Fibroblast starvation activates ECM remodeling gene transcription and putative enhancers despite inducing quiescence [bruseq]
Depletion of growth factors and nutrients induces cellular quiescence, which often accompanies transcriptional silencing and chromatin compaction. Paradoxically, such depletion occurs in pathological microenvironments in which fibroblasts are activated to orchestrate tissue remodeling. The relationship between fibroblast activation and growth factor and nutrient depletion remains unclear. Here, we report that serum depletion in cell culture, a model for growth factor and nutrient depletions, extensively activates transcription in fibroblasts, despite inducing quiescence. Activated genes were enriched for extracellular matrix (ECM) structural components and proteases. The ECM-related transcription accompanied activation of putative distal enhancers, but not promoters. The activated putative enhancers were enriched for non-coding variants associated with inflammatory bowel disease (IBD) risk, suggesting an alteration in the ECM remodeling gene regulatory network in IBD. This study implicates nutrient and growth factor depletion in activating the ECM remodeling gene program in fibroblasts, challenging the prevailing view linking such depletion to transcriptional dormancy. Overall design: To define the transcriptional state of fibroblasts undergoing nutrient deprivation, primary dermal fibroblasts (GM07492) maintained in 10% serum (“proliferation”) were subjected to 1% serum for 48 hours (“starvation”). Starved cells were then subjected to a recovery phase with 10% serum for 24 hours ("recovery"). To determine genes transcribed during proliferation, starvation, and recovery, we performed Bru-seq, in which nascent transcripts are labeled with 5-bromouridine (BrU) in cell culture, purified by anti-BrU immunoprecipitation, and quantified by high-throughput sequencing. We labeled transcripts for 2 hours, either during proliferation, at the end of starvation, or at the end of recovery.