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Gene expression during hormone-induced shoot regeneration in Arabidopsis thaliana explants exposed to different temperatures

ABSTRACT: Gene expression during hormone-induced shoot regeneration in Arabidopsis thaliana explants exposed to different temperatures

PROVIDER: PRJNA735204 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14731468.fastq.gz	Fastqsanger.gz
	SRR14731469.fastq.gz	Fastqsanger.gz
	SRR14731470.fastq.gz	Fastqsanger.gz
	SRR14731471.fastq.gz	Fastqsanger.gz
	SRR14731472.fastq.gz	Fastqsanger.gz

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Gene expression during hormone-induced shoot regeneration in Arabidopsis thaliana explants exposed to different temperatures

Project description:Many plants are able to regenerate upon cutting, and this process can be enhanced in vitro by incubating explants on hormone-supplemented media. While such protocols have been used for decades, little is known about the molecular details of how incubation conditions influence their efficiency. In this study, we show that warm temperature promotes both callus formation and shoot regeneration efficiency in Arabidopsis thaliana. Our RNA sequencing analysis unveil that this accompanied by the enhanced expression of several regeneration-associated genes, such as CUP-SHAPED COTYLEDON 1 (CUC1), encoding a transcription factor involved in shoot meristem formation, and ISOPENTENYLTRANSFERASE (IPT1) and YUCCA1/4 (YUC1/4), encoding key enzymes for cytokinin and auxin biosynthesis, respectively. Consistently, mutations in CUC1 and IPT1 or chemical inhibition of YUCs reduce the enhancement of shoot regeneration at warm temperature. When combined with ChIP sequencing analyses, our RNA sequencing data further reveal that histone variant H2A.Z is enriched on these differentially expressed loci at 17°C and that its occupancy level decreases when the ambient temperature increases to 27°C. This study thus unveil a new epigenetic mechanism that influences hormone-induced regeneration and brings further insights on how incubation temperature is a crucial parameter in optimizing protocols for in vitro tissue culture.

2022-02-15 | GSE176161 | GEO

Histidine Kinase Inhibitors Impair Shoot Regeneration in Arabidopsis thaliana via Cytokinin Signalling and SAM Patterning Determinants

Project description:Reversible protein phosphorylation is a post-translational modification involved in virtually all plant processes, as it mediates protein activity and signal transduction. Here, we probe dynamic protein phosphorylation during de novo shoot organogenesis in Arabidopsis thaliana. We find that application of three kinase inhibitors in various time intervals has different effects on root explants. We furthermore show that short exposures to the putative His kinase inhibitor TCSA during the initial days on shoot induction medium (SIM) are detrimental for regeneration in seven natural accessions. Investigation of ahk and ahp mutants, as well as reporter lines for shoot markers and hormone responses suggests that TCSA at least partially works by impeding cytokinin signal transduction via AHK3, AHK4, AHP2, AHP3, and AHP5. A mass spectrometry-based phosphoproteome analysis further reveals profound deregulation of Ser/Thr/Tyr phosphoproteins related to protein modification, transcriptional regulation, vesicle trafficking, organ morphogenesis, and cation transport. Among TCSA-responsive factors are prior candidates with a role in shoot apical meristem patterning, such as AGO1, BAM1, PLL5, FIP37, TOP1ALPHA, and RBR1, but also proteins involved in polar auxin transport (e.g., PIN1) and brassinosteroid signalling (e.g., BIN2). Potentially novel regeneration determinants regulated by TCSA include RD2, AT1G52780, PVA11, and AVT1C, while NAIP2, OPS, ARR1, QKY, and aquaporins exhibit differential phospholevels on control SIM.

2022-09-28 | PXD030754 | Pride

Expression data from ectodermal explants following activation of hormone-inducible zic1

2009-07-01 | GSE12128 | GEO

Transcription profiling of Xenopus laevis ectodermal explants following activation of hormone-inducible zic1

Project description:The response of ectodermal explants, neuralized by noggin and treated with cycloheximide, following activation of hormone-inducible zic1 injected into the parent embryos compared to those from beta globin injected embryos as controls, is expected to provide information on the direct targets of the Zic1 transcription factor. Experiment Overall Design: Activation of zic1 in ectodermal explants following inhibition of new protein synthesis allowed the direct targets of zic1 to be identified by comparison with controls. After RNA extraction, purification and checks with PCR with actin primers for any mesoderm contamination samples were prepared for hybridization to Xenopus laevis Affymetrix GeneChip arrays.

2009-07-10 | E-GEOD-12128 | biostudies-arrayexpress

ELONGATED HYPOCOTYL5-mediated light signaling promotes shoot regeneration in Arabidopsis thaliana

Project description:Injured plant somatic tissues regenerate themselves by establishing the shoot or root meristems. In Arabidopsis (Arabidopsis thaliana) a two-step culture system ensures regeneration by first promoting the acquisition of pluripotency and subsequently specifying the fate of new meristems. Although previous studies have reported the importance of phytohormones auxin and cytokinin in determining the fate of new meristems, it remains elusive whether and how the environmental factors influence this process. In this study, we investigated the impact of light signals on shoot regeneration using Arabidopsis hypocotyl as explants. We found that light signals promote shoot regeneration while inhibiting root formation. ELONGATED HYPOCOTYL 5 (HY5), the pivotal transcriptional factor in light signaling, plays a central role in this process by mediating the expression of key genes controlling the fate of new meristems. Specifically, HY5 directly represses root development genes and activates shoot meristem genes, leading to the establishment of shoot progenitor from pluripotent callus. We further demonstrated that the early activation of photosynthesis is critical for shoot initiation, and this is transcriptionally regulated downstream of the HY5-dependent pathways. In conclusion, we uncovered the intricate molecular mechanisms by which light signals control the establishment of new meristem through the regulatory network governed by HY5, thus, highlighting the influence of light signals on plant developmental plasticity.

2024-09-16 | GSE236147 | GEO

Optimization of Callus Induction and Shoot Regeneration from Tomato Cotyledon Explants

Project description:Cultivated tomato (Solanum lycopersicum L.) is one of the most important horticultural crops in the world. The optimization of culture media for callus formation and tissue regeneration of different tomato genotypes presents numerous biotechnological applications. In this work, we have analyzed the effect of different concentrations of zeatin and indole-3-acetic acid on the regeneration of cotyledon explants in tomato cultivars M82 and Micro-Tom. We evaluated regeneration parameters such as the percentage of callus formation and the area of callus formed, as well as the initiation percentage and the number of adventitious shoots. The best hormone combination produced shoot-like structures after 2–3 weeks. We observed the formation of leaf primordia from these structures after about 3–4 weeks. Upon transferring the regenerating micro-stems to a defined growth medium, it was possible to obtain whole plantlets between 4 and 6 weeks. This hormone combination was applied to other genotypes of S. lycopersicum, including commercial varieties and ancestral tomato varieties. Our method is suitable for obtaining many plantlets of different tomato genotypes from cotyledon explants in a very short time, with direct applications for plant transformation, use of gene editing techniques, and vegetative propagation of elite cultivars.

| S-EPMC10459365 | biostudies-literature

Plant Regeneration via Adventitious Shoot Formation from Immature Zygotic Embryo Explants of Camelina.

Project description:Camelina is an oil seed crop that is enjoying increasing interest because it has a particularly valuable fatty acid profile, is modest regarding its water and nutrient requirements, and is comparatively resilient to abiotic and biotic stress factors. The regeneration of plants from cells accessible to genetic manipulation is an essential prerequisite for the generation of genetically engineered plants, be it by transgenesis or genome editing. Here, immature embryos were used on the assumption that their incomplete differentiation was associated with totipotency. In culture, regenerative structures appeared adventitiously at the embryos' hypocotyls. For this, the application of auxin- or cytokinin-type growth regulators was essential. The formation of regenerative structures was most efficient when indole-3-acetic acid was added to the induction medium at 1 mg/L, zygotic embryos of the medium walking stick stage were used, and their hypocotyls were stimulated by pricking to a wound response. Histological examinations revealed that the formation of adventitious shoots was initiated by locally activated cell division and proliferation in the epidermis and the outer cortex of the hypocotyl. While the regeneration of plants was established in principle using the experimental line Cam139, the method proved to be similarly applicable to the current cultivar Ligena, and hence it constitutes a vital basis for future genetic engineering approaches.

| S-EPMC10892543 | biostudies-literature

Potential link between biotic defense activation and recalcitrance to induction of somatic embryogenesis in shoot primordia from adult trees of white spruce (Picea glauca)

Project description:The goal is to examine the molecular aspects underpinning somatic embryogenesis (SE) within shoot tissues of adult white spruce trees by conducting transcriptome-wide expression profiling of shoot explants taken from responsive and nonresponsive genotypes.

2013-10-17 | GSE46977 | GEO

Transcriptional profiling by array of Amphiura filiformis arm explants during regeneration

Project description:Gene expression profiling of the proximal, medial and distal parts of Amphiura filiformis arm explants.

2012-01-11 | E-MEXP-3413 | biostudies-arrayexpress

Transcriptomic analysis of pig intestinal explants exposed or not to deoxynivalenol

Project description:Intestinal explants from 5-weeks old piglets were exposed 4h to control or 10 µM deoxynivalenol-contaminated cell culture medium. Explants were nitrogen frozen. RNA were extracted, quantified and their quality was checked with Tapestation 4200 device. RNA samples were used to perform a microarray experiment

2021-06-30 | GSE165968 | GEO

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