Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Expression data from Arabidopsis wild type and ibr1 ibr3 ibr10 triple mutant seedlings root tip segments treated with indole-3-butyric acid (IBA)

ABSTRACT: The root cap-specific conversion of the auxin precursor indole-3-butyric acid (IBA) into the main auxin indole-3-acetic acid (IAA) generates a local auxin source which subsequently modulates both the periodicity and intensity of auxin response oscillations in the root tip of Arabidopsis, and consequently fine-tunes the spatiotemporal patterning of lateral roots. To explore downstream components of this signaling process, we investigated the early transcriptional regulations happening in the root tip during IBA-to-IAA conversion in Col-0 and ibr1 ibr3 ibr10 triple mutant after 6 hours of IBA treatment. Arabidopsis thaliana (L). Heynh., Col-0 and ibr1ibr3ibr10 seeds were germinated vertically on solid medium derived from standard Murashige and Skoog (MS) medium. Three days after germination, Col-0 and ibr1ibr3ibr10 seedlings were transferred to a fresh MS medium supplemented with or without 10 ?M indole-3-buytric acid (IBA) for 6 hours. Then, root tip segments (~4mm) were dissected from the primary root and harvested for further RNA extraction. For each treatment, at least 120 individual Col-0 or ibr1ibr3ibr10 mutant root tip segments were sampled and three independent biological replicates were performed. Hormone and DMSO solution were filer-sterilized before being added to the medium.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Wouter Van Delm

PROVIDER: E-GEOD-59426 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Root Cap-Derived Auxin Pre-patterns the Longitudinal Axis of the Arabidopsis Root.

Xuan Wei W Audenaert Dominique D Parizot Boris B Möller Barbara K BK Njo Maria F MF De Rybel Bert B De Rop Gieljan G Van Isterdael Gert G Mähönen Ari Pekka AP Vanneste Steffen S Beeckman Tom T

Current biology : CB 20150507 10

During the exploration of the soil by plant roots, uptake of water and nutrients can be greatly fostered by a regular spacing of lateral roots (LRs). In the Arabidopsis root, a regular branching pattern depends on oscillatory gene activity to create prebranch sites, patches of cells competent to form LRs. Thus far, the molecular components regulating the oscillations still remain unclear. Here, we show that a local auxin source in the root cap, derived from the auxin precursor indole-3-butyric a ...[more]

PMID: 25959963

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Project description: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. Experiment 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

Dataset Information

Expression data from Arabidopsis wild type and ibr1 ibr3 ibr10 triple mutant seedlings root tip segments treated with indole-3-butyric acid (IBA)

Publications

Root Cap-Derived Auxin Pre-patterns the Longitudinal Axis of the Arabidopsis Root.

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