Histone arginine methylation and transcriptionally active chromosomal domains

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The eukaryotic genome is organized into domains, which contain one or more genes. Some domains contain expressed genes, while others have silenced genes. This research field called epigenetics is the study of the organization and expression of genes that is not dependent upon changes in the DNA sequence. For more than three decades, my research group has focused on the study of histones which play a key role in epigenetic regulation of gene expression. Histones bind to DNA forming a structure called the nucleosome. The nucleosomes are joined by a stretch of DNA to form chromatin. Histone modifications, which are different in expressed gene and silent gene chromatin, play a key role in the organization and expression of genes. My research uses red blood cells from egg-laying chickens to characterize the organization of expressed genes. My research group discovered a method to separate expressed gene chromatin from silent gene chromatin, and when combined with state-of-the-art DNA sequencing methods, we identified all the chromatin domains containing expressed genes in chicken red blood cells. Surprisingly the red blood cell expressed genes involved in the innate immune response, which defends the bird from infection by other organisms (viruses). My proposed discovery research will explore the role of two enzymes called protein arginine methyltransferases, PRMT1 and 5, in maintaining the histone modifications associated with the expressed gene chromatin domains. We believe that these enzymes are essential to maintaining the chromatin organization needed for expression of genes involved in oxygen transport and innate immunity. Three graduate and four summer students will be trained in state-of-the-art epigenetic methodology. Sanzida Jahan, a PhD trainee, and a Masters trainee, Tasnim Hussain, will determine the location of PRMT1/5 and the histone modifications produced by these enzymes (histone H3 dimethylated (symmetric) at R2 (H3R2me2s) and histone H4 dimethylated (asymmetric) at R3 (H4R3me2a)) using the chromatin immunoprecipitation (ChIP) assay and next generation DNA sequencing with chicken red blood cells and avian 6C2 cells, which are arrested at the colony forming unit erythrocyte stage. The second aim will find out how PRMT1 and 5 are directed to expressed genes. Sanzida and Tasnim will identify the proteins associated with these enzymes. In the third aim, the graduate students will use methods that reduce the expression of or inhibit PRMT1 and 5 and determine the consequences of the loss/inhibition of the enzyme's activity on the organization of expressed gene chromatin in chicken red blood cells. This discovery research will enhance our understanding of the mechanisms involved in epigenetic regulation of gene expression and highlight the central role of PRMTs in establishing a chromatin structure that is supportive of gene expression in a background of highly condensed chromatin.