Transcriptional outcomes and kinetic patterning of gene expression in response to NF-κB activation

• Published in: PLoS biology Vol. 16; no. 9; p. e2006347
• Main Authors: Zhao, Mingming, Joy, Jaimy, Zhou, Weiqiang, De, Supriyo, Wood, 3rd, William H, Becker, Kevin G, Ji, Hongkai, Sen, Ranjan
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01-09-2018; Public Library of Science (PLoS)
• Subjects: Biology and life sciences; Research and analysis methods
• ISSN: 1545-7885; 1544-9173; 1545-7885
• DOI: 10.1371/journal.pbio.2006347

Transcription factor nuclear factor kappa B (NF-κB) regulates cellular responses to environmental cues. Many stimuli induce NF-κB transiently, making time-dependent transcriptional outputs a fundamental feature of NF-κB activation. Here we show that NF-κB target genes have distinct kinetic patterns in activated B lymphoma cells. By combining RELA binding, RNA polymerase II (Pol II) recruitment, and perturbation of NF-κB activation, we demonstrate that kinetic differences amongst early- and late-activated RELA target genes can be understood based on chromatin configuration prior to cell activation and RELA-dependent priming, respectively. We also identified genes that were repressed by RELA activation and others that responded to RELA-activated transcription factors. Cumulatively, our studies define an NF-κB-responsive inducible gene cascade in activated B cells.