Cork Oak Young and Traumatic Periderms Show PCD Typical Chromatin Patterns but Different Chromatin-Modifying Genes Expression

Abstract

Plants are subjected to adverse conditions being outer protective tissues fundamental to their survival. Tree stems are enveloped by a periderm made of cork cells, resulting from the activity of the meristem phellogen. DNA methylation and histone modifications have important roles in the regulation of plant cell differentiation. However, studies on its involvement in cork differentiation are scarce despite periderm importance. Cork oak periderm development was used as a model to study the formation and differentiation of secondary protective tissues, and their behavior after traumatic wounding (traumatic periderm). Nuclei structural changes, dynamics of DNA methylation, and posttranslational histone modifications were assessed in young and traumatic periderms, after cork harvesting. Lenticular phellogen producing atypical non-suberized cells that disaggregate and form pores was also studied, due to high impact for cork industrial uses. Immunolocalization of active and repressive marks, transcription analysis of the corresponding genes, and correlations between gene expression and cork porosity were investigated. During young periderm development, a reduction in nuclei area along with high levels of DNA methylation occurred throughout epidermis disruption. As cork cells became more differentiated, whole nuclei progressive chromatin condensation with accumulation in the nuclear periphery and increasing DNA methylation was observed. Lenticular cells nuclei were highly fragmented with faint 5-mC labeling. Phellogen nuclei were less methylated than in cork cells, and in lenticular phellogen were even lower. No significant differences were detected in H3K4me3 and H3K18ac signals between cork cells layers, although an increase in H3K4me3 signals was found from the phellogen to cork cells. Distinct gene expression patterns in young and traumatic periderms suggest that cork differentiation might be under specific silencing regulatory pathways. Significant correlations were found between QsMET1, QsMET2, and QsSUVH4 gene expression and cork porosity. This work evidences that DNA methylation and histone modifications play a role in cork differentiation and epidermis induced tension-stress. It also provides the first insights into chromatin dynamics during cork and lenticular cells differentiation pointing to a distinct type of remodeling associated with cell death.

Genome-Wide Identification of Epigenetic Regulators in Quercus suber

“…Interestingly, in Q. suber the lower expression level of the presumed DNA methylation maintenance genes QsCMT-and QsMET-like is counterbalanced by the higher expression of the putative de novo DNA methylation gene QsDRM2. This result was already observed in previous works [78,79]. QsDRM2 higher expression is well noticed in cork and buds (containing vegetative and reproductive tissues) (Fig 8, Table S3).…”

“…DNA methylation variability may contribute to cork cell characteristics linked to quality [86]. Inácio et al (2018) emphasized the presence of both DNA and H3K9 methylation silencing pathways in cork. Here, we show that QsSUVH4 is expressed in cork (Fig 8) but also in the other tissues analyzed.…”

A cost-effective approach to DNA methylation detection by Methyl Sensitive DArT sequencing

“…Either increase [50,51] or decrease [52] in methylation levels has been observed in different species as tissues mature. Other evidence come from elevated expression of the RdDM (RNA directed DNA methylation) pathway and other chromatin regulators in meristems suggesting they act as a relay mechanism to ensure correct propagation of silent states to new tissues and organs [53], from epigenomic diversity observed between cell types within root meristem [54] and from highly dynamic DNA methylation during cork cells differentiation [55]).…”

Four hundred years of cork imaging: New advances in the characterization of the cork structure

“…Plasmodesmata act as intercellular channels that mediate the cell-to-cell transport of signaling molecules, such as non-cell autonomous proteins or RNAs, in the living cells 14 . After their development, cork cells are autolyzed and undergo programmed cell death in response to environmental cues 15,16 . Thus, the resulting layer of phellem, which is composed of dead cells, is an efficient insulator, either acting as a barrier to dehydration or as protection against fire for the oak tree in the Mediterranean peninsula.…”

“…A higher number of lenticels indicates a lower quality of the cork. Several other imaging techniques have been applied to study cork, such as terahertz millimeter wave 21 , near-infrared spectroscopies 22 and more recently confocal microscopy 16 (Fig. 1) X-ray 23,24 and neutron tomographies 19 were also used, showing that lenticels are not interconnected within a cork stopper.…”