Nuclear microenvironments modulate transcription from low-affinity enhancers

Abstract

Transcription factors bind low-affinity DNA sequences for only short durations. It is not clear how brief, low-affinity interactions can drive efficient transcription. Here, we report that the transcription factor Ultrabithorax (Ubx) utilizes low-affinity binding sites in the Drosophila melanogaster shavenbaby (svb) locus and related enhancers in nuclear microenvironments of high Ubx concentrations. Related enhancers colocalize to the same microenvironments independently of their chromosomal location, suggesting that microenvironments are highly differentiated transcription domains. Manipulating the affinity of svb enhancers revealed an inverse relationship between enhancer affinity and Ubx concentration required for transcriptional activation. The Ubx cofactor, Homothorax (Hth), was co-enriched with Ubx near enhancers that require Hth, even though Ubx and Hth did not co-localize throughout the nucleus. Thus, microenvironments of high local transcription factor and cofactor concentrations could help low-affinity sites overcome their kinetic inefficiency. Mechanisms that generate these microenvironments could be a general feature of eukaryotic transcriptional regulation.

Decoding the Notch signal

“…In agreement with this model, several TFs (Bicoid [Mir et al, 2017[Mir et al, , 2018, Dorsal [Yamada et al, 2019], Zelda [Dufourt et al, 2018;Mir et al, 2018] and Ultrabithorax [Tsai, Alves, & Crocker, 2019;Tsai et al, 2017]) are present in foci or "hubs" in the nucleus. interact with nascent sites of transcription, suggesting a "hit and run" mechanism for initiating transcription (Mir et al, 2018), rather than a model where TFs become integrated with stable PolII/Med clusters.…”

“…This "bursty" transcription has been formalized as a two state model of a promoter's activity, which cycles between ON and OFF states with stochastic rate constants (Larson, Singer, & Zenklusen, 2009;Peccoud & Ycart, 1995 The formation of PolII clusters or aggregates is thought to be driven by weak interactions between intrinsically disordered regions/low complexity domains (LCD) in PolII and other proteins (Boehning et al, 2018;Cho et al, 2018;Lu et al, 2018). Similarly, many TFs In agreement with this model, several TFs (Bicoid [Mir et al, 2017[Mir et al, , 2018, Dorsal [Yamada et al, 2019], Zelda [Dufourt et al, 2018;Mir et al, 2018] and Ultrabithorax [Tsai, Alves, & Crocker, 2019;Tsai et al, 2017]) are present in foci or "hubs" in the nucleus. Similarly, many TFs In agreement with this model, several TFs (Bicoid [Mir et al, 2017[Mir et al, , 2018, Dorsal [Yamada et al, 2019], Zelda [Dufourt et al, 2018;Mir et al, 2018] and Ultrabithorax [Tsai, Alves, & Crocker, 2019;Tsai et al, 2017]) are present in foci or "hubs" in the nucleus.…”

Enhancer features that drive formation of transcriptional condensates

“…Recent studies have suggested that phase-separated condensates of molecules involved in transcription form at enhancers (Boija et al, 2018;Cho et al, 2018;Chong et al, 2018;Fukaya et al, 2016;Hnisz et al, 2017;Sabari et al, 2018;Tsai et al, 2017), providing a potential mechanism for concentrating transcriptional machinery at specific loci. Here we investigated how features encoded in a DNA element regulate the formation of transcriptional condensates.…”

“…Recent studies suggest that the cooperative process of phase separation can also contribute to assembling dynamic clusters or condensates of TFs, coactivators, and RNA polymerase II at active enhancer elements, especially super-enhancers (Boija et al, 2018;Cho et al, 2018;Chong et al, 2018;Fukaya et al, 2016;Hnisz et al, 2017;Sabari et al, 2018;Tsai et al, 2017). Some of these transcriptional condensates contain hundreds of coactivator and RNA polymerase II molecules (Cho et al, 2018).…”

Enhancer priming enables fast and sustained transcriptional responses to Notch signaling

“…In the first model, increasing the concentration of NICD when the enhancer is activated would create larger PolII clusters. This is based on the observation that low complexity activation domains in transcription factors can form local regions of high concentration of transcription factors, so-called "hubs", which in turn are able to recruit PolII (Mir et al 2017;Tsai et al 2017;Lu et al 2018). As the lifetime of PolII clusters appears to correlate with transcriptional output (Cho et al 2016), the formation of larger PolII clusters would in turn drive larger bursts.…”