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Enhancers are DNA elements that are bound by transcription factors (TFs), which recruit coactivators and the transcriptional machinery to genes. Phase-separated condensates of TFs and coactivators have been implicated in assembling the transcription machinery at particular enhancers, yet the role of DNA sequence in this process has not been explored. We show that DNA sequences encoding TF binding site number, density, and affinity above sharply defined thresholds drive condensation of TFs and coactivators. A combination of specific structured (TF-DNA) and weak multivalent (TF-coactivator) interactions allows for condensates to form at particular genomic loci determined by the DNA sequence and the complement of expressed TFs. DNA features found to drive condensation promote enhancer activity and transcription in cells. Our study provides a framework to understand how the genome can scaffold transcriptional condensates at specific loci and how the universal phenomenon of phase separation might regulate this process., (Copyright © 2019 Elsevier Inc. All rights reserved.)

In order for a new organism to form, the genomes of the highly specialized egg and sperm need to be reprogrammed into a totipotent state that is capable of generating all of the cell types that comprise an organism. This reprogramming occurs by erasing chromatin modifications, leaving the cells in a naïve state, followed by the induction of specialized programming events. Pioneer factors bind to the genome prior to zygotic genome activation, followed by acetylation of histones and further chromatin specialization by the addition of methylation marks later during differentiation. Genome-wide approaches have provided insight into the genomic and epigenomic regulation of gene expression during development, providing a new perspective on the process of cell specification and differentiation. In this review, we discuss how distal DNA and core promoter elements, RNA polymerase pausing, transcription factors, and co-regulators interact to shape the chromatin landscape and direct tissue-specific expression patterns during embryo development, focusing on the well-characterized Drosophila embryo., (© 2015 Wiley Periodicals, Inc.)

Maintenance of appropriate cell states involves epigenetic mechanisms, including Polycomb-group (PcG)-mediated transcriptional repression. While PcG proteins are known to induce chromatin compaction, how PcG proteins gain access to DNA in compact chromatin to achieve long-term silencing is poorly understood. Here, we show that the p300/CREB-binding protein (CBP) co-activator is associated with two-thirds of PcG regions and required for PcG occupancy at many of these in Drosophila and mouse cells. CBP stabilizes RNA polymerase II (Pol II) at PcG-bound repressive sites and promotes Pol II pausing independently of its histone acetyltransferase activity. CBP and Pol II pausing are necessary for RNA-DNA hybrid (R-loop) formation and nucleosome depletion at Polycomb Response Elements (PREs), whereas transcription beyond the pause region is not. These results suggest that non-enzymatic activities of the CBP co-activator have been repurposed to support PcG-mediated silencing, revealing how chromatin regulator interplay maintains transcriptional states. [Display omitted] • p300/CBP occupies Polycomb-repressed H3K27me3 regions in Drosophila and mouse cells • p300/CBP is required for Polycomb group (PcG) occupancy by promoting RNA Pol II pausing • Pol II pausing establishes R-loops and open chromatin to sustain PcG occupancy • p300/CBP catalytic activity is dispensable for Pol II pausing and PcG silencing Polycomb group (PcG) proteins induce chromatin compaction but require access to DNA for maintenance of long-term gene silencing. Hunt et al. show that p300/CBP promotes Pol II pausing, local nucleosome depletion, and formation of R-loops in repressive regions by a non-enzymatic mechanism, which is necessary for PcG occupancy and silencing. [ABSTRACT FROM AUTHOR]

Summary Transcription activation involves RNA polymerase II (Pol II) recruitment and release from the promoter into productive elongation, but how specific chromatin regulators control these steps is unclear. Here, we identify a novel activity of the histone acetyltransferase p300/CREB-binding protein (CBP) in regulating promoter-proximal paused Pol II. We find that Drosophila CBP inhibition results in “dribbling” of Pol II from the pause site to positions further downstream but impedes transcription through the +1 nucleosome genome-wide. Promoters strongly occupied by CBP and GAGA factor have high levels of paused Pol II, a unique chromatin signature, and are highly expressed regardless of cell type. Interestingly, CBP activity is rate limiting for Pol II recruitment to these highly paused promoters through an interaction with TFIIB but for transit into elongation by histone acetylation at other genes. Thus, CBP directly stimulates both Pol II recruitment and the ability to traverse the first nucleosome, thereby promoting transcription of most genes. [ABSTRACT FROM AUTHOR]