The candidate is currently a postdoctoral fellow at NHLBI in the laboratory of Dr. Keji Zhao. The proposal describes a combined research and training program leading to independence. During the mentored phase of this project, the candidate will continue training in computational data analysis necessary for the application of modern high- throughput techniques such as ChIP-Seq and RNA-Seq, as well as develop other skills necessary for a successful academic career. The research goal of this project is to understand the role of chromatin and gene poising in T helper cell differentiation and function. Upon initial antigen stimulation, naive T cells differentiate into effector and then into memory T cells. As a result of previous antigen exposure, memory T cells are able to produce cytokines and fight infection more rapidly than naive T cells. This ability of memory T cells is likely mediated by the epigenetic mechanisms. Recently, we developed ChIP-Seq, a novel method to study genome-wide distribution of chromatin modifications. Applying this method to resting T cells, we discovered that some silent genes posses "active" chromatin modifications normally associated with expressed genes and even have RNA Polymerase II (Pol II) at their promoters. We called these genes poised, because the majority of the genes that were actually induced during T cell activation belonged to this gene set. To test whether poising may occur de novo or has to be a result of prior expression we propose to follow changes in chromatin and Pol II binding and gene expression during in vitro differentiation of naive T helper cells into Th1/Th2 cells. Further, we hypothesize that the ability of effector memory T helper cells to quickly produce cytokines is mediated by poising of these genes. We will correlate chromatin structure at cytokine and other important genes in naive and subsets of memory T cells with the ability of these genes to be rapidly expressed in these cell types (Aim 1). Poised genes possess Pol II and all the necessary chromatin modifications at their promoters, but are not transcribed. Upon T cell activation only a minority of poised genes are expressed. We will dissect the mechanism of transcription inhibition at the poised genes and identify factors responsible for the release of this inhibition in a gene specific manner upon T cell activation (Aim 2). Taken together, results of these studies will contribute to our understanding of acquired immune response.
This project aims to explore the role of chromatin modifications and gene poising in T helper cell differentiation and activation. The studies will lead to better understanding of adaptive immune response and acquired immunity.
|Barski, Artem; Chepelev, Iouri; Liko, Dritan et al. (2010) Pol II and its associated epigenetic marks are present at Pol III-transcribed noncoding RNA genes. Nat Struct Mol Biol 17:629-34|
|Cuddapah, Suresh; Barski, Artem; Zhao, Keji (2010) Epigenomics of T cell activation, differentiation, and memory. Curr Opin Immunol 22:341-7|