title: Capturing the dynamic nascent transcriptome during acute cellular responses: The serum response.
abstract: 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.
authors.affiliation: Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, and Translational Oncology Program, University of Michigan, Ann Arbor, MI 48109, USA Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
authors.forename: Killeen S
authors.initials: KS
authors.lastname: Kirkconnell
authors.affiliation: Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, and Translational Oncology Program, University of Michigan, Ann Arbor, MI 48109, USA.
authors.forename: Michelle T
authors.initials: MT
authors.lastname: Paulsen
authors.affiliation: Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, and Translational Oncology Program, University of Michigan, Ann Arbor, MI 48109, USA Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA.
authors.forename: Brian
authors.initials: B
authors.lastname: Magnuson
authors.affiliation: Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, and Translational Oncology Program, University of Michigan, Ann Arbor, MI 48109, USA.
authors.forename: Karan
authors.initials: K
authors.lastname: Bedi
authors.affiliation: Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, and Translational Oncology Program, University of Michigan, Ann Arbor, MI 48109, USA Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA ljungman@umich.edu.
authors.forename: Mats
authors.identifier: http://orcid.org/0000-0003-1553-6695
authors.initials: M
authors.lastname: Ljungman
keywords: Gene length; Regulation of transcription; Signal transduction; Transcription elongation