6C). Both tested cell lines selleck chemicals llc being transfected with the expression construct encoding c-Jun displayed a significantly more open chromatin configuration at the TNF TSS, as compared with cells transfected with control vector (Fig. 6D). The classical method to probe chromatin conformation—DNase I sensitivity assay [53, 54]—was previously

applied to the TNF/lymphotoxin (LT) genomic locus in different types of immune cells [14-17, 19-22, 24, 55]. DNase I hypersensitivity (DH) sites, the hallmarks of open chromatin, were found at the proximal TNF promoter and at TSS in primary and cultivated myeloid cells from mice, humans, and pigs [14-17, 19-22], and were confirmed by restriction enzyme accessibility assay in the mouse macrophage cell line J774 [18]. Results obtained with MNase Palbociclib cell line digestion assay applied to human myeloid cell lines appeared controversial: closed chromatin configuration (putative nucleosomal positions) was identified either at the proximal

promoter [56] or at the proximal promoter and TSS of the TNF gene [57]. However, open conformation of TNF proximal promoter/TSS in mouse BMDM (GEO entry GSE26550 [58]) and human CD14+ monocytes (GEO sample GSM1008582) was confirmed by genome-wide DNase-seq analysis (Supporting Information Fig. 1). Open chromatin conformation at the TNF promoter in Jurkat T-cell line was detected only after stimulation or ectopic expression of viral proteins [15, 21, 55], and no studies were performed in primary

PAK5 human T cells. The exact position of the DH site upstream of the TNF gene in primary mouse T cells was a matter of controversy. It was originally mapped to the middle of the intergenic region between TNF and LTα genes and designated “HSS-0.8” (hypersensitive site; “0.8 kb upstream of the first exon” [24]), but was recently remapped to the proximal part of TNF promoter [59]. This DH site appeared more prominent in cells polarized under Th1 conditions [24]. Analysis of recent DNase-seq data deposited to ENCODE [60] and GEO databases (GSE33802 [61]) confirmed the presence of DH site at the proximal TNF promoter with enhanced DNA accessibility at TNF TSS upon polarization of naive CD4+ T cells under Th1 conditions (Supporting Information Fig. 1A). DNase-seq analysis of the TNF/LT locus in human immune cells also revealed an open chromatin conformation at TNF promoter (Supporting Information Fig. 1B). In our study, we detected inducible chromatin remodeling at the TNF TSS of both mouse and human primary T cells by restriction enzyme accessibility assay (Fig. 1). We also confirmed the open status of TNF TSS in BMDM and detected inducible changes of chromatin conformation at TNF TSS in T cells by MNase digestion assay (Fig. 2).