(
A) Cross-correlation plots for Pol 2 and NELF-E ChIP-seq datasets generated in this study. Relative strand cross-correlations were calculated using CLC BIO Genomics Workbench. A plot of log transformed per gene read counts for Pol 2 replicas is shown for each treatment condition; r
s - Spearman’s correlation between replicas. (
B) A pie chart shows the percentage of all paused (23%) and non-paused (70%) LPS-induced Dex-insensitive transcripts that exhibit NELF-E binding (81.1% and 44.2%, respectively) in untreated BMDM. Paused and non-paused transcripts were identified as described in Materials and methods. (
C) RNA-seq expression levels of indicated genes in untreated WT and NELF-B KO BMDM (n = 2). (
D) The volcano plots compare gene expression in L + D (1 hr) treated WT vs. NELF-B KO BMDM (n = 3, fold change = 1.5, FDR p<0.05). Pausing indexes for LPS-induced Dex-insensitive genes from
Figure 1A (left) and LPS-insensitive genes (right) are shown in colors, as indicated.