CTCF regulates chromatin accessibility of the HBAD gene promoter during erythroid differentiation [ChIP-Seq]

Chromatin structure undergoes dynamic rearrangements during cell differentiation. The architectural protein CTCF plays diverse roles in this process. Here, we demonstrate that a subset of gene promoters alters their chromatin accessibility profiles upon CTCF binding during differentiation of the chicken erythroblast cell line HD3. Furthermore, we show that CTCF contributes to establishing a specific 3D chromatin architecture in the a-globin multigenic domain prior to differentiation in HD3 cells. Overall design: To characterize CTCF's role during in vitro chicken erythroid differentiation, we performed CTCF ChIP-seq in both uninduced HD3 cells and HD3 cells induced for 24 hours. We then generated a promoter-specific mutant lacking the CTCF binding site in the HBAD globin gene and analyzed resulting changes using ATAC-seq, to assess chromatin accessibility, and UMI-4C, to evaluate local chromatin interactions.