Transcriptional outcomes and kinetic patterning of gene expression in response to NF-?B activation [ChIA-PET]

Transcription factor NF-?B regulates cellular responses to environmental cues. For many stimuli NF-?B resides only transiently in the nucleus. Consequently, time-dependent transcriptional outputs are a fundamental feature of NF-?B activation. Here we identify mechanisms that direct kinetic patterns of NF-?B-dependent gene expression and transcriptional outcomes in response to a transient NF-?B-inducing stimulus in B cells. By combining RELA binding, RNA polymerase II (Pol II) recruitment, and perturbation of NF-?B 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. Additionally, we identified genes that were repressed by RELA activation and others that responded to RELA-activated transcription factors. Cumulatively, our studies define an NF-?B-responsive inducible gene cascade in activated B cells. Overall design: kinetic patterning of direct and indirect NF-?B targets

转录因子NF-κB（Transcription factor NF-κB）可调控细胞对环境信号的应答。在多数刺激条件下，NF-κB仅短暂驻留于细胞核内。因此，时序依赖性的转录输出是NF-κB激活的核心特征之一。本研究以B细胞为模型，针对瞬时性NF-κB诱导刺激，解析了调控NF-κB依赖性基因表达动力学模式及转录结局的分子机制。通过整合RELA结合分析、RNA聚合酶II（RNA polymerase II, Pol II）招募检测以及NF-κB激活扰动实验，本研究证实：早期与晚期激活的RELA靶基因之间的动力学差异，可分别归因于细胞激活前的染色质构型以及RELA依赖性的预激活。此外，本研究还鉴定出受RELA激活抑制的基因，以及可响应RELA激活型转录因子的基因。综上，本研究明确了激活B细胞中响应NF-κB的诱导型基因级联调控网络。整体实验设计：直接与间接NF-κB靶基因的动力学模式分析。