H3K27me3 chromatin heterogeneity reveals variable cell responses to estrogen and endocrine treatment [CUT&Tag]

Gene expression heterogeneity creates subpopulations of tumor cells with increased resistance, posing a challenge to effective cancer treatment. This non-genetic variability stems from the stochastic nature of transcription, where gene activation occurs in bursts of RNA synthesis. The estrogen-responsive TFF1 gene is heterogeneously expressed due to periods of inactivity lasting several days. Here we uncover the mechanism driving heterogeneous TFF1 activity by examining cells sorted based on TFF1 activity levels (High vs Low TFF1 expressing cells). In both populations, genome-wide assays and live cell imaging were performed to assess chromatin state, ERa occupancy, allele activation and transcriptional bursting behavior. Overall design: Nascent and total RNA levels measured in MCF7 cells treated with 1nM of Estrogen to evaluate the transcriptome. NUN refers to Nascent RNA sequencing and pA-RNA refers to total RNA sequencing. All experiments have been performed in triplicates (referred as Rep 1, 2, 3 or A, B, C)