Investigating the Role of Active Chromatin Dynamics in T Cell Activation and Differentiation

University Of Maryland, College Park, College Park MD

Investigators

Abstract

The two-meter-long genetic material in human cells is tightly packed into the nucleus that is a million times smaller. To accomplish this packing, DNA, the primary genetic material, is tightly wound around proteins called histones which are then hierarchically organized as chromatin. In a process called transcription, specialized proteins read out the information contained in the DNA sequences to make new proteins that then carry out all cellular functions. Chromatin, rather than being an inert template, is a dynamic polymer, which undergoes further reorganization when cells undergo changes in their state, such as during development. How this information is read out from the tightly packed, dynamic chromatin is poorly understood as are the physical rules of spatial organization of chromatin. Cells of the adaptive immune system, which help the body fight infection offer a tractable system to study the interplay between gene transcription and dynamic chromatin. When exposed to foreign proteins, these cells undergo extensive changes in chromatin organization as they fight the infection and subsequently develop a memory for it. In this award the investigators will use quantitative experimental approaches and theories from physics to address long standing gaps in our knowledge of critical processes in development, immune response and disease states such as cancer. This project will also provide novel educational and training opportunities for undergraduate and graduate students in advanced optical microscopy techniques, image processing, and data analysis as well as polymer physics and biophysics. Genomic techniques have established the basic structural rules of hierarchical organization of chromatin but they offer only a static, cell-averaged snapshot. Transcriptional readout of the genetic information contained in chromatin does not occur on a static template. Rather, chromatin exhibits dynamics at multiple time scales, ranging from the sub-second scale thermal motion of the chromatin polymer to minutes and hours long reorganization in response to developmental programs and external chemical and mechanical stimuli. When cells undergo differentiation, the genome undergoes extensive structural reorganization of chromatin leading to functionally appropriate gene expression. How sequence specific proteins that bind DNA and regulate transcription, known as transcription factors (TF), interact with dynamic chromatin to regulate gene expression remains poorly understood. This award will use CD8+ T cells (also called “killer T cells”) as a model system to study this question. Upon antigen exposure, T cells rapidly differentiate into effector cells and memory cells. Effector T cells ultimately kill infected target cells, while memory T cells circulate in the body in a “naive-like” state and rapidly recall re-exposure to antigen and transform into effector cells. Genomic studies have revealed that T cell activation and differentiation is accompanied by extensive reorganization of the genome, but how these changes affect chromatin dynamics and interactions with transcription factors is not well understood. The Principal Investigator’s laboratory have developed a suite of techniques – from single molecule tracking to whole genome imaging to study the dynamics of chromatin and TFs over transcriptionally relevant timescales. In this award they propose to elucidate the driving forces for chromatin patterning, its dynamical evolution and the resulting impact on transcriptional dynamics with T cell activation and differentiation as a model. More generally, this work will have implications in understanding the fundamental principles underlying chromatin dynamics and TF/chromatin interactions during cell differentiation. This research, which lies at the nexus of physics and biology, will provide interdisciplinary training opportunities for graduate and undergraduate students. The project will also provide STEM research experiences for undergraduate students and high school students. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.