A Targeted RNA Interference Screen Reveals Novel Epigenetic Factors
That Regulate Herpesviral Gene Expression
Hyung Suk Oh,a Kevin F. Bryant,a Thomas J. F. Nieland,b Aprotim Mazumder,c Mukta Bagul,b Mark Bathe,b,c David E. Root,b
David M. Knipea
Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USAa; Broad Institute of Massachusetts Institute of Technology and
Harvard, Cambridge, Massachusetts, USAb; Department of Biological Engineering and Center for Environmental Health Sciences, Laboratory for Computational Biology &
Biophysics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USAc
ABSTRACT Herpes simplex virus (HSV) utilizes and subverts host chromatin mechanisms to express its lytic gene products in mammalian cells. The host cell attempts to silence the incoming viral genome by epigenetic mechanisms, but the viral VP16 and
ICP0 proteins promote active chromatin on the viral genome by recruiting other host epigenetic factors. However, the dependence on VP16 and ICP0 differs in different cell lines, implying cell type-dependent functional contributions of epigenetic factors for HSV gene expression. In this study, we performed a targeted RNA interference (RNAi) screen for cellular chromatin factors that are involved in regulation of herpes simplex virus (HSV) gene expression in U2OS osteosarcoma cells, a cell line that complements ICP0 mutant and VP16 mutant virus replication. In this screen, we found the same general classes of chromatin factors that regulate HSV gene expression in U2OS cells as in other cell types, including histone demethylases (HDMs), histone deacetylases (HDACs), histone acetyltransferases (HATs), and chromatin-remodeling factors, but the specific factors within these classes are different from those identified previously for other cell types. For example, KDM3A and KDM1A (LSD1) both demethylate mono- and dimethylated H3K9, but KDM3A emerged in our screen of U2OS cells. Further, small interfering RNA
(siRNA) and inhibitor studies support the idea that KDM1A is more critical in HeLa cells, as observed previously, while KDM3A is more critical in U2OS cells. These results argue that different cellular chromatin factors are critical in different cell lines to carry out the positive and negative epigenetic effects exerted on the HSV genome.
IMPORTANCE Upon entry into the host cell nucleus, the herpes simplex virus genome is subjected to host epigenetic silencing
