Coordinated Regulation of Synthesis and Stability of RNA During the Acute TNF-Induced Proinflammatory Response
Coordinated regulation of synthesis and stability of RNA during the acute TNF-induced proinflammatory response Michelle T. Paulsena, Artur Velosoa,b, Jayendra Prasada, Karan Bedia,c, Emily A. Ljungmana, Ya-Chun Tsana,c, Ching-Wei Changa,d, Brendan Tarriere, Joseph G. Washburne, Robert Lyonse, Daniel R. Robinsonf, Chandan Kumar-Sinhaf, Thomas E. Wilsonf,g, and Mats Ljungmana,c,1 aDepartment of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, bBioinformatics Program, Department of Computational Medicine and Bioinformatics, cDepartment of Environmental Health Sciences, School of Public Health, dBiomedical Engineering, fDepartment of Pathology, gDepartment of Human Genetics, and eUniversity of Michigan DNA Sequencing Core, University of Michigan, Ann Arbor, MI 48109 Edited by Roy Parker, University of Colorado, Boulder, CO, and approved December 20, 2012 (received for review November 5, 2012) Steady-state gene expression is a coordination of synthesis and homeostasis and in the reprogramming of gene expression dur- decay of RNA through epigenetic regulation, transcription factors, ing the acute TNF-induced proinflammatory response. micro RNAs (miRNAs), and RNA-binding proteins. Here, we present bromouride labeling and sequencing (Bru-Seq) and bromouridine Results pulse-chase and sequencing (BruChase-Seq) to assess genome- Metabolic Labeling of Nascent RNA with Bromouridine. To explore wide changes to RNA synthesis and stability in human fibroblasts the contributions of both transcriptional
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