Ontology highlight
ABSTRACT:
PROVIDER: PRJNA432269 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10058116.fastq.gz | Fastqsanger.gz | |||
| SRR10058117.fastq.gz | Fastqsanger.gz | |||
| SRR6655826.fastq.gz | Fastqsanger.gz | |||
| SRR6655827.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 4 of 4 |
Similar Datasets
Project description:This model is from the article:
The auxin signalling network translates dynamic input into robust patterning at the shoot apex.
Vernoux T, Brunoud G, Farcot E, Morin V, Van den Daele H, Legrand J, Oliva M, Das P, Larrieu A, Wells D, Guédon Y, Armitage L, Picard F, Guyomarc'h S, Cellier C, Parry G, Koumproglou R, Doonan JH, Estelle M, Godin C, Kepinski S, Bennett M, De Veylder L, Traas J. Mol Syst Biol.
2011 Jul 5;7:508. 21734647
,
Abstract:
The plant hormone auxin is thought to provide positional information for patterning during development. It is still unclear, however, precisely how auxin is distributed across tissues and how the hormone is sensed in space and time. The control of gene expression in response to auxin involves a complex network of over 50 potentially interacting transcriptional activators and repressors, the auxin response factors (ARFs) and Aux/IAAs. Here, we perform a large-scale analysis of the Aux/IAA-ARF pathway in the shoot apex of Arabidopsis, where dynamic auxin-based patterning controls organogenesis. A comprehensive expression map and full interactome uncovered an unexpectedly simple distribution and structure of this pathway in the shoot apex. A mathematical model of the Aux/IAA-ARF network predicted a strong buffering capacity along with spatial differences in auxin sensitivity. We then tested and confirmed these predictions using a novel auxin signalling sensor that reports input into the signalling pathway, in conjunction with the published DR5 transcriptional output reporter. Our results provide evidence that the auxin signalling network is essential to create robust patterns at the shoot apex. Note:
Figure 4 of the supplementary material of the reference article has been reproduced here. In this model, the fluctuations of auxin level is represented using sinux function. Time evolution of the variables AUX/IAA (I) and mRNA (R) are plotted, under the influence of fluctuations of auxin level. pi_A is varied between 0 and 2 by steps of 0.1.
This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
For more information see the terms of use
.
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
2024-09-02 | BIOMD0000000352 | BioModels
Project description:This model is from the article:
The auxin signalling network translates dynamic input into robust patterning at the shoo
t apex.
Vernoux T, Brunoud G, Farcot E, Morin V, Van den Daele H, Legrand J, Oliva M, Das P, Larrieu A, Wells D
, Guédon Y, Armitage L, Picard F, Guyomarc'h S, Cellier C, Parry G, Koumproglou R, Doonan JH, Estelle M
, Godin C, Kepinski S, Bennett M, De Veylder L, Traas J. Mol Syst Biol.
2011 Jul 5;7:508. 21734647
,
Abstract:
The plant hormone auxin is thought to provide positional information for patterning during development.
It is still unclear, however, precisely how auxin is distributed across tissues and how the hormone is
sensed in space and time. The control of gene expression in response to auxin involves a complex netwo
rk of over 50 potentially interacting transcriptional activators and repressors, the auxin response fac
tors (ARFs) and Aux/IAAs. Here, we perform a large-scale analysis of the Aux/IAA-ARF pathway in the sho
ot apex of Arabidopsis, where dynamic auxin-based patterning controls organogenesis. A comprehensive ex
pression map and full interactome uncovered an unexpectedly simple distribution and structure of this p
athway in the shoot apex. A mathematical model of the Aux/IAA-ARF network predicted a strong buffering
capacity along with spatial differences in auxin sensitivity. We then tested and confirmed these predic
tions using a novel auxin signalling sensor that reports input into the signalling pathway, in conjunct
ion with the published DR5 transcriptional output reporter. Our results provide evidence that the auxin
signalling network is essential to create robust patterns at the shoot apex. Note:
Figure 3 of the supplementary material of the reference article has been reproduced here. Time evolution of all the variables in the model are plotted, under the influence of a step input of auxin level (auxin=5, when time>1000; 0.11, otherwise). pi_A is varied between 0 and 2 by steps of 0.1.
This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
For more information see the terms of use
.
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
2024-09-02 | BIOMD0000000351 | BioModels
Project description:Gene expression in the shoot apex of 3-week old Arabidopsis thaliana (ecotype Col-0) was compared to DRB2 (AT2G28380) null mutants.
2014-07-01 | E-MTAB-2586 | biostudies-arrayexpress
Project description:We take the two year old plant for sampling.Use the Affymetrix poplar gene chip to elucidate the gene functions and mechanisms in Populus tomentosa shoot apex and mature xylem. We used microarrays to detail the global programme of gene expression in shoot apex and mature xylem. Populus tomentosa shoot apex and mature xylem were taken for RNA extraction and hybridization on Affymetrix microarrays.CB2009304-C and CB2009304-D from shoot apex, CB2009304-G and CB2009304-H from mature xylem.
2013-04-23 | E-GEOD-46312 | biostudies-arrayexpress
Project description:We take the two year old plant for sampling.Use the Affymetrix poplar gene chip to elucidate the gene functions and mechanisms in Populus tomentosa shoot apex and mature xylem. We used microarrays to detail the global programme of gene expression in shoot apex and mature xylem.
2013-04-23 | GSE46312 | GEO
Project description:Plants grow continuously and undergo numerous changes in their vegetative morphology and physiology during their life span. The molecular basis of these changes is largely unknown. To provide a more comprehensive picture of shoot development in Arabidopsis, microarray analysis was used to profile the mRNA content of shoot apices of different ages, as well as leaf primordia and fully-expanded leaves from 6 different positions on the shoot, in early-flowering and late-flowering genotypes. This extensive dataset provides a new and unexpectedly complex picture of shoot development in Arabidopsis. At any given time, the pattern of gene expression is different in every leaf on the shoot, and reflects the activity at least 6 developmental programs. Three of these are specific to individual leaves (leaf maturation, leaf aging, leaf senescence), two occur at the level of the shoot apex (vegetative phase change, floral induction), and one involves the entire shoot (shoot aging). Our results demonstrate that vegetative development is a much more dynamic process that previously imagined, and provide new insights into the underlying mechanism of this process.
2019-11-30 | GSE122691 | GEO
Project description:This data is was generated in connection with a study on the 'Opposing influences of TAC1 and LAZY1 on Lateral Shoot Orientation in Arabidopsis'. RNA was extracted from individual shoot tips from wild type (Columbia; Col), tac1, and lazy1 plants that experienced either 0 or 45 minutes of gravistimulation by 90-degree reorientation. The summary of the entire project is as follows: TAC1 and LAZY1 are members of a gene family that regulates lateral shoot orientation in plants. TAC1 promotes outward orientations in response to light, while LAZY1 promotes upward shoot orientations in response to gravity via altered auxin transport. We performed genetic, molecular, and biochemical assays to investigate possible interactions between these genes. In Arabidopsis they were expressed in similar tissues and double mutants revealed the wide-angled lazy1 branch phenotype, indicating it is epistatic to the tac1 shoot phenotype. Surprisingly, the lack of TAC1 did not influence gravitropic shoot curvature responses. Combined, these results suggest TAC1 might negatively regulate LAZY1 to promote outward shoot orientations. However, additional results revealed that TAC1- and LAZY1 influence on shoot orientation is more complex than a simple direct negative regulatory pathway. Transcriptomes of Arabidopsis tac1 and lazy1 mutants compared to wild type under normal and gravistimulated conditions revealed few overlapping differentially expressed genes. Overexpression of each gene did not result in major branch angle differences. Shoot tip hormone levels were similar between tac1, lazy1, and Col, apart from exceptionally elevated levels of salicylic acid in lazy1. The data presented here provide a foundation for future study of TAC1 and LAZY1 regulation of shoot architecture.
2020-03-21 | GSE147254 | GEO
Project description:Flowering of several plant species is induced by exposure to specific photoperiods that promote the expression of florigenic proteins in the leaves and their subsequent translocation to the shoot apex, where they commit the meristem to a reproductive fate. Transition to reproductive growth at the apex is often accompanied by stem elongation, to expose flowers above the leaves and facilitate fertilization. However, how growth and inflorescence formation are coupled and how photoperiodic signals coordinate these processes at the apex is still unclear. We studied these mechanisms in rice, a short day plant. Here, we show that HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1), encoding components of the rice florigenic signal, are sufficient to repress expression of PREMATURE INTERNODE ELONGATION 1 (PINE1) at the shoot apex during the transition to flowering, thus promoting culm elongation. PINE1 encodes a nuclear C2H2 zinc finger transcriptional repressor that controls the mRNA abundance of GA3ox2, a gibberellin (GA) biosynthetic gene. These data uncover the existence of a regulatory network coordinating multiple aspects of phase transition, and indicate that GA-induced growth and activity of florigenic proteins at the shoot apex need to be strictly coupled.
2018-11-30 | GSE90493 | GEO