GSE131356
CTCF confers local nucleosome resiliency after DNA replication and during mitosis
The access of Transcription Factors (TFs) to their cognate DNA binding motifs requires a precise control over nucleosome positioning. This is especially important following DNA replication and during mitosis, both resulting in profound changes in nucleosome organization over TF binding regions. Using mouse Embryonic Stem (ES) cells, we show that the TF CTCF displaces nucleosomes from its binding site and locally organizes large and phased nucleosomal arrays, not only in interphase steady-state but also immediately after replication and during mitosis. While regions bound by other TFs, such as Oct4 and Sox2, display major rearrangement, the post-replication and mitotic nucleosome organization activity of CTCF is not likely to be unique: Esrrb binding regions are also characterized by persistent nucleosome positioning. Therefore, selected TFs such as CTCF and Esrrb act as resilient TFs governing the inheritance of nucleosome positioning at gene regulatory regions throughout the ES cell-cycle. Overall design: Examination of binding of CTCF and SMC1 in mouse ES cells, fibroblasts and myoblasts in interphase and mitosis by ChIP-seq.  Examination of nucleosome positioning at CTCF sites in interphase, mitosis and immediately after replication by MNase-seq and MINCE-seq, including investigation of nucleosome positioning at CTCF sites in interphase and mitosis with auxin inducible depletion of CTCF.