Chd4 regulates intra-chromatin looping by concealing CTCF sites from B2 SINEs in mESCs

CTCF plays a critical role in maintaining the three-dimensional (3D) chromatin organization, which is important for gene regulation, as it allows distal regulatory elements to come into proximity with one another. However, the detailed mechanism responsible for establishing and maintaining the recruitment of CTCF remains elusive. Here, we use in situ Hi-C to show that the ATP-dependent chromatin remodeler, Chd4, regulates intra-chromatin looping by controlling chromatin accessibility to conceal aberrant CTCF-binding sites in mouse embryonic stem cells (mESCs). These aberrant CTCF-binding sites are embedded in B2 SINEs and are localized within the interior of chromatin loops. In the absence of Chd4, the aberrant CTCF-binding sites become accessible and improper CTCF recruitment occurs, resulting in disorganization of the 3D chromatin architecture and subsequent disruption of enhancer-promoter interactions and the transcription of the corresponding genes. These results indicate that Chd4 regulates adequate transcription of mESCs by securing the proper 3D chromatin organization. For in situ Hi-C experiment : Genome-wide chromatin conformation capture upon CHD4 loss (Chd4 knockdown using siRNA and auxin treatment for CHD4-mAID) in mouse embryonic stem cells (mESCs). For MNase-seq experiment : Genome-wide analysis of nucleosomes upon CHD4 loss in mESCs. For ATAC-seq experiment : Genome-wide analysis of chromatin accessibility upon CHD4 loss in mESCs. For ChIP-seq experiment : Genome-wide distributions of various factors upon CHD4 loss in mESCs. For CUT&RUN experiment : Genome-wide distributions of various factors upon CHD4 loss in mESCs. For RNA-seq experiment : Strand-specific totalRNA-seq and mRNA-Seq upon CHD4 loss in mESCs. For GRO-seq experiment : Genome-wide analysis of nascent transcripts upon CHD4 loss in mESCs.