Grant: Discovery Grants Program - Individual

DNA of animals contains the genetic information. Each cell type receives instructions from a subset of the genetic information. The turning on and off genes is critically important in the functioning of the different cell types that make up the body of the animal. The long-term goal of my research program is to understand the ways that genes are turned off and on. Vertebrate genomic DNA is associated with proteins forming a structure called chromatin. The basic repeating structural unit of chromatin is the nucleosome, which consists of two each of four proteins called histones, forming an octamer around which is wrapped a short stretch of genomic DNA. The vertebrate genome is organized into lightly compacted euchromatin with expressed genes and highly compacted heterochromatin with silenced genes. For more than three decades, I have been studying the histones and enzymes that play key roles in chromatin structure and function. Chemical tags (modifications) onto the histone are different for expressed versus silent gene chromatin. Although we know that these different types of histone modifications play a key role in the expression of genes, there is still much to be learned as to the function of these histone modifications in turning genes on and off. The chicken model organism has advanced the areas of regulation of gene expression, conservation biology, and genomics of domestication. My research uses nucleated red blood cells from chickens to characterize the chromatin organization of expressed genes. Most chromatin in these cells is highly condensed, more so than in other vertebrate cells; it is in this repressive chromatin environment that the euchromatin structure allows gene expression to occur. My research group discovered a method to separate chicken erythroid expressed gene chromatin from silent gene chromatin, and when combined with state-of-the-art DNA sequencing methods, we identified the euchromatin regions in chicken red blood cells. The short-term goals of my proposed research are to characterize the chromatin structure of expressed genes and to train highly qualified personnel in a variety of approaches. In objective 1, methods will be applied to map the genomic location of the histone modifications of interest and determine the position of these proteins relative to nucleosome free regions which locate to regulatory DNA elements such as promoters and enhancers. In objective 2, molecular biology approaches will be applied to learn what happens to expressed gene chromatin structure when transcriptional activity and specific chromatin modifying enzyme activity are halted. We will apply state-of-the-art imaging methods to learn where in the red blood cell nucleus expressed genes and modified histones are located. Such information will lead to a better understanding of how expressed gene chromatin maintains a structure and composition that operates in a highly condensed chromatin environment.