Chromatin profiling of GM12878 cells with and without a predicted enhancer element
We test the predicted interferon-inducible enhancer activity of a LINE within the first intron of the IFNAR1 gene (IFNAR1.L1M2a) by knocking out the predicted enhancer using CRISPR, and assessing chromatin and polymerase II occupancy in untreated and interferon beta-treated conditions compared to wildtype cells Overall design: Profiling of histone marks H3K27ac, H3K9me3, as well as PolII were conducted by CUT&Tag in human lymphoblastoid cell line GM12878. Cells were either wildtype, clonal wildtype lines, or CRISPR knockout clonal lines lacking a LINE-derived predicted enhancer within the first intron of the IFNAR1 gene. Cells were either untreated, or treated for 4 hours with 10 units per mL of human interferon beta