Theoretical analysis of the role of chromatin interactions in long-range action of enhancers and insulators

Abstract

Long-distance regulatory interactions between enhancers and their target genes are commonplace in higher eukaryotes. Interposed boundaries or insulators are able to block these long-distance regulatory interactions. The mechanistic basis for insulator activity and how it relates to enhancer action-at-a-distance remains unclear. Here we explore the idea that topological loops could simultaneously account for regulatory interactions of distal enhancers and the insulating activity of boundary elements. We show that while loop formation is not in itself sufficient to explain action at a distance, incorporating transient nonspecific and moderate attractive interactions between the chromatin fibers strongly enhances long-distance regulatory interactions and is sufficient to generate a euchromatin-like state. Under these same conditions, the subdivision of the loop into two topologically independent loops by insulators inhibits interdomain interactions. The underlying cause of this effect is a suppression of crossings in the contact map at intermediate distances. Thus our model simultaneously accounts for regulatory interactions at a distance and the insulator activity of boundary elements. This unified model of the regulatory roles of chromatin loops makes several testable predictions that could be confronted with in vitro experiments, as well as genomic chromatin conformation capture and fluorescent microscopic approaches. chromatin-polymer model | enhancer-promoter | long-range gene regulation U nlike most known cases of transcriptional regulation in prokaryotes and lower eukaryotes, metazoan genes are often regulated by enhancers placed tens to hundreds of kilobases away from the promoter (1-4). Facilitating mechanisms are necessary for such long-range enhancer action, as we shall explain below. Widespread distant regulation also requires additional mechanisms to ensure specificity. Enhancer-blocking DNA sequences, known as boundaries or insulators, define chromatin domains within which enhancer action is limited (5-11). While it is known that insulator elements bind to particular proteins (12) how these protein complexes manage to block enhancer action across domains remains controversial.Several different models for long-range enhancer-promoter communication have been proposed, for review see refs. 5, 10. One model hypothesizes a tracking mechanism that involves the processive movement of regulatory machines launched from the enhancer towards the promoter. Another model hypothesizes that transcriptional up-regulation requires direct physical contact between proteins assembled at the enhancer and the transcriptional apparatus at promoter. This process necessarily leads to looping out the intervening chromatin. Looping model has received significant support in the context of the control of the betaglobin locus by the LCR (13,14). For each of these models of enhancer-promoter communication, one needs a corresponding mechanism of action for insulators (9, 10, 15, 16). For the tracking model, insulators are assumed to...

Distant Activation of Transcription: Mechanisms of Enhancer Action

“…In mechanism 1, termed brachiation, transient internucleosomal interactions mediated by histone tails could keep chromatin arrays or fibers in close proximity and allow relocation of the interacting partners relative to each other at a high rate. In mechanism 2, termed transient collapse, multiple intrafiber interactions mediated by histone tails could be fully disrupted and reestablished in a different register (36). this case it is unclear how the target promoter is identified.…”

“…3B, mechanism 1) or by reestablishing internucleosomal interactions de novo (Fig. 3B, mechanism 2) (36).…”

Quantitation of interactions between two DNA loops demonstrates loop domain insulation in E. coli cells

“…Further experiments are needed to confirm the involvement of DNA supercoiling in the loop interference we measured in vivo. Of particular interest is whether the prevalent DNA supercoiling in eukaryotic genomes (61) plays a role in the efficiency and specificity of enhancer-promoter contact, or whether more complex mechanisms such as nucleosome-nucleosome interactions are also involved (62,63).…”

Promoter architectures and developmental gene regulation

“…Several models have been proposed to describe how enhancers may communicate with their target gene promoter [112]. Currently the most plausible model supported by both theoretical [113] and experimental [114,115] observations is the "looping" model in which the remote enhancer "loops out" the intervening DNA to reach the target promoter. It was shown that the formation of these chromatin loops depends on sequence-specific TFs bound to the enhancer and the promoter [115].…”