Chromatin Manipulation and Editing: Challenges, New Technologies and Their Use in Plants

Abstract

An ongoing challenge in functional epigenomics is to develop tools for precise manipulation of epigenetic marks. These tools would allow moving from correlation-based to causal-based findings, a necessary step to reach conclusions on mechanistic principles. In this review, we describe and discuss the advantages and limits of tools and technologies developed to impact epigenetic marks, and which could be employed to study their direct effect on nuclear and chromatin structure, on transcription, and their further genuine role in plant cell fate and development. On one hand, epigenome-wide approaches include drug inhibitors for chromatin modifiers or readers, nanobodies against histone marks or lines expressing modified histones or mutant chromatin effectors. On the other hand, locus-specific approaches consist in targeting precise regions on the chromatin, with engineered proteins able to modify epigenetic marks. Early systems use effectors in fusion with protein domains that recognize a specific DNA sequence (Zinc Finger or TALEs), while the more recent dCas9 approach operates through RNA-DNA interaction, thereby providing more flexibility and modularity for tool designs. Current developments of “second generation”, chimeric dCas9 systems, aiming at better targeting efficiency and modifier capacity have recently been tested in plants and provided promising results. Finally, recent proof-of-concept studies forecast even finer tools, such as inducible/switchable systems, that will allow temporal analyses of the molecular events that follow a change in a specific chromatin mark.

Lysine 27 of histone H3.3 is a fine modulator of developmental gene expression and stands as an epigenetic checkpoint for lignin biosynthesis in Arabidopsis

“…Loss of function of EMF2, another Arabidopsis PRC2 sub‐unit, homologue of the Drosophila Su(z)12 protein and containing a VEFS (VRN2‐EMF2‐FIS2‐Su(z)12) domain, leads to direct flowering upon germination and sterility (Chanvivattana et al ., 2004). Thus, despite our knowledge of PRC2 components in plants, the plurality of sub‐units, may they be redundant or alternative, does not allow to get a clear idea of the function of the deposited marks themselves (Fal et al ., 2021).…”

Lysine 27 of histone H3.3 is a fine modulator of developmental gene expression and stands as an epigenetic checkpoint for lignin biosynthesis in Arabidopsis

“…Loss of function of EMF2, another Arabidopsis PRC2 sub-unit, homologue of the Drosophila Su(z)12 protein and containing a VEFS (VRN2-EMF2-FIS2-Su(z)12) domain, leads to direct flowering upon germination, and sterility (Chanvivattana et al ., 2004). Thus, despite our knowledge of PRC2 components in plants, the plurality of sub-units, may they be redundant or alternative, does not allow to get a clear idea of the function of the deposited marks themselves (Fal et al ., 2021).…”

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

“…Therefore, to gain resolution on the genuine function of histone marks, approaches and tools for their direct edition have been developed 11 . Manipulation of histone residues allowed revealing the key role of H3 methylations in animal and plant cell differentiation and specific developmental programs [12][13][14][15] .…”