RT Journal Article
SR Electronic
T1 Stage-specific transcriptomes and DNA methylomes indicate an early and transient loss of transposon control in Arabidopsis shoot stem cells
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 430447
DO 10.1101/430447
A1 Ruben Gutzat
A1 Klaus Rembart
A1 Thomas Nussbaumer
A1 Rahul Pisupati
A1 Falko Hofmann
A1 Gabriele Bradamante
A1 Nina Daubel
A1 Angelika Gaidora
A1 Nicole Lettner
A1 Mattia Donà
A1 Magnus Nordborg
A1 Michael Nodine
A1 Ortrun Mittelsten Scheid
YR 2018
UL http://biorxiv.org/content/early/2018/09/29/430447.abstract
AB In contrast to animals, postembryonic development in plants is modular, and aerial organs originate from stem cells in the center of the shoot apical meristem (SAM) throughout life. Descendants of SAM stem cells in the subepidermal layer (L2) will give also rise to male and female gametes 1 and therefore can be considered primordial germ cells. In these cells, transmission of somatic mutations including virus and TE insertions must be avoided. Despite their essential role for plant development and intergenerational continuity, a comprehensive molecular analysis of SAM plant stem cells has been missing, due to their low number, deep embedding among non-stem cells and difficult isolation. Here we present a comprehensive analysis of stage-specific gene expression and DNA methylation dynamics in Arabidopsis SAM stem cells. This revealed that stem cell expression signatures are mostly defined by development, but we also identified a core set of differentially expressed stemness genes. Surprisingly, vegetative SAM stem cells showed increased expression of transposable elements (TEs) relative to surrounding cells, despite high expression of genes connected to epigenetic silencing. We also find increasing methylation at CHG and a drop in CHH methylation at TEs before stem cells enter the reproductive lineage, indicating an onset of epigenetic reprogramming at an early stage. Transiently elevated TE expression is reminiscent of that in animal primordial germ cells (PGCs)2 and demonstrates commonality of transposon biology. Our results connect SAM stem cells with germline development and transposon evolution and will allow future experiments to determine the degree of epigenetic heritability between generations.