Interactome Rewiring Following Pharmacological Targeting of BET Bromodomains

Lambert, Jean-Philippe; Picaud, S.; Fujisawa, Takao; Hou, Huayun; Savitsky, P.; Uusküla-Reimand, Liis; Gupta, Gagan D.; Abdouni, Hala; Lin, Zhen‐Yuan; Tucholska, Monika; Knight, James D.R.; Gonzalez-Badillo, Beatriz; St‐Denis, Nicole; Newman, Joseph A.; Stucki, Manuel; Pelletier, Laurence; Bandeira, Nuno; Wilson, Michael D.; Filippakopoulos, P.; Gingras, Anne‐Claude

doi:10.1016/j.molcel.2018.11.006

Cited by 134 publications

(174 citation statements)

References 74 publications

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“…In our SAXS analyses, BrdT, Brd2, Brd3 and Brd4 all demonstrated similar R g (48.6-55.4 Å) and D max (181-200 Å) values (Figure 2A-B and S2, Table S1) consistent with previous SAXS measurements (73). Consequently, the high degree of inter-bromodomain flexibility demonstrated by our SAXS-guided Rosetta ab initio modeling of the Brd4 linker sequence is likely conserved across all four BET proteins.…”

Section: Discussionsupporting

confidence: 89%

“…For instance, Brd4 binds acetylated forms of cyclin T1 (55, 72), the RelA subunit of NF- κ B (77, 78), and the transcription factor Twist (79). In addition, a recent study by Lambert et al (73) suggests BET protein interactions are more widespread than previously appreciated and demonstrated structural evidence of Brd4 bromodomain binding to numerous acetylated nuclear proteins. However, the ability of tandem bromodomains to simultaneously engage separate acetylated proteins had not been tested directly.…”

Section: Discussionmentioning

confidence: 99%

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Nucleosome scaffolding by Brd4 tandem bromodomains in acetylation-dependent chromatin compartmentalization

Olp

Jackson

Smith

2019

Preprint

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Bromodomain binding of acetyl-lysine residues is a crucial step in many epigenetic mechanisms governing transcription. Nearly half of human bromodomains exist in tandem with at least one other bromodomain on a single protein. The Bromodomain and ExtraTerminal domain (BET) family of proteins (BrdT, Brd2, Brd3 and Brd4) each encode two bromodomains at their N-termini and are important regulators of acetylation-dependent transcription in homeostasis and disease. Previous efforts have focused on identifying protein acetylation sites bound by individual bromodomains. However, the mechanisms through which tandem bromodomains act cooperatively on chromatin are largely unknown. Here, we first used small angle xray scattering combined with Rosetta ab initio modeling to explore conformational space available to BET tandem bromodomains. For Brd4, the flexible tandem bromodomain linker allows for distances between the two acetyl-lysine binding sites ranging from 15 to 157 Å. Using a bioluminescence resonance energy transfer assay, we show a clear distance dependence for Brd4 tandem bromodomain bivalent binding of multiply acetylated histone H4 peptides. However, isothermal titration calorimetry studies revealed Brd4 binding affinity toward multiply acetylated peptides does not correlate with the potential for bivalent binding. We used sucrose gradient assays to provide direct evidence in vitro that Brd4 tandem bromodomains can simultaneously bind and scaffold multiple acetylated nucleosomes. Intriguingly, our bioinformatic analysis of deposited chromatin immunoprecipitation sequencing data indicates that Brd4 colocalizes with subsets of histone acetyl-lysine sites across transcriptionally active chromatin compartments. These findings support our hypothesis that scaffolding of acetylated nucleosomes by Brd4 tandem bromodomains contributes to higher-order chromatin architecture.family of bromodomains (BrdT, Brd2, Brd3 and Brd4) were 49 discovered in 2010 (20, 21) and since have entered clinical trials 50 as potential treatment for cancer (22)(23)(24)(25)(26)(27) and inflammation-51 driven disease (28, 29). However, the molecular mechanisms 52 underlying the potential therapeutic effects of bromodomain 53 inhibitors are poorly understood. As isolated bromodomains 54 harbor relatively weak affinity toward monoacetylated histone 55 tail peptides in vitro (K d = 10 µM -1 mM) (13), multivalency 56 is emerging as an increasingly crucial concept in bromodomain 57 binding of modified chromatin (30, 31). One category of po-58 tential multivalent interactions is the recognition of multiple 59 sites on one histone tail by an individual bromodomain. For 60 instance, the N -terminal bromodomains (BD1) of Brd4 and 61BrdT cooperatively bind two adjacent acetyl-lysine residues 62 (i.e. lysines 5 and 8) on the histone H4 tail (13, 32) with 3-63 to 20-fold tighter affinity compared to either acetylation in 64 isolation (33, 34) suggesting that multiple neighboring acety-65 lation sites are necessary to recruit these bromodomains to 66 D R A F ...

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Section: Discussionsupporting

confidence: 89%

Section: Discussionmentioning

confidence: 99%

Nucleosome scaffolding by Brd4 tandem bromodomains in acetylation-dependent chromatin compartmentalization

Olp

Jackson

Smith

2019

Preprint

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“…For example, the BRD4 C-terminal domain interacts with the PTEFb complex 16,17 and the BRD4 extra-terminal domain interacts with the histone methyltransferase NSD3 68,69 . Unbiased protein-protein interaction screens for BET family members have been performed both in the presence and absence of JQ1, demonstrating a number of BD-independent interacting partners for each of the ubiquitously expressed BET family members 70 . Our data identify a novel, BD-independent interaction between BRD4 and GATA4, suggesting a mechanism by which a broadly expressed chromatin coactivator can be preferentially targeted to specific genomic loci by associating with a tissue-enriched DNA-binding TF.…”

Section: Discussionmentioning

confidence: 99%

BRD4 Interacts with GATA4 to Govern Mitochondrial Homeostasis in Adult Cardiomyocytes

Padmanabhan

Alexanian

Linares-Saldana

et al. 2020

Preprint

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Gene regulatory networks control tissue plasticity during basal homeostasis and disease in a cell-type specific manner. Ubiquitously expressed chromatin regulators modulate these networks, yet the mechanisms governing how tissue-specificity of their function is achieved are poorly understood. BRD4, a member of the BET (Bromo-and Extra-Terminal domain) family of ubiquitously expressed acetyl-lysine reader proteins, plays a pivotal role as a coactivator of enhancer signaling across diverse tissue types in both health and disease, and has been implicated as a pharmacologic target in heart failure.However, the cell-specific role of BRD4 in adult cardiomyocytes remains unknown. Here, we show that cardiomyocyte-specific deletion of BRD4 in adult mice leads to acute deterioration of cardiac contractile function with mutant animals demonstrating a transcriptomic signature enriched for decreased expression of genes critical for mitochondrial energy production. Genome-wide occupancy data show that BRD4 enriches at many downregulated genes and preferentially co-localizes with GATA4, a lineage determining cardiac transcription factor not previously implicated in regulation of adult cardiac metabolism. Co-immunoprecipitation assays demonstrate that BRD4 and GATA4 form a complex in a bromodomain-independent manner, revealing a new interaction partner for BRD4 that has functional consequences for target transactivation and may allow for locus and tissue specificity. These results highlight a novel role for a BRD4-GATA4 module in cooperative regulation of a cardiomyocyte specific gene program governing bioenergetic homeostasis in the adult heart.

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“…Along with other related pan-BET BRD compounds JQ1 was also associated with improvement of associated memory and enhancement of special memory precision in mice, showing potential for treatment of dementia (Benito et al, 2017). Given the therapeutic potential of JQ1 significant efforts have been made to understand the mechanisms of its action on the BET BRD family, giving insight into the intricate proteinprotein interactions (PPI) with transcriptional complexes, and most importantly, providing means for enhancing inhibition specificity for a single BET (Lambert et al, 2019).…”

Section: Targets That Reside On the Testis Side Of The Blood-testis Bmentioning

confidence: 99%

Toward Development of the Male Pill: A Decade of Potential Non-hormonal Contraceptive Targets

Kent

Johnston

Strump

et al. 2020

Front. Cell Dev. Biol.

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With the continued steep rise of the global human population, and the paucity of safe and practical contraceptive options available to men, the need for development of effective and reversible non-hormonal methods of male fertility control is widely recognized. Currently there are several contraceptive options available to men, however, none of the non-hormonal alternatives have been clinically approved. To advance progress in the development of a safe and reversible contraceptive for men, further identification of novel reproductive tract-specific druggable protein targets is required. Here we provide an overview of genes/proteins identified in the last decade as specific or highly expressed in the male reproductive tract, with deletion phenotypes leading to complete male infertility in mice. These phenotypes include arrest of spermatogenesis and/or spermiogenesis, abnormal spermiation, abnormal spermatid morphology, abnormal sperm motility, azoospermia, globozoospermia, asthenozoospermia, and/or teratozoospermia, which are all desirable outcomes for a novel male contraceptive. We also consider other associated deletion phenotypes that could impact the desirability of a potential contraceptive. We further discuss novel contraceptive targets underscoring promising leads with the objective of presenting data for potential druggability and whether collateral effects may exist from paralogs with close sequence similarity.

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Interactome Rewiring Following Pharmacological Targeting of BET Bromodomains

Cited by 134 publications

References 74 publications

Nucleosome scaffolding by Brd4 tandem bromodomains in acetylation-dependent chromatin compartmentalization

Nucleosome scaffolding by Brd4 tandem bromodomains in acetylation-dependent chromatin compartmentalization

BRD4 Interacts with GATA4 to Govern Mitochondrial Homeostasis in Adult Cardiomyocytes

Toward Development of the Male Pill: A Decade of Potential Non-hormonal Contraceptive Targets

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