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.
Highlights
Chromatin mechanisms play a major role in fine-tuning gene regulation in eukaryotes
In vitro assays in plants showed that the binding of over three quarters of Arabidopsis transcription factors (248 TFs out of 327 tested) is sensitive to DNA methylation, which either inhibits (72%) or favours (4.3%) its binding to a DNA motif [69]
While in vivo studies based on dead Cas9 (dCas9)-based approaches are slowly cranking up in plants, they should be more generally accompanied by transcriptomic and epigenomic analyses to verify target specificity and to assess efficiency and consequences in distinct cellular and molecular contexts
Summary
Chromatin mechanisms play a major role in fine-tuning gene regulation in eukaryotes. The main feature of chromatin is the wrapping of genomic DNA around a protein octamer of four pairs of histones H2A, H2B, H3 and H4, altogether constituting the nucleosome. In a variety of applications including epigenome editing, this catalytically dead Cas (dCas9) is used as a synthetic platform to recruit specific proteins or enzymes to a given locus, without affecting its DNA sequence. Transcriptional engineering in which a transacting factor is targeted to a gene regulatory region and destabilizes or triggers a shift in the local chromatin state, and direct epigenome editing in which a chromatin modifier is recruited through dCas for locus-specific perturbation of a specific epigenetic regulation. Each of those synthetic approaches was shown to function to some extent in plant and animal systems. This domain seems very promising to achieve locus-specific repression in plants
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