Genome-wide maps of SP100A binding chromatin.

Sp100 protein has been previously reported to contain direct DNA binding domains or to interact with chromosomal proteins to regulate transcription of genes of both cellular and viral origin. Thus, investigation of how IFNß shifted chromosomal association pattern of Sp100A may help to elucidate the biological function of this isoform in response to IFN. Herein this study, Cleavage Under Targets and Tagmentation (CUT&Tag) technique plus Illumina deep sequencing(deep-seq) was employed to analyze Sp100A associated host chromosomal regions in NT and IFNß treated Sp100Aoe cells. The sample from HEp-2 cells served as negative control as it lacked Flag-Sp100A expression61. General chromosome association pattern profiling of Sp100A showed that the protein was preferentially associated with promoter region within -3kb to 3kb distance to the transcription start site (TSS) and was most frequently located within the transcription regulation area less than 1kb from the TSS, reinforcing its major role as a transcriptional regulator. Further in-depth comparison of the enrichment level of Sp100A in the promoter regions between NT and IFNß groups revealed the following findings: I) IFN stimulation substantially changed the promoter region binding affinity of Sp100A on a huge group of targeted genes. Among the promoters with increased Sp100A association frequency in response to IFNß, the top ones include promoters of ISGs such as OAS2P, DDX58P, IFI16P, MX2P and ISG15P . II) Comparison of the enrichment degree of Sp100A in the promoter regions of a set of experimentally confirmed antiviral ISGs, reviewed by Charles Rice in 2011, revealed an overall enrichment of Sp100A on these ISGs upon IFN signaling .Specifically, Sp100A was preferential assembled on promoters of OAS2, RIG-I (DDX58), IFI16, RSAD2 (Viperin), MX2, SLC15A3 and ISG15 with more than 5-fold higher enrichment in IFNß group over NT group. Overall design: Examination of Genome-wide maps of SP100A binding chromatin under IFNß or Mock treated conditions.