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The way a stretch of DNA is organized inside the cell—whether it is loosely or compactly packaged by associated proteins—is believed to reflect the activity level of the genes it contains. The Risca lab studies how the three-dimensional architecture of the mammalian genome helps to precisely control transcriptional programs and genome maintenance in both healthy cells undergoing differentiation and in cells exposed to stressors, such as DNA damage.

The 46 chromosomes of the human genome would measure almost two meters if stretched out end-to-end as pure DNA. To fit into the roughly five-micron-wide cell nucleus, DNA is wrapped around histone proteins into repeating bobbin-like structures called nucleosomes, which make up the chromatin fiber. Chromatin organizes the genome within the nucleus to control transcription, DNA replication, and DNA repair. Defects in chromatin organization can perturb gene expression, leading to serious consequences that include developmental disorders and cancer.

The Risca lab investigates the three-dimensional architecture of chromatin and the basic biophysical mechanisms by which it defines and maintains stable states in the regulation of transcription and other DNA-based processes.

Risca’s postdoctoral studies helped to fill a significant gap in the field of chromatin biology: The high density of chromatin packing made it challenging to study how nearby nucleosomes fold together in the chromatin fiber. Risca and her colleagues developed a technique, called RICC-seq, capable of examining the configuration of one to three nucleosomes. This length scale is particularly important because it corresponds to the length of genetic elements that contain binding sites for transcription factors.

RICC-seq uses ionizing radiation to create spatially distinct clusters of DNA strand breaks within intact cells. DNA fragments spanning break sites are sequenced and the resulting data aggregated across many cells to create a high-resolution map of DNA folding. Using RICC-seq, Risca and colleagues uncovered accordion-like compaction of chromatin fibers within repressed regions of chromosomes. Meanwhile, within active regions, they found evidence of a looser folding with few contacts between neighboring nucleosomes, consistent with previous data.

In addition to RICC-seq, the Risca lab uses computer simulation, microscopy, and other sequencing-based methods to study genome architecture in order to understand how it is regulated and how it, in turn, controls regulatory molecules’ access to DNA.

To better understand these relationships, the lab focuses on two natural perturbations in chromatin states. First, they study X-chromosome inactivation, which occurs when female mammalian cells must repress large portions of one of their X chromosomes during development. Using mouse embryonic stem cells, Risca is interested in the biophysical mechanisms that control this large-scale silencing of transcription. Secondly, the lab investigates senescence, a state in which cells irreversibly exit the cell cycle and undergo associated changes in genome organization. Because senescence can shut down the replication of cells in response to DNA damage or oncogene activation, it acts as a first line of defense against cancer.

The new mechanistic insights that result from this work may make it possible to better understand how cells respond to perturbations brought on by mutations or chromatin-targeting drugs, potentially leading to more precise tailoring of cancer therapies and control of cell differentiation.