Capturing the dynamic nascent transcriptome during acute cellular responses: the serum response

Dynamic regulation of gene expression via signal transduction pathways is of fundamental importance during many biological processes such as cell state transitioning, cell cycle progression and stress responses. In this study we used serum stimulation as a cell response paradigm to apply the nascent RNA Bru-seq technique in order to capture early dynamic changes in the nascent transcriptome. Our data provides an unprecedented view of the dynamics of genome- wide transcription during the first two hours of serum stimulation in human fibroblasts. While some genes showed sustained induction or repression, other genes showed transient or delayed responses. Surprisingly, the dynamic patterns of induction and suppression of response genes showed a high degree of similarity, suggesting that these opposite outcomes are triggered by a common set of signals. As expected, early response genes such as those encoding components of the AP-1 transcription factor and those involved in the circadian clock were immediately but transiently induced. Surprisingly, transcription of important DNA damage response genes and histone genes were rapidly repressed.We also show that RNA polymerase II accelerates as it transcribes large genes and this was independent of whether the gene was induced or not. These results provide a unique genome-wide depiction of dynamic patterns of transcription of serum response genes and demonstrate the utility of Bru-seq to comprehensively capture rapid and dynamic changes of the nascent transcriptome. Overall design: One cell line was used (normal human foreskin fibroblasts; HF1, referred to as "nf" in the sample names). HF1 cells were serum-starved for 48 h. One sample ("starved") was then labeled with bromouridine (2 mM) for 30 min. For the remaining samples, serum was added and bromouridine added immediately ("30 min serum") or 30 min, 60 min, or 90 min post serum addition ("60 min serum", "90 min serum", and "120 min serum", respectively). RNA was collected immediately after the 30 min bromouridine labeling period.