Deciphering histone mark-specific fine-scale chromatin organization at high resolution with Micro-C-ChIP.

The regulation of cell-type-specific transcription relies on complex 3D interactions between promoters and distal regulatory elements. Although Hi-C has advanced our understanding of genome architecture, its high sequencing demand limits use in large-scale or time course experiments. We introduce Micro-C-ChIP, a strategy combining Micro-C with chromatin immunoprecipitation to map 3D genome organization at nucleosome resolution for defined histone modifications. We profile H3K4me3 and H3K27me3-specific 3D genome architecture in mouse embryonic stem cells (mESC), hTERT-immortalized human retinal pigment epithelial (hTERT-RPE1) cells, and HCT-116 RAD21-mAID-mClover (HCT-116 RAD21-mAC) cells. We validate that Micro-C-ChIP reveals genuine 3D genome features that are not driven by ChIP-enrichment bias. We identify extensive promoter-promoter contact networks in mESCs and hTERT-RPE1, and resolve the distinct 3D architecture of bivalent promoters in mESCs. Together, our results demonstrate that Micro-C-ChIP is a high-resolution, cost-efficient approach to study histone-modification-specific chromatin folding.