Endocrine Abstracts

The human genome is over 2 meters in length, which has to be folded in micrometer-sized nuclear space for proper functions. Although most of our understandings in the human genome are based on linear explanations, it has been speculated that the three-dimensional (3D) and high-order organization of the genome must play important roles in framing the mechanisms of nuclear process such as transcription regulation. Recent advance in 3D genome mapping technologies and sophisticated computational programs have enabled us to reconstitute the 3D models of the genome, and allowed us to investigate the functions of protein factors involved in 3D genome folding and transcription regulation. In this effort, we developed ChIA-PET to comprehensively map specific chromatin interactions mediated by protein factors with haplotype-specificity and nucleotide-resolution. Using ChIA-PET, we have studied the roles of chromatin architecture factors like CTCF, nuclear receptors (NR) such as ER, AR and RARA, and transcription factors (TF) including RNA Polymerase II (RNAPII) in 3D genome organization and transcription regulation. We demonstrated that CTCF-mediated chromatin interaction anchors serve as 3D organizational foci, where constitutive genes are positioned in concordance with the orientation of CTCF binding motifs, whereas RNAPII and other TFs interacts within these structures by drawing cell-type-specific genes towards CTCF-foci for coordinated transcription. We further found that fusion protein PML/RARA could alter the 3D genome configuration of normal cells and become cancerous. In addition, we have shown that haplotype-resolved chromatin interactions have allelic-specific effects on chromatin interactions, thus revise the expression of genes residing in the topological domains, and lead to different traits or diseases. Together, these mechanistic insights establish a topological basis of 3D genome folding and transcription regulation that links genetic variation to phenotype diversity.

DOI: 10.1530/endoabs.54.IS11