The three-dimensional (3D) organisation of the genome is fundamental to establishing and maintaining cell identity. While all cells of the body share the same DNA sequence, they possess distinct 3D genomes that shape gene regulatory interactions between gene promoters, enhancers, and other genomic elements. Lineage specific transcription factors (TFs) can regulate cell identity, and in a limited number of cell types have been shown to also regulate genome organisation. However, in many cell types the factors that establish and maintain cell type specific genome organisation remains are unknown.
To reveal TFs that regulate cell type specific 3D genome organisation, we leveraged mouse genetics and the ~21 million single nucleotide polymorphisms (SNPs) between the Castaneous (Cast) and C57BL/6 (B6) mouse strains as a source of nucleotide sequence variability. TFs bind to DNA at consistent motifs where the nucleotide sequence influences binding. SNPs within these motifs can disrupt this interaction.
Using immune cells from Cast/B6 first generation offspring, we generated 3D genome (Hi-C), chromatin accessibility (ATAC-seq) and gene expression (RNA-seq) data. The well-defined SNPs between the strains enable the separation of genomic data into haplotypes (phasing) and analysis with a novel, statistically robust method, based on edgeR revealed haplotype- and cell type-specific regions. We then performed motif enrichment analysis to identify DNA motifs disrupted by SNPs, resulting in altered transcription factor binding and subsequent changes in chromatin organisation and/or accessibility. Understanding how SNPs influence TF binding and genome organisation is a powerful method to identify which TFs are responsible for establishing and maintaining cell type defining epigenetics.