Deciphering Plant Chromatin Regulation via CRISPR/dCas9-Based Epigenome Engineering

Abstract

CRISPR-based epigenome editing uses dCas9 as a platform to recruit transcription or chromatin regulators at chosen loci. Despite recent and ongoing advances, the full potential of these approaches to studying chromatin functions in vivo remains challenging to exploit. In this review we discuss how recent progress in plants and animals provides new routes to investigate the function of chromatin regulators and address the complexity of associated regulations that are often interconnected. While efficient transcriptional engineering methodologies have been developed and can be used as tools to alter the chromatin state of a locus, examples of direct manipulation of chromatin regulators remain scarce in plants. These reports also reveal pitfalls and limitations of epigenome engineering approaches that are nevertheless informative as they are often associated with locus- and context-dependent features, which include DNA accessibility, initial chromatin and transcriptional state or cellular dynamics. Strategies implemented in different organisms to overcome and even take advantage of these limitations are highlighted, which will further improve our ability to establish the causality and hierarchy of chromatin dynamics on genome regulation.

Manipulating plant development by editing histone methylation with the dCas9 tool: theCUC3boundary gene as a case study

“…While such global approaches have provided valuable insights, they affect the entire epigenome simultaneously, making it challenging to pinpoint the direct effect of a specific mark on a target gene 11 . Hence, novel CRISPR-Cas derived tools have been developed for various model organisms, serving as a platform to tether an effector capable of modifying the expression or epigenetic marks at a precise genomic locus 11,[17][18][19] . These tools harbour a catalytically inactive (referred to as "dead") form of Cas9 (dCas9), lacking endonuclease activity but retaining the ability to bind a single guide RNA (sgRNA) 20 .…”

When an Intruder Comes Home: GM and GE Strategies to Combat Virus Infection in Plants

“…dCas9 can be used as a transcriptional activator (CRISPRa) or transcriptional repressor (CRISPRi) [227]. There is enormous potential for dCas9 to gain insights into plant-virus interactions and for performing transcriptional engineering and chromatin alterations [228].…”