Gene expression map of the Arabidopsis shoot apical meristem stem cell niche

Abstract

Despite the central importance of stem cells in plant growth and development, the molecular signatures associated with them have not been revealed. Shoot apical meristems (SAMs) harbor a small set of stem cells located at the tip of each plant and they are surrounded by several million differentiating cells. This imposes a major limitation in isolating pure populations of stem cells for genomic analyses. We have developed a system to isolate pure populations of distinct cell types of the SAMs, including stem cells. We have used this system to profile gene expression from 4 different cell samples of SAMs. The cell sample-specific gene expression profiling has resulted in a highresolution gene expression map to reveal gene expression networks specific to individual spatial domains of SAMs. We demonstrate that the cell sample-specific expression profiling is sensitive in identifying rare transcripts expressed in a few specific subsets of cells of SAMs. Our extensive RNA in situ analysis reveals that the expression map can be used as a predictive tool in analyzing the spatial expression patterns of genes and it has led to the identification of unique gene expression patterns within the SAMs. Furthermore, our work reveals an enrichment of DNA repair and chromatin modification pathways in stem cells suggesting that maintenance of genome stability and flexible chromatin may be crucial for stem cell function. The gene expression map should guide future reverse genetics experiments, high-resolution analyses of cell-cell communication networks and epigenetic modifications.central zone ͉ CLAVATA3 ͉ fluorescence-activated cell sorting ͉ WUSCHEL S patiotemporal regulation of transcriptional programs mediated by cell-cell communication networks is crucial in stem cell maintenance (1, 2). Understanding the complexity of transcriptional programs requires a high resolution analysis of gene expression, preferably at a cell type-specific resolution (3). Shoot apical meristems (SAMs) of higher plants represent a dynamic and interconnected network of distinct cell types. In Arabidopsis thaliana, the SAM consists of Ϸ35 stem cells, located within the central zone (CZ) (4). Stem cells are surrounded by several million differentiating cells that are part of the adjacent peripheral zone (PZ) and developing organs. The cells of the Rib-meristem (RM) that are located just beneath the CZ provide positional cues necessary for stem cell maintenance ( Fig. 1 D and E). Earlier studies have revealed molecular mechanisms involved in stem cell maintenance (5). However, gene networks that underlie the stem cell maintenance process are far from understood. The development of high resolution gene expression map of distinct cell types of SAMs could enable network analysis of pathways involved in stem cell maintenance.Expression profiling studies of specific cell types have been performed on Arabidopsis root system (3, 6), however, studies on the SAMs have been restricted to experiments of the entire tissue (7). This is because the domains of specific...

Hypersensitivity to DNA damage in plant stem cell niches

“…Our observation that root and shoot stem cells have specialized responses to DNA damage is in agreement with the enrichment for DNA repair genes seen in the transcription profile of shoot stem cells (38). Expression of DNA repair genes could be a sign that the stem cells are under stress, as suggested (38), or that these cells have a low threshold for activation of DNA repair, consistent with a general hypersensitivity to DNA damage.…”

“…Expression of DNA repair genes could be a sign that the stem cells are under stress, as suggested (38), or that these cells have a low threshold for activation of DNA repair, consistent with a general hypersensitivity to DNA damage. However, examination of the cell type-specific transcription profiles in the shoot and root meristems (38,39) did not provide obvious clues to the molecular basis for this hypersensitivity and did not reveal clear candidate genes that might mediate the cell death response downstream of ATM/ATR in the stem cells, except perhaps for the detection of AUTOPHAGY 8G (ATG8G) as one of the genes preferentially expressed in shoot stem cells (38).…”

Seed Production Affects Maternal Growth and Senescence in Arabidopsis

“…3A), together with previously published data from cellsorted domains of the shoot apical meristem, i.e. domains expressing the CLAVATA3 or WUSCHEL (WUS) protein (Yadav et al, 2009). The whole inflorescence nodes from this study were only loosely connected to the shoot meristem nodes.…”

High-resolution metabolic mapping of cell types in plant roots

“…Their work characterized a multitude of developmental transcriptional programs that are controlled in space and time. Profiling of gene expression from different cell samples of shoot apical meristems by Yadav et al (10) has further expanded the use of this approach. They isolated three celltype populations from shoot apical meristems and demonstrated that cell-type-expression profiling is sensitive in identifying transcripts expressed in specific subsets of shoot-meristem cells.…”