Epigenetic engineering
Genome editing technologies have revolutionized biomedical research and hold the promise to decipher the genetic basis of health and may permanently reverse disease processes. Typical epigentic editing tools are composed of inactive, RNA-guided endonuclease Cas9 from Streptococcus pyogenes fused to transcriptional regulators or enzymes such as DNA methyltransferases and histone modifying enzymes. A major challenge for genome editing is that such “editors” have many unintended off-target effects including promiscuous binding of Cas9 to loci with high sequence similarity to the intended target site and unspecific enzymatic activity of editors leading to unwanted modifications. We recently described a novel tool for targeted DNA methylation by tethering a “split-fusion” methyltransferase to an endonuclease-deficient mutant Cas9. Our split-fusion approach minimizes off-target effects by ensuring that enzyme activity is specifically reconstituted at the targeted locus. We are working with Dan Bauer’s group to develop tools that improve Cas9 binding specificity to DNA and limit off-target activities of the fused editing enzymes. We are also building modular tools that recruit multiple different readers to a single Cas9 bound to DNA.
We are using these tools to ask fundamental questions about epigenetic gene regulation: How are epigenetic marks set, maintained, spread and inherited? How does establishing DNA marks relate to establishing histone marks? These fundamentally important questions must be answered to realize the full potential of epigenetic engineering in the clinic.
These tools can also be used to modulate expression of interesting ncRNAs and protein-coding genes to model therapy. We have identified interesting targets in certain cancers, cancer-infiltrating lymphocytes and antigen presenting cells, which we hope to develop for cancer immunotherapy. We have also identified ncRNAs in bone marrow progenitors of patients with Diamond Blackfan Anemia (DBA) and Shwachman Diamond Syndrome (SDS) that are interesting targets for epigenetic reprogramming. Together with the Bauer lab we are working on developing these tools for sickle cell and thalassemia therapies.
Projects are available to (1) reprogram methylation states at disease-relevant loci for therapy, in particular for cancer immunotherapy; (2) compare methylation-dependent changes in microRNA transcription to oncogenic phenotypes; and (3) relate differential promoter methylation to changes in chromatin architecture and transcription factor binding at promoters.
We are using these tools to ask fundamental questions about epigenetic gene regulation: How are epigenetic marks set, maintained, spread and inherited? How does establishing DNA marks relate to establishing histone marks? These fundamentally important questions must be answered to realize the full potential of epigenetic engineering in the clinic.
These tools can also be used to modulate expression of interesting ncRNAs and protein-coding genes to model therapy. We have identified interesting targets in certain cancers, cancer-infiltrating lymphocytes and antigen presenting cells, which we hope to develop for cancer immunotherapy. We have also identified ncRNAs in bone marrow progenitors of patients with Diamond Blackfan Anemia (DBA) and Shwachman Diamond Syndrome (SDS) that are interesting targets for epigenetic reprogramming. Together with the Bauer lab we are working on developing these tools for sickle cell and thalassemia therapies.
Projects are available to (1) reprogram methylation states at disease-relevant loci for therapy, in particular for cancer immunotherapy; (2) compare methylation-dependent changes in microRNA transcription to oncogenic phenotypes; and (3) relate differential promoter methylation to changes in chromatin architecture and transcription factor binding at promoters.
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