Enhancers are regulatory DNA sequences that activate transcription over long distances. Recent studies revealed a widespread role of distant activation in eukaryotic gene regulation and in development of various human diseases, including cancer. Genomic and gene-targeted studies of enhancer action revealed novel mechanisms of transcriptional activation over a distance. They include formation of stable, inactive DNA-protein complexes at the enhancer and target promoter before activation, facilitated distant communication by looping of the spacer chromatin-covered DNA, and promoter activation by mechanisms that are different from classic recruiting. These studies suggest the similarity between the looping mechanisms involved in enhancer action on DNA in bacteria and in chromatin of higher organisms. E nhancers (Es) are short (20-to 400-bp) DNA sequences that can activate transcription from target promoters (P) in trans and over various distances (more than 100 kb) (7). Enhancers operate in pro-and eukaryotes; in the majority of cases, action of Es involves direct E-P interaction through proteins bound at the E and P, accompanied by formation of an intervening chromatin loop (7,24,38). Recent genomic studies using various versions of the 3C approach revealed widespread use of gene regulation by enhancers (see reference 32 for a review). In parallel, genomic studies identified specific signatures (histone modifications and associated proteins) of enhancers that greatly facilitated analysis of the databases (32).At the same time, understanding of mechanistic aspects of enhancer action trails behind, primarily due to the lack of in vitro systems faithfully recapitulating distant activation. The enhancer field remains driven by the concept of recruiting that was proposed to explain short-distance activation of transcription in prokaryotes (Fig. 1A) (44). During recruiting, an activator protein increases the local concentration of another protein/protein complex (e.g., RNA polymerase [RNAP]) in the vicinity of its binding site. The local increase of protein concentration results in relief of a step limiting the rate of initiation (usually binding of RNAP to a promoter nearby) and induces transcription. During distant action, even if a protein complex was recruited to the enhancer, its concentration at the target would not necessarily be increased because E/P do not typically colocalize. Furthermore, enhancers typically activate preformed complexes already recruited to DNA ( Fig. 1B; also see below). Thus, the concept of recruiting cannot explain some principal aspects of enhancer action; instead, the presence of preformed enhancer targets raises questions about efficient E-P communication and activation of transcription (Fig. 1B). In this review, we focus primarily on mechanistic aspects of enhancer action; other recent studies were covered in several excellent reviews (7,24,32,38). ENHANCER ACTION ON DNAIn prokaryotes, there are two types of transcriptional enhancers using tracking and looping mechanisms for enhancer-...

Recently we characterized a class of anti-cancer agents (curaxins) that disturbs DNA/histone interactions within nucleosomes. Here, using a combination of genomic and in vitro approaches, we demonstrate that curaxins strongly affect spatial genome organization and compromise enhancer-promoter communication, which is necessary for the expression of several oncogenes, including MYC . We further show that curaxins selectively inhibit enhancer-regulated transcription of chromatinized templates in cell-free conditions. Genomic studies also suggest that curaxins induce partial depletion of CTCF from its binding sites, which contributes to the observed changes in genome topology. Thus, curaxins can be classified as epigenetic drugs that target the 3D genome organization.

The dynamic organization of chromatin plays an essential role in the regulation of gene expression and in other fundamental cellular processes. The underlying physical basis of these activities lies in the sequential positioning, chemical composition, and intermolecular interactions of the nucleosomes—the familiar assemblies of ~ 150 DNA base pairs and eight histone proteins—found on chromatin fibers. Here we introduce a mesoscale model of short nucleosomal arrays and a computational framework that make it possible to incorporate detailed structural features of DNA and histones in simulations of short chromatin constructs. We explore the effects of nucleosome positioning and the presence or absence of cationic N-terminal histone tails on the ‘local’ inter-nucleosomal interactions and the global deformations of the simulated chains. The correspondence between the predicted and observed effects of nucleosome composition and numbers on the long-range communication between the ends of designed nucleosome arrays lends credence to the model and to the molecular insights gleaned from the simulated structures. We also extract effective nucleosome-nucleosome potentials from the simulations and implement the potentials in a larger-scale computational treatment of regularly repeating chromatin fibers. Our results reveal a remarkable effect of nucleosome spacing on chromatin flexibility, with small changes in DNA linker length significantly altering the interactions of nucleosomes and the dimensions of the fiber as a whole. In addition, we find that these changes in nucleosome positioning influence the statistical properties of long chromatin constructs. That is, simulated chromatin fibers with the same number of nucleosomes exhibit polymeric behaviors ranging from Gaussian to worm-like, depending upon nucleosome spacing. These findings suggest that the physical and mechanical properties of chromatin can span a wide range of behaviors, depending on nucleosome positioning, and that care must be taken in the choice of models used to interpret the experimental properties of long chromatin fibers.

Communication between distantly spaced genomic regions is one of the key features of gene regulation in eukaryotes. Chromatin per se can stimulate efficient enhancer-promoter communication (EPC); however, the role of chromatin structure and dynamics in this process remains poorly understood. Here we show that nucleosome spacing and the presence of nucleosome-free DNA regions can modulate chromatin structure/dynamics and, in turn, affect the rate of EPC in vitro and in silico. Increasing the length of internucleosomal linker DNA from 25 to 60 bp results in more efficient EPC. The presence of longer nucleosome-free DNA regions can positively or negatively affect the rate of EPC, depending upon the length and location of the DNA region within the chromatin fiber. Thus the presence of histone-free DNA regions can differentially affect the efficiency of EPC, suggesting that gene regulation over a distance could be modulated by changes in the length of internucleosomal DNA spacers.