Slow chromatin dynamics enhances promoter accessibility to transcriptional condensates

Research output: Contribution to journalResearch articleContributedpeer-review



Enhancers are DNA sequences at a long genomic distance from target genes. Recent experiments sug- gest that enhancers are anchored to the surfaces of condensates of transcription machinery and that the loop extrusion process enhances the transcrip- tion level of their target genes. Here, we theoretically study the polymer dynamics driven by the loop extru- sion of the linker DNA between an enhancer and the promoter of its target gene to calculate the contact probability of the promoter to the transcription ma- chinery in the condensate. Our theory predicts that when the loop extrusion process is active, the con- tact probability increases with increasing linker DNA length. This finding reflects the fact that the relax- ation time, with which the promoter stays in proximity to the surface of the transcriptional condensate, in- creases as the length of the linker DNA increases. This contrasts the equilibrium case for which the contact probability between the promoter and the transcription machineries is smaller for longer linker DNA lengths.


Original languageEnglish
Pages (from-to)5017–5027
Number of pages11
JournalNucleic Acids Research
Issue number9
Publication statusPublished - 22 Apr 2021

External IDs

Scopus 85107087029