Phase separation of ligand-activated enhancers licenses cooperative chromosomal enhancer assembly

Nair, Sreejith J.; Lu, Yang; Meluzzi, Dario; Oh, Soohwan; Yang, Feng; Friedman, Meyer J.; Wang, Susan; Suter, Tom; Alshareedah, Ibraheem; Gamliel, Amir; Ma, Qi; Zhang, Jie; Hu, Yiren; Tan, Yuliang; Ohgi, Kenneth A.; Jayani, Ranveer Singh; Banerjee, Priya R.; Aggarwal, Aneel K.; Rosenfeld, Michael G.

doi:10.1038/s41594-019-0190-5

Cited by 290 publications

(261 citation statements)

References 71 publications

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“…Computational simulation has suggested that formation of these structures may promote long-range chromatin interactions 3 , and BRD4 is capable of driving clustering of acetylated chromatin in vitro 68 . In support of this, BRD4 intrinsically disordered regions (IDRs) targeted to telomeric sequences appear to bring loci together 35 and dissolution of phase condensate structures prevents the estrogen-induced colocalization of enhancers 69 . However, it is unclear how closely these observations represent physiological enhancer-promoter interactions, or whether these results are representative of mechanisms functioning generally at most enhancers.…”

Section: Discussionmentioning

confidence: 94%

BET inhibition disrupts transcription but retains enhancer-promoter contact

Crump

Ballabio

Godfrey

et al. 2019

Preprint

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In higher eukaryotes, enhancers are DNA sequences that enable complex temporal and tissue-specific regulation of genes. Although it is not entirely clear how enhancer-promoter interactions can increase gene expression, this proximity has been observed in multiple systems at multiple loci and is thought to be essential for the maintenance of gene expression. The formation of phase condensates is thought to be an essential component of enhancer function. Here, we show that pharmacological targeting of cells with inhibitors of BET (Bromodomain and Extra-Terminal domain) proteins can have a strong impact on transcription but very little impact on enhancer-promoter interactions. Treatment with 1,6-hexanediol, which dissolves phase condensate structures and reduces BET and Mediator protein binding at enhancers, can also have a strong effect on gene transcription, without disrupting enhancer-promoter interactions. These results suggest that activation of transcription and maintenance of enhancerpromoter interactions are separable events. Our findings further suggest that enhancer-promoter interactions are not dependent on high levels of BRD4 (Bromodomain-containing protein 4) and Mediator, and are likely maintained by a complex set of factors including additional activator complexes and loop extrusion by CTCF/cohesin.

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Section: Discussionmentioning

confidence: 94%

BET inhibition disrupts transcription but retains enhancer-promoter contact

Crump

Ballabio

Godfrey

et al. 2019

Preprint

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“…Phase separation describes the large-scale, three-dimensional concentration of proteins and nucleic acids (Box 1) and is a means by which transcriptional machinery and multiple regulatory elements are brought together. Phase separation of enhancers has been shown at super enhancers and at enhancers utilizing the MegaTrans complex Nair et al, 2019). While much remains to be learned, the literature overall supports a model wherein eRNAs contribute to enhancer function by interacting with nuclear proteins to promote enhancer-promoter looping, chromatin modification, and regulation of transcriptional machinery, possibly through phase separation.…”

Section: Mechanisms Of Actionmentioning

confidence: 94%

Diversity and Emerging Roles of Enhancer RNA in Regulation of Gene Expression and Cell Fate

Arnold

Wells

2020

Front. Cell Dev. Biol.

178

157

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Enhancers are cis-regulatory elements in the genome that cooperate with promoters to control target gene transcription. Unlike promoters, enhancers are not necessarily adjacent to target genes and can exert their functions regardless of enhancer orientations, positions and spatial segregations from target genes. Thus, for a long time, the question as to how enhancers act in a temporal and spatial manner attracted considerable attention. The recent discovery that enhancers are also abundantly transcribed raises interesting questions about the exact roles of enhancer RNA (eRNA) in gene regulation. In this review, we highlight the process of enhancer transcription and the diverse features of eRNA. We review eRNA functions, which include enhancer-promoter looping, chromatin modifying, and transcription regulating. As eRNA are transcribed from active enhancers, they exhibit tissue and lineage specificity, and serve as markers of cell state and function. Finally, we discuss the unique relationship between eRNA and super enhancers in phase separation wherein eRNA may contribute significantly to cell fate decisions.

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“…Given the conservation of protein disorder ( Figure 1A) and recent evidence that the CTD can form and interact with phase separated droplets (Kwon et al, 2013;Chong et al, 2018;Boehning et al, 2018;Cho et al, 2018;Nair et al, 2019), we hypothesized that the function of the CTD's long disorder could be supplied by other proteins of similar chemical and structural features. We tested this idea by fusing the low complexity domains (LCD) of the human proteins FUS and TAF15, which are not present in the yeast genome, to the C-terminus of a 10CTDr truncated RPB1.…”

Section: Fusion To Disordered Proteins Can Rescue the Function Of A Cmentioning

confidence: 99%

“…CTD length has also been implicated in its ability to form (Boehning et al, 2018) and bind phase-separated droplets, with a minimum threshold that parallels its viability requirement (Kwon et al, 2013). In addition, the interaction of the CTD with these droplets can be dynamically modulated by phosphorylation (Kwon et al, 2013;Chong et al, 2018;Boehning et al, 2018;Cho et al, 2018;Nair et al, 2019), a major post-translational modification that precedes transcription initiation (Payne et al, 1989;Svejstrup et al, 1997). In light of these observations, phase separation provides an appealing framework to explain certain transcriptional phenomena.…”

Section: Introductionmentioning

confidence: 99%

RNA Pol II Length and Disorder Enable Cooperative Scaling of Transcriptional Bursting

Quintero-Cadena¹,

Lenstra

Sternberg³

2019

Preprint

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RNA Polymerase II contains a disordered C-terminal domain (CTD) whose length enigmatically correlates with genome size. The CTD is crucial to eukaryotic transcription, yet the functional and evolutionary relevance of this variation remains unclear. Here, we use smFISH, live imaging, and RNA-seq to investigate how CTD length and disorder influence transcription. We find that length modulates the size and frequency of transcriptional bursting. Disorder is highly conserved and mediates CTD-CTD interactions, an ability we show is separable from protein sequence and necessary for efficient transcription. We build a data-driven quantitative model, simulations of which recapitulate experiments and support CTD length promotes initial polymerase recruitment to the promoter but slows down its release from it, and that CTD-CTD interactions enable promoter recruitment of multiple polymerases. Our results reveal how these tunable parameters provide access to a range of transcriptional activity, offering a new perspective for the mechanistic significance of CTD length and disorder in transcription across eukaryotes.

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Phase separation of ligand-activated enhancers licenses cooperative chromosomal enhancer assembly

Abstract: A crucial feature of differentiated cells is the rapid activation of enhancer-driven transcriptional programs in response to signals. The potential contributions of physicochemical properties of

Cited by 290 publications

References 71 publications

BET inhibition disrupts transcription but retains enhancer-promoter contact

BET inhibition disrupts transcription but retains enhancer-promoter contact

Diversity and Emerging Roles of Enhancer RNA in Regulation of Gene Expression and Cell Fate

RNA Pol II Length and Disorder Enable Cooperative Scaling of Transcriptional Bursting

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