Solid Phase Condensates RNASeq and HiC

Abstract

Ultra long-range genomic contacts, which emerge as prominent components of neuronal genome architecture1-3, constitute a biochemical enigma. This is because regulatory DNA elements make selective and stable contacts with DNA sequences located hundreds of Kbs away, instead of interacting with proximal sequences occupied by the same exact transcription factors (TFs)1,4. This is exemplified in olfactory sensory neurons (OSNs), where only a fraction of Lhx2/Ebf1/Ldb1-bound sites interact with each other, converging into highly selective multi-chromosomal enhancer hubs5.

To obtain biochemical insight to this process, we assembled OR enhancer hubs in vitro with recombinant proteins and enhancer DNA. Cell-free enhancer hub reconstitution revealed that OR enhancers form nucleoprotein condensates with unusual, solid-like characteristics. Assembly of these solid condensates is orchestrated by specific DNA motifs enriched in OR enhancers, which likely impose distinct homotypic properties to their resident Lhx2/Ebf1/Ldb1 complexes.

Single molecule tracking and pulse/chase experiments in vivo confirm that Lhx2 and Ebf1 assemble OR transcription-competent condensates with solid properties in OSN nuclei, under physiological protein concentrations. Thus, DNA sequence-influenced homophilic nucleoprotein interactions generate new types of biomolecular condensates, which may provide a generalizable explanation for the stability and specificity of long-range genomic contacts across cell types.