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. Author manuscript; available in PMC: 2021 Jul 1.
Published in final edited form as: Nat Cancer. 2020 Nov 9;2(1):34–48. doi: 10.1038/s43018-020-00135-y

Extended Data Fig. 6. CDK4/6 inhibitor-activated LTR enhancers are predicted to regulate immune genes.

Extended Data Fig. 6

a, Gene Ontology analysis of interferon-related signatures using genes predicted to be regulated by all abemaciclib-activated enhancers, abemaciclib-activated SEs, or abemaciclib-activated LTR enhancers in MCF7 cells treated with DMSO or abemaciclib for 7 days. Odds ratios and P-values calculated by ChIP-Enrich.

b, ATAC-seq and H3K27ac ChIP-seq tracks near representative immune genes in MCF7 and MDA-MB-453 treated with DMSO or abemaciclib for 7 days. LTRs annotated using Repeat Masker are shown as blue bars. Yellow highlights indicate H3K27ac up-peaks that align with an LTR.

c, Relative RNA-seq normalized reads of immune genes in MCF7 parental and shRB1 cells treated with DMSO or abemaciclib for 7 days, measured by RNA-seq (parental: n=3; shRB1: n=2). Means ± s.d. are shown. DESeq2 was used to calculated adjusted P-values.