Competition between transcription and loop extrusion modulates promoter and enhancer dynamics

Abstract

The spatiotemporal configuration of genes with distal regulatory elements, and the impact of chromatin mobility on transcription, remain unclear. Loop extrusion is an attractive model for bringing genetic elements together, but how this functionally interacts with transcription is also largely unknown. We combine live tracking of genomic loci and nascent transcripts with molecular dynamics simulations to assess the 4D arrangement of the Sox2 gene and its enhancer, in response to a battery of perturbations. We find that alterations in chromatin mobility, not promoter-enhancer distance, is more informative about transcriptional status. Active elements display more constrained mobility, consistent with confinement within specialized nuclear sites, and alterations in enhancer mobility distinguish poised from transcribing alleles. Strikingly, we find that whereas loop extrusion and transcription factor-mediated clustering contribute to promoter-enhancer proximity, they have antagonistic effects on chromatin dynamics. This provides an experimental framework for the underappreciated role of chromatin dynamics in genome regulation.

Connecting Chromatin Structures to Gene Regulation Using Dynamic Polymer Simulations

“…The simulations presented here suggest that the sigmoidal relationship could emerge from productive interactions being limited to long events (> 1min) within a larger capture radius (∼400 nm) than that of Hi-C. In support of this idea, the time- and distance-gated model proposed here recapitulates several observations: the increased dependence of loop extrusion for transcription activation from long distances (27,32); the stronger effect of loop extrusion perturbations on the frequency of activation intervals compared to their duration (23); the fact that Sox2 transcription exhibits little temporal correlation with distance to its SCR enhancer - since the SCR lies within <400 nm of the promoter the vast majority of the time, the model predicts near uninterrupted enhancer-promoter communication (33,34); the strong temporal correlation between enhancer-promoter distance and transcription activity for artificial systems where the enhancer regularly explores distances outside of the ∼400 nm capture radius from the promoter (35,36). While other mechanisms have also been proposed to account for the non-linearity observed between chromatin contact matrices and transcription regulation (17,37,38), the simulations presented here demonstrate that the choice of a specific contact observable as a metric is not a neutral decision, but in itself can introduce non-linearities.…”

Tracking pairwise genomic loci by the ParB–ParS and Noc-NBS systems in living cells

“…It has been reported that the ParB/ParS system has minimal transcription disruption ( 21 , 28 ). Here we compared the effect of 8XLacO, 8XParSc or U2OS-8XNBS integration (P1 locus) on the transcription repression of the PPP1R2 gene ( Supplementary Figure S7A ).…”

“…Although there are four to ten nucleotide differences between Bc ParS1 or Bc ParS2 and the other ParSs, Bc ParB2/ Bc ParS2 (ANCHOR2) formed many non-specific foci regardless of the presence or absence of ParS in mammalian cells, which is excluded us from being utilized in the multicolor DNA labeling system. Bc ParB1/ Bc ParS1 (ANCHOR1) was recently used in the mESCs ( 28 ), but its robustness of labeling needs to be further validated. ANCHOR3 has been used successfully in several cases ( 21 , 27 , 28 ).…”

“…Bc ParB1/ Bc ParS1 (ANCHOR1) was recently used in the mESCs ( 28 ), but its robustness of labeling needs to be further validated. ANCHOR3 has been used successfully in several cases ( 21 , 27 , 28 ). Unfortunately, the ANCHOR3 system is not publicly available.…”

“…Recently the ANCHOR system has been used to study 3D genome organization in drosophila or mammalian cells ( 25–27 ). ANCHOR3 has been optimized to use in mammalian cells, and ANCHOR1 has recently been used in mESCs with a low signal-to-noise ratio ( 28 ). Thus, it is important to develop a multicolor ParB/ParS system for live-tracking multiple or pairs of genomic loci.…”