Chromatin Structure and Gene Expression

Division Of Basic Sciences - Nci

Investigators

Linked publications, trials & patents

Abstract

1 Reprogramming of the chromatin landscape is a critical component to the transcriptional response in breast cancer. Effects of sex hormones such as estrogens and progesterone have been well described to have a critical impact on breast cancer proliferation. However, the complex network of the chromatin landscape, enhancer regions and mode of function of steroid receptors (SRs) and other transcription factors (TFs), is an intricate web of signaling and functional processes that is still largely misunderstood at the mechanistic level. We are exploring the dynamic interplay between TFs with chromatin and the reprogramming of enhancer elements. We characterize the different modes of action of TFs in regulating enhancer activity, specifically, how different SRs target enhancer regions to reprogram chromatin. 2 We are adapting recent advances in live cell imaging technology to study the function of T factors in single cells in real time. Single Molecule Tracking (SMT) allows the study of TF dynamics in the nucleus, giving important information regarding the search and binding behavior of these proteins with chromatin in vivo. However, how TFs navigate within the intricate nuclear environment to find and bind their response elements on chromatin, recruit the transcription machinery, and ultimately regulate gene expression remains largely unknown. By the implementation of proper photobleaching kinetics, theory-based models and an unbiased model selection approach, we revealed a new model of TF dynamics where TFs binding times are power-law distributed. Previous models suggested that TFs bound either non-specifically or specifically, with each mode of binding having their own distribution that was largely discrete from the other. The power-law model, on the other hand, indicates that TFs bind not discretely in these two modes, but with a continuous distribution from fast to very slow kinetics. These results are aligned with the theoretical underpinnings of TF motions in the crowded nuclear space and exploration of a complex DNA space. Our approaches enable the coupling of population based assays with real time studies to address many unsolved questions about SRs and chromatin dynamics in normal mammalian cells, in breast cancer cells, and prostate cancer cells. 3 Cancer discovery has been focused primarily on the identification of critical mutated pathways, and the development of drugs to target the gene products of these so called "driver" mutants. Critical driver mutants are not commonly identified, and therapies targeting these pathways are frequently followed by relapse. In fact, the regulatory networks that control global gene expression are massively transformed during cancer initiation and progression. The failure to normalize gene regulation and return cells to normal growth control is likely a major factor in treatment failure. To treat cancer effectively, a key issue is to identify the regulatory elements that create this abnormal expression pattern, rather than simply describing the gene expression pattern in tumor cells. Our primary goal is to analyze the status of enhancer networks in cancer cells, and identify enhancer "signatures" characteristic of progression and metastasis. Enhancer signatures predictive of cancer progression can then inform threat level for a specific tumor, appropriate patient therapy, and treatment progress for favorable response in enhancer status.