SUMMARY Histone modifications regulate chromatin-dependent processes, yet the mechanisms by which they contribute to specific outcomes remain unclear. H3K4me3 is a prominent histone mark that is associated with active genes and promotes transcription through interactions with effector proteins that include initiation factor TFIID. We demonstrate that H3K4me3-TAF3 interactions direct global TFIID recruitment to active genes, some of which are p53 targets. Further analyses show that (i) H3K4me3 enhances p53-dependent transcription by stimulating preinitiation complex (PIC) formation; (ii) H3K4me3, through TAF3 interactions, can act either independently or cooperatively with the TATA box to direct PIC formation and transcription; and (iii) H3K4me3-TAF3/TFIID interactions regulate gene-selective functions of p53 in response to genotoxic stress. Our findings indicate a mechanism by which H3K4me3 directs PIC assembly for the rapid induction of specific p53 target genes.

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Sall1 is a multi-zinc finger transcription factor that represses gene expression and regulates organogenesis. In this report, we further characterize the domain of Sall1 necessary for repression. We show that endogenous Sall1 binds to the nucleosome remodeling and deacetylase corepressor complex (NuRD) and confirm the functionality of the Sall1-associating macromolecular complex by showing that the complex possesses HDAC activity. NuRD is involved in global transcriptional repression and regulation of specific developmental processes. The mechanism by which sequence-specific DNA-binding proteins associate with NuRD is not well understood. We have identified a highly conserved 12-amino acid motif in the transcription factor Sall1 that is sufficient for the recruitment of NuRD. Single amino acid substitutions defined the critical amino acid peptide motif as RRKQXK-PXXF. This motif probably exhibits a more general role in regulating gene expression, since other proteins containing this domain, including all Sall family members and an unrelated zinc finger protein Ebfaz, mediate transcriptional repression and associate with NuRD. These results also have important implications for the pathogenesis of TownesBrocks, a syndrome caused by SALL1 mutations.It is well established that changes in chromatin structure are associated with activation and silencing of gene expression. The packaging of DNA in the nucleosome acts to inhibit the accessibility of DNA to transcriptional regulators and the molecular machinery required for gene expression. Gaining accessibility to DNA relies on two major mechanisms that include ATP-dependent chromatin remodeling and multiple types of modifications of nucleosomal histones (1-3). Two well described macromoleclar complexes, NuRD 2 and Sin3 (reviewed in Ref. 4), are instrumental in facilitating these enzymatic activities to establish transcriptional repression.The NuRD complex is distinguished by its ability to exhibit both histone deacetylase and ATP-dependent nucleosome remodeling activity. NuRD has been purified from mammalian and Xenopus cells and is ϳ2 MDa in size (5-9). The mammalian complex is composed of at least eight polypeptides. The histone deacetylase proteins, HDAC1 and HDAC2, and two associated proteins, RbAp46 and RbAp48, are core components that are common to both the NuRD and Sin3 repression complexes. In addition to histone deacetylase activity, the NuRD complex has ATP-dependent nucleosome remodeling activity because of its association with the ATPase, Mi-2. The biochemical functions of the remaining NuRD-specific components, the methyl-CpGbinding protein, MBD3, and MTA1 and MTA2 are not well defined (reviewed in Ref. 4).NuRD is widely conserved across the animal and plant kingdoms and has been shown to play a critical role in regulating gene expression during embryonic development (reviewed in Ref. 4). NuRD has been shown to inhibit Ras signaling during vulval development through effects on both the synMuvA and synMuvB pathways in Caenorhabditis elegans (10 -15). In Dro...

The bromodomain and extra-terminal motif (BET) protein BRD4 binds to acetylated histones at enhancers and promoters via its bromodomains (BDs) to regulate transcriptional elongation. In human colorectal cancer cells, we found that BRD4 was recruited to enhancers that were co-occupied by mutant p53 and supported the synthesis of enhancer-directed transcripts (eRNAs) in response to chronic immune signaling. BRD4 selectively associated with eRNAs that were produced from BRD4-bound enhancers. Using biochemical and biophysical methods, we found that BRD4 BDs function cooperatively as docking sites for eRNAs and that the BDs of BRD2, BRD3, BRDT, BRG1, and BRD7 directly interact with eRNAs. BRD4-eRNA interactions increased BRD4 binding to acetylated histones in vitro and augmented BRD4 enhancer recruitment and transcriptional cofactor activities. Our results suggest a mechanism by which eRNAs are directly involved in gene regulation by modulating enhancer interactions and transcriptional functions of BRD4.

Inflammation influences cancer development, progression, and the efficacy of cancer treatments, yet the mechanisms by which immune signaling drives alterations in the cancer cell transcriptome remain unclear. Using ChIP-seq, RNA-seq, and GRO-seq, here we demonstrate a global overlap in the binding of tumor-promoting p53 mutants and the master proinflammatory regulator NFκB that drives alterations in enhancer and gene activation in response to chronic TNF-α signaling. We show that p53 mutants interact directly with NFκB and that both factors impact the other’s binding at diverse sets of active enhancers. In turn, the simultaneous and cooperative binding of these factors is required to regulate RNAPII recruitment, the synthesis of enhancer RNAs, and the activation of tumor-promoting genes. Collectively, these findings establish a mechanism by which chronic TNF-α signaling orchestrates a functional interplay between mutant p53 and NFκB that underlies altered patterns of cancer-promoting gene expression.