Individual transcription factors modulate both the micromovement of chromatin and its long-range structure

Abstract

The control of eukaryotic gene expression is intimately connected to highly dynamic chromatin structures. Gene regulation relies on activator and repressor transcription factors (TFs) that induce local chromatin opening and closing. However, it is unclear how nucleus-wide chromatin organization responds dynamically to the activity of specific TFs. Here we examined how two TFs with opposite effects on local chromatin accessibility modulate chromatin dynamics nucleus-wide. We combine High-resolution Diffusion mapping (Hi-D) and Dense Flow reConstruction and Correlation (DFCC) in living cells to obtain an imaging-based, nanometer-scale analysis of local diffusion processes and long-range coordinated movements of both chromatin and TFs. We show that the expression of either an individual transcriptional activator (CDX2) or repressor (SIX6) increases local chromatin mobility nucleus-wide, yet induces opposite coherent chromatin motions at the micron scale. Hi-C analysis of higher-order chromatin structures shows that induction of CDX2 leads to changes in local chromatin interactions and compartmentalization. These results thus document a close relation between chromatin dynamics on the microscale and changes in compartmental structures. Given that inhibition of transcription initiation and elongation by RNA Pol II have almost no impact on the global chromatin dynamics induced by CDX2, we suggest that CDX2 alters chromatin structures independently from transcription. Our biophysical analysis shows that sequence-specific TFs mobilize long-range chromatin structure on multiple levels, providing evidence that local chromatin changes brought about by TFs can alter both the dynamics and the long-range organization of chromatin in living cells. Significance statementIn eukaryotes, DNA is embedded into a higher-order structure called chromatin that varies between a closed state that is inaccessible to DNA-binding proteins, and an open state that allows the assembly of the transcriptional machinery on DNA. The state of chromatin is dynamic and locally controlled by sequence-specific transcription factors (TFs). How local chromatin opening and closing initiated by TFs alter long-range dynamics of chromatin structures is unknown. Here we combine two nucleus-wide live-imaging techniques, Hi-D and DFCC, along with Hi-C (genomic analysis technique) to quantify both local and global chromatin dynamics, then to correlate these dynamics to structural changes. Our quantitative analysis reveals a differential impact of TFs in shaping and mobilizing long-range chromatin structures in living cells.