Table 1 Role of transcriptional condensates on transcriptional activity: evidence and experimental strategies
From: Transcriptional condensates: a blessing or a curse for gene regulation?
Cell lines or organisms (live/fixed) | TF or transcription-related molecule | Strategy (tools) | Role of condensates in transcription | Key results and conclusions | Ref. |
|---|---|---|---|---|---|
Stem cells (fixed) | Natural TFs | Correlative (colocalization) | Activation | TFs form condensates with Med1 through their activation domains. | |
Stem cells (live and fixed) | Natural TFs | Correlative (colocalization) | Activation | Condensates of a coactivator and Med1 form at super-enhancers. | |
Cancer cells (live) | Synthetic coactivator + MS2 reporter gene | Correlative (colocalization); Causal (pharmacology, optogenetics) | Activation | 1) Coactivator forms condensates with Pol II CTD; 2) light-induced condensates amplify transcription. | |
Cancer cells (live and fixed) | Negative transcriptional regulator | Correlative (condensates visualization and gene expression assays); Causal (domain swapping) | Inhibition | 1) Natural IDR is required for heat-shock-dependent condensate formation and transcriptional repression; 2) other IDRs promote condensate formation and gene repression independently of heat-shock. | |
Stem and cancer cells (live and fixed) | Natural and synthetic TFs + PP7 reporter gene | Correlative (colocalization); Causal (domain swapping, optogenetics) | Activation | 1) TFs and p300 form condensates through IDR-IDR interactions; 2) p300 is acetylated (active) at condensates; 3) condensates modulate initiation rate and burst duration. | |
Immortalized cells and adult mice (live and fixed) | Synthetic TFs + enzymatic reporter gene | Causal (domain swapping, optogenetics) | Activation | 1) IDR promote formation of synthetic TF condensates; 2) light-induced TF condensates increase transcription. | |
Immortalized cells and primary cultures (live and fixed) | Onco-fusion and synthetic TFs | Causal (domain swapping, deletions, mutations pharmacology) | Activation | 1) Onco-fusion TF IDR promotes formation of condensates, chromatin looping, oncogenes activation and oncogenesis; 2) swapping with other IDRs also promotes condensate formation with similar oncogenic properties. | |
Cancer cells (fixed) | Natural coactivator | Correlative (colocalization) | Inhibition | p300 coactivator condensates colocalize with repressive histone marks. | |
Cancer cells (live and fixed) | Onco-fusion TF | Causal (competition with exogenous IDRs) | Inhibition | 1) Excess in homotypic IDR-IDR interactions represses onco-fusion TF-driven transcription; 2) larger condensates formed by heterotypic IDR-IDR interactions exert more severe transcriptional repression. | |
Cancer cells (live and fixed) | Synthetic TFs + MS2 reporter gene | Causal (domain swapping, optogenetics) | None / Inhibition | 1) Strength of TFs activation domains correlates with their propensity to form condensates; 2) condensate formation per se does not enhance transcriptional activity; 3) increasing valency might inhibit transcription. | |
Cancer cells (live and fixed) | Natural chromatin reader | Correlative (colocalization); Causal (mutations, deletions, insertions) | Activation (only at endogenous levels) | 1) Chromatin reader and oncogenic mutants form condensates at specific loci; 2) degree of condensation correlates with gene expression level; 3) overexpressed mutants form non-functional condensates. | |
Prostate-derived cells (live and fixed) | Natural TF | Correlative (colocalization) Causal (pharmacology, mutations, truncations, optogenetics) | Activation | 1) Ligand-activation triggers the formation of TF condensates with Med1, H3K27ac, and Pol II Ser-5-P; 2) a small inhibitor compound targeting TF IDR disrupts TF condensates. | |
Cancer and epithelial cells (live and fixed) | Synthetic TFs + PP7 reporter gene | Correlative (colocalization); Causal (pharmacology, domain swapping) | Activation | 1) TF clustering propensity modulates gene expression; 2) only 4% of TF condensates colocalize with nascent RNA sites. | |
Cancer cells (fixed) | Natural TF | Correlative (colocalization); Causal (mutations) | Activation | 1) Heat-shock stimulation triggers the formation of TF condensates at targeted loci; 2) TF condensates include cofactors, Pol II, and H3K4me3; 3) a mutant TF that does not form condensates presents impaired binding to chromatin and lower activity. | |
Immortalized and cancer cells (live and fixed) | Synthetic TFs | Causal (mutations, truncations) | Activation | 1) TF condensate formation increases chromatin accessibility and looping at targeted genes and is linked to gene activation; 2) proteomic analysis identifies Pol II, other TFs, coactivators, Mediator, and chromatin remodelers at condensates. | |
Drosophila embryos (live cells) | Synthetic TF + MS2 reporter gene | Correlative (condensates visualization and gene expression assays); Causal (mutations, insertions) | Activation | 1) Formation of TF condensates at enhancers correlates with transcriptional bursting; 2) longer synthetic IDRs increase RNA production, but there is a sweet spot for optimal transcription; 3) TF clustering favors the interactions between distal enhancer and promoter. | |
Yeast (live) | Natural TF + PP7 reporter gene | Causal (truncations, mutations) | Neutral or inhibitory | 1) TF form condensates at endogenous target genes; 2) both IDRs and DBD contribute to but are not essential for condensate formation; 3) the activity of a reporter gene does not depend on the presence of a colocalized condensate; 4) a DBD-mutant TF recruited to condensates does not contribute to transcriptional activation and may actually inhibit transcription. | |
Immortalized and cancer cells (live and fixed) | Natural and synthetic TFs | Casual (truncations, mutations, pharmacological) | Activation or inhibition (fine tuning of optimal IDR interactions) | 1) TF IDR is necessary but not sufficient for condensate formation; 2) swapping IDRs has different effects on condensate formation and transcriptional activity; 3) poly-glutamine track extension within the IDR favors condensate formation but decreases transcriptional activity. | |
Cancer cells (live) | Natural TFs | Causal (mutations, truncations) | Inhibition | TF with an additional IDR increases transcription below critical concentration (no condensate formation) but decreases transcription when forming condensates at higher concentrations | |
Mice liver (fixed), cancer cell lines (live) and mice (live?) | Natural TF | Correlative (colocalization); Causal (truncations) | Inhibition | 1) Donut-shape condensates containing TF and corepressor; 2) IDR necessary for condensation and transcriptional repression. |
