CRISPR-based epigenome editing for targeted gene regulation

Abstract

The discovery of CRISPR (clustered regularly interspaced short palindromic repeats) gene editing technology has increased the repertoire of methods to target and test specific gene functions. CRISPR-Cas system has been modified by fusing epigenetic modifiers to a “dead” Cas9 endonuclease (dCas9) to target epigenome using guide RNA as a docking tool. Fusion of repressive epigenetic factors to the dCas9 result in specific guide RNA-targeted repression of gene function (CRISPR interference). Generation of CRISPRi (CRISPR interference) constructs using variety of epigenetic modifiers will increase the potential of gene repression. This project aims to expand on the versatility of CRISPRi system, by fusing different epigenetic modifiers and test their potencies to specifically repress target gene expression via epigenetic modifications. Previously, lentiviral-based CRISPRi constructs using KRAB, HP1a and LSD1 were generated in the lab. Our transduction experiments with CRISPRi constructs and specific guide RNA targeting HS2 enhancer of globin gene in K562 leukemia cells demonstrated that they are effective in gene repression, albeit with variable strength. Generation of novel CRISPRi constructs can help in high-throughput genome-wide CRISPRi screening which currently employs dCas9 with KRAB effector domain. The coupling of new epigenetic effector domains could provide deeper insights on gene regulatory networks in different cell types and context.