Arabidopsis shoot stem cells display dynamic transcription and DNA methylation patterns

Abstract

In plants, aerial organs originate continuously from stem cells in the center of the shoot apical meristem. Descendants of stem cells in the subepidermal layer are progenitors of germ cells, giving rise to male and female gametes. In these cells, mutations, including insertions of transposable elements or viruses, must be avoided to preserve genome integrity across generations. To investigate the molecular characteristics of stem cells in Arabidopsis, we isolated their nuclei and analyzed stage-specific gene expression and DNA methylation in plants of different ages. Stem cell expression signatures are largely defined by developmental stage but include a core set of stem cell-specific genes, among which are genes implicated in epigenetic silencing. Transiently increased expression of transposable elements in meristems prior to flower induction correlates with increasing CHG methylation during development and decreased CHH methylation, before stem cells enter the reproductive lineage. These results suggest that epigenetic reprogramming may occur at an early stage in this lineage and could contribute to genome protection in stem cells during germline development.

Gene Expression Variation in Arabidopsis Embryos at Single-Nucleus Resolution

“…By contrast, genes encoding ARGONAUTE (AGO; AGO1/5/8/9/10) proteins, which bind to small RNAs and mediate gene repression, were enriched in the precursors of the shoot meristem initials. The enrichment of AGOs in shoot meristem initials is supported by previous reports (Gutzat et al, 2020; Jullien et al, 2020; Tucker et al, 2008) and is consistent with small RNA-mediated surveillance pathways that prevent transposon mobilization and other genome de-stabilizing events being enriched in the precursors to all aerial tissues including the gametes. Altogether, these results suggest that small RNA-dependent and -independent pathways establish distinct chromatin environments in individual cell lineage precursors.…”

Repression of CHROMOMETHYLASE 3 Prevents Epigenetic Collateral Damage in Arabidopsis

“…The copyright holder for this preprint (which this version posted April 14, 2021. ; https://doi.org/10.1101/2021.04.14.439682 doi: bioRxiv preprint opment can readily explain the genome-wide patterns of non-CG methylation reported thus far (Borges et al, 2021;Calarco et al, 2012;Gutzat et al, 2020;Ji et al, 2019;Kawakatsu et al, 2016Kawakatsu et al, , 2017Lin et al, 2017;Narsai et al, 2017;Papareddy and Nodine, 2021).…”

Role of Chromatin Architecture in Plant Stress Responses: An Update

“…In meristems before flower induction, increased expression of transposable elements correlates with enhanced CHG methylation during development and reduced CHH methylation, before stem cells enter the reproductive lineage ( Sasaki et al, 2019 ). This shows the occurrence of epigenetic reprogramming at an early stage and its role in genome protection in stem cells during germline development ( Gutzat et al, 2020 ). In the Arabidopsis leaf tissue, after prolonged heat stress, centromeric repeats and 5S rDNA decondensation occur ( Pecinka et al, 2010 ).…”