Nonlinear control of transcription through enhancer–promoter interactions

Abstract

Chromosome structure in mammals is thought to regulate transcription by modulating three-dimensional interactions between enhancers and promoters, notably through CTCF-mediated loops and topologically associating domains (TADs)1–4. However, how chromosome interactions are actually translated into transcriptional outputs remains unclear. Here, to address this question, we use an assay to position an enhancer at large numbers of densely spaced chromosomal locations relative to a fixed promoter, and measure promoter output and interactions within a genomic region with minimal regulatory and structural complexity. A quantitative analysis of hundreds of cell lines reveals that the transcriptional effect of an enhancer depends on its contact probabilities with the promoter through a nonlinear relationship. Mathematical modelling suggests that nonlinearity might arise from transient enhancer–promoter interactions being translated into slower promoter bursting dynamics in individual cells, therefore uncoupling the temporal dynamics of interactions from those of transcription. This uncovers a potential mechanism of how distal enhancers act from large genomic distances, and of how topologically associating domain boundaries block distal enhancers. Finally, we show that enhancer strength also determines absolute transcription levels as well as the sensitivity of a promoter to CTCF-mediated transcriptional insulation. Our measurements establish general principles for the context-dependent role of chromosome structure in long-range transcriptional regulation.

Building regulatory landscapes reveals that an enhancer can recruit cohesin to create contact domains, engage CTCF sites and activate distant genes

“…2b,c ) (see also below). Collectively these results support other recent data that the relationship between gene activity and E-P contact frequencies is non-linear and that subtle changes in contact frequencies can lead to large changes in expression 36 , 45 , 46 .…”

“…We propose this is a consequence of concentrated loop extrusion activity. We, like others, find that transcriptional activity is controlled by more than just E-P contact frequencies 36 , 45 , 46 . Preformed contacts established prior to gene activation have been observed at, for example, the Hoxd locus, and such ‘permissive’ structures 58 may be reminiscent of the topologies that we detect here.…”

In vivo dissection of a clustered-CTCF domain boundary reveals developmental principles of regulatory insulation

“…Besides boundary insulation, we observe that enhancer–promoter communication may be influenced by genomic distances. Indeed, analyses in mESCs demonstrated that the transcriptional output depends on the genomic distance between an enhancer and its promoter 44 . Moreover, reduced distances between the ZRS enhancer and the Shh gene, in inverted alleles, can overcome boundary insulation and cause gene activation 45 .…”

Chromatin Hubs: A biological and computational outlook

“…A similar pattern is followed by the promoter's transcriptional output, where transcriptional levels decrease with increasing genomic distance and fall to promoter-only levels when the enhancer is located outside of the TAD and is not able to activate the promoter. Therefore, the authors built a mathematical model to explain transcriptional output in terms of contact probabilities: Transcription is described by a two-state (on–off) model where the frequency of transcriptional bursts depends on the enhancer-promoter contact probability through a Hill function [169] .…”