A Novel Epigenetic Gene Silencing Technology

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DESCRIPTION (provided by applicant): This research proposal, entitled "A Novel Epigenetic Gene Silencing Technology", addresses the broad Challenge Area: (06) Enabling Technologies, and specific Challenge Topic, 01-OD-107: Functional Modulation of Epigenomic Modifications. The ability to modulate gene expression holds great promise for genome biology research and for novel treatments of intractable human diseases caused by the dysfunction of genes. RNA interference (RNAi) that blocks gene translation to protein by small interfering RNA (siRNA)-triggered messenger RNA destruction has had transformative impact in research and also generated enormous excitement and hope for new therapies. However, due to daunting challenges in siRNA delivery and off-target side effects, the RNAi gene silencing technology has yet to produce new therapeutics. On the other hand, recent advances in the field of epigenetics show that site-specific modifications in chromosomal DNA-packing histones dictate gene expression or silencing in response to physiological and environmental stimuli. For instance, histone H3 lysine 4 methylation (H3K4me) directed by the Trithorax group complex signifies for gene activation, whereas H3 lysine 27 methylation (H3K27me) controlled by the Polycomb group complex is an epigenetic marker for gene silencing resulting from chromatin compaction. While effective in mammalian gene transcriptional control, the Trithorax or Polycomb group complex works through multiple proteins in a highly coordinated fashion. Thus, it is not feasible to direct Trithorax or Polycomb proteins for targeted gene activation or silencing for the purpose of research or therapeutic disease treatments. We have recently discovered a novel viral mechanism for host transcriptional repression centered on histone methylation (Nature Cell Biology, 2008). We show that the chlorella virus uses a viral protein (termed vSET) to modify specifically host histone H3 lysine 27 in the infected cells, thereby switching host transcription machinery for viral replication. Given that this epigenetic silencing mechanism is conserved in eukaryotes, we show that vSET can effectively suppress transcriptional expression of Polycomb target genes in human cells such as the HOX genes. Because of its exquisite activity for methylation of histone H3 at lysine 27, vSET can in principle be developed into a selective epigenetic gene silencing technology by fusing itself to a gene sequence-specific recognition domain, which is the goal of our proposed research. We expect that this novel gene silencing technology, which fills an important technological gap of controlling gene silencing at the transcription level, will have broad impact as a powerful tool in genome research of human biology and disease. Post-translational histone modifications determine transcriptional activation or silencing of human genes. While the importance of histone modifications in gene regulation is well recognized, it remains a major challenge to modulate the functions of histone modifying enzymes for the purpose of research or disease treatments. To address this scientific challenge, we propose to develop a new histone lysine methylation-directed gene silencing technology that is based on our recent discovery of a novel viral gene silencing mechanism, which we expect will be a new transformative tool for both the mechanistic genome biology research and for future development of novel epigenetic therapies to intractable human diseases.