Chromatin Mechanics: Starting Local, Going Global

Exogenous Chromatin Damage or Alteration, or CDA, represents an existential threat to the viability of the cell. It is important to understand the cause of various types of CDA, the direct effect that they have upon the chromatin, and the cell’s natural response in order to either counteract them, in the case of disease or injury, or amplify them in a targeted manner, in the case of cancer treatment. One of the main challenges to overcome is the complexity of biology. One way to simplify this complexity is the use of an orthogonal method, such as measuring the mechanical properties of the system, that takes into account all the individual contributions simultaneously without parsing them out individually. Analogous to this is the way an integral finds the area under a strangely shaped curve by summing an infinite number of infinitesimally thin slices. Directly measuring the motion of chromatin will allow us to study the effect of a particular CDA upon the chromatin without individually measuring the contributions of many participating proteins or pathways. We have specialized in one particular method to accomplish this goal called Sensors from IntraNuclear Kinetics (SINK). Here we demonstrate how SINK can be used to study CDA in vastly different contexts. We begin with site-specific DNA damage (Chapter III) and expand to widespread DNA damage due to chemotherapeutic treatment (Chapter IV). Next, we examine total nuclear remodeling due to viral infection (Chapter V), then move on to remodeling of both chromatin and cytoskeleton for genome-wide damage prevention in response to mechanical stimulus (Chapter VI). We find that SINK allows us to detect patterns other methods could not, which improves our understanding of processes that are already well-studied and enables us to make new discoveries about phenomena that have previously been difficult to study.