Numerous DNA transactions in eukaryotic nuclei are regulated by elements (enhancers) that can directly interact with their targets over large regions of DNA organized into chromatin. The mechanisms allowing communication over a distance in chromatin are unknown. We have established an experimental system allowing quantitative analysis of the impact of chromatin structure on distant transcriptional regulation. Assembly of relaxed or linear DNA templates into subsaturated chromatin results in a strong increase of the efficiency of distant enhancer-promoter E-P communication and activation of transcription. The effect is directly proportional to the efficiency of chromatin assembly and cannot be explained only by DNA compaction. Transcription activation on chromatin templates is enhancer-and activator-dependent, and must be accompanied by direct E-P interaction and formation of a chromatin loop. Previously we have shown that DNA supercoiling can strongly facilitate E-P communication on histone-free DNA. The effects of chromatin assembly and DNA supercoiling on the communication are quantitatively similar, but the efficiency of enhancer action in subsaturated chromatin does not depend on the level of unconstrained DNA supercoiling. Thus chromatin structure per se can support highly efficient communication over a distance and functionally mimic the supercoiled state characteristic for prokaryotic DNA.activation ͉ nucleosome ͉ transcription R egulation of many processes of DNA metabolism often occurs by DNA sequences positioned over a large distance from the site of action. Thus transcription of many eukaryotic and some prokaryotic genes is regulated by enhancers, short DNA sequences usually composed of several binding sites for activator proteins and capable of activating target genes over Ͼ80 kb in vivo (1). Most likely, enhancer action involves direct interaction between proteins bound at the enhancer and promoter with accompanying formation of chromatin loops including the intervening DNA (1-3). Therefore, efficient enhancer action over a distance critically depends on structural and dynamic properties of the spacer chromatin that are largely unknown.Several previous studies have suggested that chromatin could facilitate interaction between spaced DNA-bound proteins involved in transcription activation (4-6). However in these cases interactions between DNA-bound proteins positioned at a relatively close distance from each other (Ͻ400 bp) were analyzed. Interaction between DNA regions in the 200-to 600-bp distance range occurs relatively efficiently both on DNA and in chromatin; the efficiency of communication is strongly decreased only when the regions are spaced by Ͼ1-2 kb (7-9). In a pioneering study, it was shown that activation of transcription of Ͼ1.3 kb by the GAL4-VP16 activator depended on packaging of the template into histone H1-containing chromatin (10). However, the mechanisms mediating action of the activator over a distance were not analyzed further.Currently there is no purified eukaryotic system su...

Chromosomal translocations are a major cause of cancer. At the same time, the mechanisms that lead to specific chromosomal translocations that associate different gene regions remain largely unknown. Translocations are induced by double strand breaks (DSBs) in DNA. Here we review recent data on the mechanisms of generation, mobility and repair of DSBs and stress the importance of the nuclear organization in this process.

Design of selective anticancer drugs that are targeting RGD-binding integrin receptors which are known to be one of the perspective directions in the field of oncology. Significant progress in the development and application of these types compounds is already demonstrated. The accumulating body of basic and clinical evidence demonstrates potential significant effects on both in vitro and in vivo experimental models. However, the specific mechanism of action of these compounds is generally not a fully elucidated or the exact target responsible for the achievement of stated effects hasn't yet been defined sufficiently. To date eight types of integrin receptors, which are capable to recognize RGD-motif in natural ligands, has in fact been identified as (namely αIIbβ3, αvβ1, αvβ3, αvβ5, αvβ6, αvβ8, α5β1, α8β1). Even so, the estimation of the affinity of one particular RGD-bearing anticancer agent is often based on the determination of the binding efficacy to only one or rarely two integrin receptors. Traditionally the range of targets is restricted by the integrins, which are known to be highly expressed in a particular model system. While potential interactions of such an agent with other RGD-recognizing receptors usually remain beyond the research. Nonetheless, such interactions may also affect the viability and behavior of cancer cells. In this review we attempt to critically analyze the principles of selectivity achievement in the case of RGD-bearing natural ligands and the applicability of these principles in the context of the anticancer drug design.

Regulation of many biological processes often occurs by DNA sequences positioned over a large distance from the site of action. Such sequences, capable of activating transcription over a distance, are termed enhancers. Several experimental approaches for analysis of the mechanisms of communication over a distance between DNA regions positioned on the same molecule and, in particular, for analysis of enhancer-promoter communication were developed recently. Most of these methods are technically complicated and not applicable for studies of various important aspects of distant interactions in chromatin. As an alternative, we propose a more efficient and versatile method for the study of enhancer-promoter communication in chromatin using a prokaryotic model enhancerpromoter system that recapitulates most of the key aspects of eukaryotic transcriptional enhancer action (including action over a large distance) both in vivo and in vitro. Below we describe the application of this highly efficient experimental system to analyze the structural and dynamic properties of chromatin that allow communication between DNA regulatory regions over a distance.