Light-activated macromolecular phase separation modulates transcription by reconfiguring chromatin interactions

Abstract

Biomolecular condensates participate in the regulation of gene transcription, yet the relationship between nuclear condensation and transcriptional activation remains elusive. Here, we devised a biotinylated CRISPR-dCas9–based optogenetic method, light-activated macromolecular phase separation (LAMPS), to enable inducible formation, affinity purification, and multiomic dissection of nuclear condensates at the targeted genomic loci. LAMPS-induced condensation at enhancers and promoters activates endogenous gene transcription by chromatin reconfiguration, causing increased chromatin accessibility and de novo formation of long-range chromosomal loops. Proteomic profiling of light-induced condensates by dCas9-mediated affinity purification uncovers multivalent interaction-dependent remodeling of macromolecular composition, resulting in the selective enrichment of transcriptional coactivators and chromatin structure proteins. Our findings support a model whereby the formation of nuclear condensates at native genomic loci reconfigures chromatin architecture and multiprotein assemblies to modulate gene transcription. Hence, LAMPS facilitates mechanistic interrogation of the relationship between nuclear condensation, genome structure, and gene transcription in living cells.

Coactivator condensation drives cardiovascular cell lineage specification

“…A few key examples using in vitro reconstituted condensates have shown that biochemical activity (e.g., nucleation of actin and microtubule polymerization) is increased upon condensate formation ( 51 – 54 ). Cell-based approaches to investigate the link between condensates and gene transcription have mainly used engineered, synthetic, or otherwise artificial approaches at supraphysiological concentrations, leading to contradictory conclusions with some reporting no link ( 55 , 56 ) and others finding a link ( 57 , 58 ). Here, we show, at endogenous protein concentrations, in both COS-7 cells with a reporter gene and 10T1/2 cells with a cell identity gene, that the gene activation function of MYOCD is coupled to and requires its formation of condensates.…”

May the force be with you: Nuclear condensates function beyond transcription control

“…The genetic function of chromatin condensates in modulating gene expression is generally accepted and proved by recent publications. [ 95 ] However, other indications question this linear relationship. In this direction, it has recently been suggested that E–P loop strength and related microcompartments are not linearly connected with the transcriptional outputs.…”

Transcriptional condensates: a blessing or a curse for gene regulation?

“…Conversely, nuclear condensates themselves can reorganize the local chromatin architecture 66 . For example, it has been shown that TFs such as FOXA1 and SOX2 co-condense with DNA in vitro, exerting a tension force on the DNA strand which can bring together distal regions 67,68 .…”