Transcriptional outcomes and kinetic patterning of gene expression in response to NF-κB activation
Fig 5
Kinetic patterning of NF-κB-dependent gene expression.
(A) Relationship of Pol II–associated chromatin looping to NF-κB-dependent gene expression. Unactivated BJAB cells were used to carry out ChIA-PET after immunoprecipitation of cross-linked chromatin with anti-Pol II antibodies. Resulting sequence data were analyzed and categorized according to the type of promoter status. Category I = genes with no Pol II (no loops); II = genes with Pol II at promoter (no loops); III = genes with single-gene-based loops, in which only 1 gene was involved; IV = genes with multi-gene-based loops that included promoter–promoter interactions in which at least 2 genes were involved. (B) Analysis of 130 direct RELA target genes and (C) 78 “indirect” RELA target genes that are induced ≥2-fold by P+I. Yellow and blue circles denote genes that have or do not have Pol II–associated loops, respectively, in unactivated BJAB cells. Average expression profiles of genes within each group were obtained from RNA-Seq analysis of Tet-inducible BJAB clones (right). The letters “Ad” after a pattern number indicate target genes that were activated by RELA binding, and the letters “Ai” indicate target genes that were indirectly activated by RELA. Genes in each category are listed in S6B Table. (D) RELA and Pol II binding over the activation time course on representative direct and indirect RELA target genes. The effect of dnIκBα expression on RNA expression is shown on the top 2 lines, followed by RELA ChIP-Seq and Pol II ChIP-Seq tracks. The bottom line summarizes loops identified by ChIA-PET. Complete RNA time courses for each gene are shown in (S6J Fig). ChIA-PET data are available on the GEO website (http://www.ncbi.nlm.nih.gov/geo/) (Accession number GSE117259). Underlying data for Fig 5B and 5C are provided in S1C and S1D Data. ChIA-PET, chromatin interaction analysis by paired-end tag sequencing; ChIP-Seq, chromatin immunoprecipitation and sequencing; dnIκBα, dominant negative NFKB inhibitor alpha; GEO, Gene Expression Omnibus; NF-κB, nuclear factor kappa B; P+I, phorbol 12-myristate 13-acetate and ionomycin; Pol II, RNA polymerase II; RNA-Seq, RNA sequencing; Tet, tetracycline.