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| Status |
Public on Oct 30, 2008 |
| Title |
Organ regeneration in plants is independent of stem cell niche activity |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by array
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| Summary |
A critical step in regeneration is recreating the cellular identities and patterns of lost organs long after embryogenesis is complete. In plants, perpetual (indeterminate) organ growth occurs in apical stem cell niches, which have been shown to re-establish quickly when damaged or removed (1,2). Here we ask whether the machinery of perpetual organ growth, stem cell activity, is needed for the phase of regeneration that leads to replenishing lost cell identities and patterning, or, whether organ re-establishment enlists a wider group of pluripotent cells. We adapt a root tip regeneration system to Arabidopsis that permits us to assess the molecular and functional recovery of specific cell fates during organ regeneration. These results suggest a rapid restoration of missing cell fate and function in advance of the recovery of stem cell activity. Surprisingly, plants with mutations that fail to maintain stem cell activity were able to re-pattern their distal tip and re-specify lost cell fates. Thus, although stem cell activity is required to resume indeterminate growth (3), our results show it is not necessary for cell re-specification and patterning steps. This implies a regeneration mechanism that coordinates patterning of the whole organ, as in embryogenesis, but is initiated from different starting morphologies. 1. Feldman, L. J. Denovo Origin of Quiescent Center Regenerating Root Apices of Zea-Mays. Planta 128, 207-212 (1976). 2. Xu, J. et al. A molecular framework for plant regeneration. Science 311, 385-8 (2006). 3. Gordon, S. P. et al. Pattern formation during de novo assembly of the Arabidopsis shoot meristem. Development 134, 3539-48 (2007).
We adapted root tip excision techniques to Arabidopsis, enabling us to perform microarray profiling of regenerating root tissue. Excisions were performed at 4 days post-germination (dpg) at a distance of 130 um from the root tip, resulting in the complete excision of QC, all surrounding stem cells along with several tiers of daughter cells, and the root cap, including all of the columella and most of the lateral root cap. The tip section and then approximately 70 um of regenerating tissue was recut at different time points post cutting. We sampled regenerating stumps at 0hrs, 5 hrs, 13 hrs, 22 hrs, and 7 days after the excision for microarray analysis (Methods). We also sampled root sections immediately above the zone competent to regenerate at 270 um to approximately 340 um.
Keywords: time course, development, root regeneration
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| Overall design |
30 samples with 4 or 3 replicates for each condition representing a time course of regenerating root stumps and including controls for root tips (regeneration endpoint) at 4 dpg and 8 dpg and a wounded set of samples representing root tissue at 270-340 mm from the root tip for non-regeneration control
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| Contributor(s) |
Birnbaum KD, Sena G, Wang X, Liu H |
| Citation(s) |
19182776 |
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| Submission date |
Dec 20, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Kenneth David Birnbaum |
| E-mail(s) |
[email protected]
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| Phone |
212-998-8257
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| Organization name |
New York University
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| Department |
Biology
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| Lab |
Birnbaum
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| Street address |
12 Waverly Place
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10003 |
| Country |
USA |
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| Platforms (1) |
| GPL198 |
[ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array |
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| Samples (30)
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| GSM252663 |
Arabidopsis Root from tip to 130 mm proximal to tip (cut 4dpg) rep1 |
| GSM252664 |
Arabidopsis Root from tip to 130 mm proximal to tip (cut 4dpg) rep2 |
| GSM252665 |
Arabidopsis Root from tip to 130 mm proximal to tip (cut 4dpg) rep3 |
| GSM252666 |
Arabidopsis Root from tip to 130 mm proximal to tip (cut 4dpg) rep4 |
| GSM252667 |
Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 0 hrs Taking 70 mm of Stump (4dpg) rep1 |
| GSM252668 |
Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 0 hrs Taking 70 mm of Stump (4dpg) rep2 |
| GSM252669 |
Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 0 hrs Taking 70 mm of Stump (4dpg) rep3 |
| GSM252670 |
Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 0 hrs Taking 70 mm of Stump (4dpg) rep4 |
| GSM252671 |
Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 5 hrs Taking 70 mm of Stump (4dpg) rep1 |
| GSM252672 |
Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 5 hrs Taking 70 mm of Stump (4dpg) rep2 |
| GSM252673 |
Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 5 hrs Taking 70 mm of Stump (4dpg) rep3 |
| GSM252674 |
Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 5 hrs Taking 70 mm of Stump (4dpg) rep4 |
| GSM252675 |
Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 13 hrs Taking 70 mm of Stump (4dpg) rep1 |
| GSM252676 |
Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 13 hrs Taking 70 mm of Stump (4dpg) rep2 |
| GSM252677 |
Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 13 hrs Taking 70 mm of Stump (4dpg) rep3 |
| GSM252678 |
Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 13 hrs Taking 70 mm of Stump (4dpg) rep4 |
| GSM252679 |
Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 22 hrs Taking 70 mm of Stump (4dpg) rep1 |
| GSM252680 |
Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 22 hrs Taking 70 mm of Stump (4dpg) rep2 |
| GSM252681 |
Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 22 hrs Taking 70 mm of Stump (4dpg) rep3 |
| GSM252682 |
Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 22 hrs Taking 70 mm of Stump (4dpg) rep4 |
| GSM252683 |
Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 22 hrs Taking 70 mm of Stump (4dpg) rep5 |
| GSM252684 |
Arabidopsis Root from tip to 130 mm proximal to tip (cut 8dpg) rep1 |
| GSM252685 |
Arabidopsis Root from tip to 130 mm proximal to tip (cut 8dpg) rep2 |
| GSM252686 |
Arabidopsis Root from tip to 130 mm proximal to tip (cut 8dpg) rep3 |
| GSM252687 |
Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 0 hrs Taking 70 mm of Stump (8 dpg) rep1 |
| GSM252688 |
Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 0 hrs Taking 70 mm of Stump (8 dpg) rep2 |
| GSM252689 |
Regenerating Stump of Root Tip Cut at 130 mm first and then Recut after 0 hrs Taking 70 mm of Stump (8 dpg) rep3 |
| GSM252690 |
Section of Root from 270 mm to 340 mm harvested immediately rep1 |
| GSM252691 |
Section of Root from 270 mm to 340 mm harvested immediately rep2 |
| GSM252692 |
Section of Root from 270 mm to 340 mm harvested immediately rep3 |
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| Relations |
| Affiliated with |
GSE69995 |
| BioProject |
PRJNA104017 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE9996_RAW.tar |
67.3 Mb |
(http)(custom) |
TAR (of CEL, EXP) |
| Processed data included within Sample table |
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