Minor Loops in Major Folds: Enhancer-Promoter Looping, Chromatin Restructuring, and Their Association with Transcriptional Regulation and Disease

Abstract

The organization and folding of chromatin within the nucleus can determine the outcome of gene expression. Recent technological advancements have enabled us to study chromatin interactions in a genome-wide manner at high resolution. These studies have increased our understanding of the hierarchy and dynamics of chromatin domains that facilitate cognate enhancer-promoter looping, defining the transcriptional program of different cell types. In this review, we focus on vertebrate chromatin long-range interactions as they relate to transcriptional regulation. In addition, we describe how the alteration of boundaries that mark discrete regions in the genome with high interaction frequencies within them, called topological associated domains (TADs), could lead to various phenotypes, including human diseases, which we term as "TADopathies."

Fig 1. Structural organization of chromatin.

(A) Chromosomes within an interphase diploid eukaryotic nucleus are found to occupy specific nuclear spaces, termed chromosomal territories [25]. (B) Each chromosome is subdivided into topological associated domains (TAD) as found in Hi-C studies. TADs with repressed transcriptional activity tend to be associated with the nuclear lamina (dashed inner nuclear membrane and its associated structures), while active TADs tend to reside more in the nuclear interior [32,33]. Each TAD is flanked by regions having low interaction frequencies, as determined by Hi-C, that are called TAD boundaries (purple hexagon) [29]. (C) An example of an active TAD with several interactions between distal regulatory elements and genes within it.

Fig 2. Mechanisms defining enhancer–promoter recognition.

(A) TAD boundaries pose spatial constraint, allowing for specific enhancer–promoter interactions. (B) Enhancer activity could be obscured by its localization to repressive chromatin compartments. (C) Enhancer–promoter targeting can depend upon the binding compatibility of the transcription factors bound to two interacting loci, termed biochemical compatibility. (D) Insulator elements bound by insulator factors facilitate specific enhancer interaction and eliminate nonspecific enhancer–promoter crosstalk. (E) Noncoding RNA or enhancer RNA (eRNA) transcribed from the enhancer can define its interaction with the target promoter.

Fig 3. Enhancer–promoter interactions and human disease.

(A) An inversion between GATA binding protein 2 (GATA2) and ecotopic viral integration site 1 (EVI1) repositions a GATA2 enhancer (green oval) near EVI1, leading to its ectopic expression while reducing GATA2 expression [65]. Inversion breakpoints are depicted by magenta and yellow dots. (B) The T-allele of rs12913832, which resides within an enhancer (green oval) of the oculocutaneous albinism II (OCA2) gene, leads to a stronger enhancer–promoter looping interaction versus the C allele, as observed by 3C [66]. (C) A 660 kb deletion that removes a TAD boundary and enhancer-A (Enh-A) leads to enhancer B (Enh-B) adoption by lamin B1 gene (LMNB1), leading to its misexpression and, subsequently, autosomal dominant adult-onset leukodystrophy (ADLD) [67]. Deletion breakpoints are depicted by magenta and yellow dots.