute to coordinated allelic transcriptional bursting to drive iPSC reprogramming

Molecular mechanisms behind the reprogramming of somatic cells to induced pluripotent stem cells (iPSC) remain poorly understood. While dynamic changes in gene expression are considered to drive reprogramming, the contribution of individual alleles of genes to reprogramming remains unexplored. It is thought that two alleles of a gene can transcribe independently or coordinatedly, which in turn can lead to temporal expression heterogeneity with potentially distinct impacts on cell fate. Here, we profiled genome-wide transcriptional burst kinetics with an allelic resolution during the reprogramming of mouse embryonic fibroblast (MEF) to iPSC. We show that many genes involved in iPSC reprogramming pathways exhibit bursty expression and contribute to dynamic autosomal random monoallelic expression (aRME). Moreover, we find that the degree of coordination of allelic bursting differs among genes and changes dynamically during iPSC reprogramming. Importantly, we show that alleles of many reprogramming-related genes burst in a highly coordinated fashion. ATAC-seq analysis revealed that coordination of allelic bursting is linked to allelic chromatin accessibility. Consistently, we show that highly coordinated genes are enriched with chromatin accessibility regulators such as H3K36me3, H3K27ac, histone variant H3.3 and BRD4. Collectively, our study demonstrates that chromatin states contribute to coordinated allelic bursting to fine-tune the expression of genes involved in iPSC reprogramming and provides insights into the implications of allelic bursting coordination in cell fate specification.