Summary
Enhancer clusters overlapping disease-associated mutations in Pierre Robin sequence (PRS) patients regulate SOX9 expression at genomic distances over 1.25 megabases. We applied optical reconstruction of chromatin architecture (ORCA) imaging to trace 3D locus topology during PRS-enhancer activation. While we observed pronounced changes in locus topology between cell-types, analysis of single chromatin fiber traces revealed that these ensemble-average differences arise not from the presence of cell-type unique conformations, but through changes in frequency of commonly sampled topologies. We further identified two CTCF-bound elements, internal to the SOX9 topologically associating domain, which are positioned near its 3D geometric center and bridge enhancer-promoter contacts in a series of chromatin loops. Ablation of these elements results in diminished SOX9 expression and altered domain-wide contacts. Polymer models with uniform loading across the domain and frequent cohesin collisions recapitulate this multiloop, centrally clustered geometry, suggesting a mechanism for gene regulation over ultralong ranges.
Four short bullet points that convey the key message of the paper SOX9 domain topology dynamically changes during a developmental transition
Structural elements promote TAD-wide interactions, stripe formation and transcription
Structural elements are CTCF-dependent and situated centrally in the 3D TAD structure
Polymer simulations of multi-loop model best recapitulate topological features
Competing Interest Statement
J.W is a paid member of Camp4 and Paratus Biosciences scientific advisory boards.
Footnotes
↵* Joint first authors
Abbreviations
- (NCC)
- neural crest cell
- (CNCC)
- cranial neural crest cell
- (PRS)
- Pierre Robin sequence
- (TAD)
- topologically associating domain
- (ORCA)
- optical reconstruction of chromatin architecture
- (SSE)
- stripe-associated structural element