# A model of repair: intercellular signaling and self-organization in plant regeneration

> **NIH NIH R35** · NEW YORK UNIVERSITY · 2021 · $385,584

## Abstract

PROJECT SUMMARY
Plants have exceptional capacity to regenerate adult body parts after injury, providing an excellent
conceptual model for organ replacement. They can even rapidly reform their adult stem cell niches after
complete excision. My lab has pioneered new systems and techniques to study plant regeneration. We
developed methods for tracking cell identity of reprogramming cells using transcriptomic and live imaging
techniques during regeneration. In connection with this work, I have led efforts to introduce new
technologies like single-cell RNA-seq into plant research. Using these and other techniques developed
under NIGMS R01GM078279, we found that regenerating roots appear to recapitulate embryonic programs
during organ regeneration. The work has led to us to propose models of how this highly self-organizing
system orchestrates the regeneration of an entire organ and its stem cell niche. However, while new tools
like in single-cell RNA-seq provide powerful approaches to dissect developmental programs cell-by-cell,
they are largely silent on the role of cell-cell communication in mediating tissue assembly. Hence, our
current efforts are focused on developing new approaches to address this gap. In one proposed system, we
inducibly block symplastic (direct) communication channels in a cell type-specific manner and use single-
cell RNA-seq to test the consequences on neighboring and distant tissues during normal post-embryonic
organogenesis and regeneration (Block-Seq). This is akin to observing the consequences of signaling from
one cell to all its neighbors but not the signals themselves. One common mode of signaling in plants is the
protein-level movement of transcription factors from one cell to its neighbors. To track protein movement
comprehensively, we are developing a click chemistry approach to incorporate labeled amino acids in
specific cell types followed by capture and mass spectrometry of the mobile proteins in neighboring cell
types (the Mobilome). This approach is designed to reveal many of the signals that plant cells use to
organize development. Overall, these approaches are motivated by a basic question that underpins a
medically relevant question: how do positional signals generate a set of rules that allow the flawless
reconstruction of organs in regeneration?

## Key facts

- **NIH application ID:** 10146430
- **Project number:** 5R35GM136362-02
- **Recipient organization:** NEW YORK UNIVERSITY
- **Principal Investigator:** Kenneth David Birnbaum
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $385,584
- **Award type:** 5
- **Project period:** 2020-04-16 → 2025-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10146430

## Citation

> US National Institutes of Health, RePORTER application 10146430, A model of repair: intercellular signaling and self-organization in plant regeneration (5R35GM136362-02). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10146430. Licensed CC0.

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