All major branches of multi-cellular life have the ability to repair damaged tissue, using cells from the adult body to generate replacement cells for tissue replenishment and organ repair. Recent work in mammals has suggested that adult stem cells arising from one tissue may have the flexibility to give rise to specialized cells of another tissue, raising the possibility that adult stem cells may provide a therapy to regenerate damaged tissue. Plants and animals share many basic cellular processes, including RNA interference, a primitive defense system that has also controls development in both kingdoms. Plants are a quintessential model for regeneration, as almost all plant species readily use cells set aside for one purpose to replace damaged cells of another purpose, analogously to adult stem cell flexibility in mammals (""""""""developmental plasticity""""""""). We use an in vivo regeneration system in plants that affords powerful analytical tools to help understand the process of cell fate plasticity in the model plant Arabidopsis thaliana. We address the hypothesis that partially differentiated cells first must revert to more basic stem cell fates perhaps similar to embryonic stem cells, in order to give rise to new cell types during regeneration. In addition, we use genomics to discover the candidate that may trigger regeneration at the cellular level. On the experimental side, we use the root tip, which has a simple and highly organized structure, and a large selection of fluorescent markers to analyze the molecular events that occur in cells in regenerating tissue.
In Aim 1, we use high-resolution microscopy to visualize individual cells, monitor their identities and their potential reversion to stem cells in order to determine how cells can transform their identity.
In Aim 2, we measure gene activity in a variety of different stem cells to obtain a comprehensive catalog of stem cell identity. This is done using new techniques we have developed to capture specific cell types and monitor their comprehensive gene activity using microarrays.
In Aim 3, we use the same methods to obtain comprehensive readouts of the cells that undergo regeneration. We then use the catalog of stem cell identity genes identified in Aim 2 to ask whether regenerating cells possess any common factors with basal stem cells.
In Aim 4, we look at mutants in genes whose expression implicates them in early regeneration. This work is aimed at understanding the fundamental mechanisms that trigger tissue regeneration at the level of the cell. These results are aimed at providing insights into the fundamental mechanisms of regeneration in plants that can be related to potentially similar mechanisms in plants either at the level of common genes or different genes that control analogous processes. ? ? ?

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Development - 1 Study Section (DEV1)
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Haynes, Susan R
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New York University
Biostatistics & Other Math Sci
Schools of Arts and Sciences
New York
United States
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Birnbaum, Kenneth D (2018) Power in Numbers: Single-Cell RNA-Seq Strategies to Dissect Complex Tissues. Annu Rev Genet 52:203-221
Ortiz-Ramírez, Carlos; Arevalo, Edgar Demesa; Xu, Xiaosa et al. (2018) An Efficient Cell Sorting Protocol for Maize Protoplasts. Curr Protoc Plant Biol 3:e20072
Birnbaum, Kenneth D; Roudier, François (2017) Epigenetic memory and cell fate reprogramming in plants. Regeneration (Oxf) 4:15-20
Efroni, Idan; Birnbaum, Kenneth D (2016) The potential of single-cell profiling in plants. Genome Biol 17:65
Efroni, Idan; Mello, Alison; Nawy, Tal et al. (2016) Root Regeneration Triggers an Embryo-like Sequence Guided by Hormonal Interactions. Cell 165:1721-1733
Rahni, Ramin; Efroni, Idan; Birnbaum, Kenneth D (2016) A Case for Distributed Control of Local Stem Cell Behavior in Plants. Dev Cell 38:635-42
Efroni, Idan; Ip, Pui-Leng; Nawy, Tal et al. (2015) Quantification of cell identity from single-cell gene expression profiles. Genome Biol 16:9
Para, Alessia; Li, Ying; Marshall-Colón, Amy et al. (2014) Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis. Proc Natl Acad Sci U S A 111:10371-6
Bargmann, Bastiaan O R; Vanneste, Steffen; Krouk, Gabriel et al. (2013) A map of cell type-specific auxin responses. Mol Syst Biol 9:688
Bargmann, Bastiaan O R; Marshall-Colon, Amy; Efroni, Idan et al. (2013) TARGET: A Transient Transformation System for Genome-Wide Transcription Factor Target Discovery. Mol Plant 6:978-80

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