Global gene-expression profiles of wild type (WT; Columbia-0; Col) and hag1 in the course of de novo shoot regeneration
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE100966 | GEO | 2018/07/29
REPOSITORIES: GEO
Similar Datasets
Project description:Genome-wide histone H3Ac maps of WT and hag1 calli were generated by chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP seq) to understand the role of HAG1 in the reprogramming of the epigenome during callus formation.
2018-07-29 | GSE100965 | GEO
Project description:De novo shoot regeneration is an essential step for massive propagation and genetic engineering of elite germplasm in forestry. Poplar that is a fast growth tree species have a very important ecologically and economically role around the world, especially in China. In this study, we found that PtWOX11 that is a homologue of AtWOX11 not only involved de novo root formation but also promote de novo shoot regeneration in poplar. We demonstrated that PtWOX11 can enhance callus regeneration competence and shoot regeneration during two-step de novo shoot regeneration. Furthermore, by using RNA-seq and qPCR, we uncovered that during callus induction stage PtWOX11 activates PtPLTs expression to promote callus formation and regeneration competence, and promote PtCUC2/3, PtWUSa and PtSTM transcription to fulfil shoot organogenesis during shoot regeneration stage. Overall, our data indicated that PtWOX11 play a new function and transcriptional regulation mechanism on de novo shoot regeneration in poplar.
2018-03-26 | GSE101922 | GEO
Project description:Plants generally possess a strong ability to regenerate organs; for example, in tissue culture, shoots can regenerate from callus, a clump of actively proliferating, undifferentiated cells. Processing of pre-mRNA and ribosomal RNAs is important for callus formation and shoot regeneration. However, our knowledge of the roles of RNA quality control via the nonsense-mediated mRNA decay (NMD) pathway in shoot regeneration is limited. Here, we examined the shoot regeneration phenotypes of the low-beta-amylase1 (lba1)/upstream frame shift1-1 (upf1-1) and upf3-1 mutants, in which the core NMD components UPF1 and UPF3 are defective. These mutants formed callus from hypocotyl explants normally, but this callus behaved abnormally during shoot regeneration: the mutant callus generated numerous adventitious root structures instead of adventitious shoots in an auxin-dependent manner. Quantitative RT-PCR and microarray analyses showed that the upf mutations had widespread effects during culture on shoot-induction medium. In particular, the expression patterns of early auxin response genes, including those encoding AUXIN/INDOLE ACETIC ACID (AUX/IAA) family members, were significantly affected in the upf mutants. Also, the upregulation of shoot apical meristem-related transcription factor genes, such as CUP-SHAPED COTYLEDON1 (CUC1) and CUC2, was inhibited in the mutants. Taken together, these results indicate that NMD-mediated transcriptomic regulation modulates the auxin response in plants and thus plays crucial roles in the early stages of shoot regeneration.
2019-09-01 | GSE134854 | GEO
Project description:De novo shoot organogenesis (DNSO) is a commonly used pathway for plant biotechnology, and is a hormonally regulated process, where auxin and cytokinin coordinates suites of genes encoding transcription factors, general transcription factors, and RNA metabolism machinery genes. Here we report that silencing Arabidopsis thaliana CTD phosphatase-like 4 (CPL4RNAi), which increases phosphorylation level of RNA polymerase II (pol II) CTD, altered lateral root development and DNSO efficiency of the host plants, suggesting an importance of precise control of pol II activities during DNSO. Under standard condition, roots of CPL4RNAi lines produced no or few lateral roots. When induced by high concentration of auxin, CPL4RNAi lines failed to produce focused auxin maxima at the meristem of lateral root primordia, and produced fasciated lateral roots. By contrast, root explants of CPL4RNAi lines were highly competent for DNSO. Efficient DNSO of CPL4RNAi lines were observed even under 10 times less cytokinin required for wild type explants. Transcriptome analysis showed CPL4RNAi but not wild type explants expressed high levels of shoot meristem related genes during priming by high auxin/cytokinin ratio, and subsequent shoot induction with cytokinin. These results indicate that CPL4 functions as a repressor of the early stage of DNSO, during acquisition of competency by high auxin/cytokinin ratio, perhaps via regulation of pol II activities.
2020-09-19 | GSE104083 | GEO
Project description:Plants have a profound capacity to regenerate organs from differentiated somatic tissues, based on which propagating plants in vitro was made possible. Beside its use in biotechnology, in vitro shoot regeneration is also an important system to study de novo organogenesis. Phytohormones and transcription factor WUSCHEL (WUS) play critical roles in this process but whether and how epigenetic modifications are involved is unknown. Here, we report that epigenetic marks of DNA methylation and histone modifications regulate de novo shoot regeneration of Arabidopsis through modulating WUS expression and auxin signaling. First, functional loss of key epigenetic genes-including METHYLTRANSFERASE1 (MET1) encoding for DNA methyltransferase, KRYPTONITE (KYP) for the histone 3 lysine 9 (H3K9) methyltransferase, JMJ14 for the histone 3 lysine 4 (H3K4) demethylase, and HAC1 for the histone acetyltransferase-resulted in altered WUS expression and developmental rates of regenerated shoots in vitro. Second, we showed that regulatory regions of WUS were developmentally regulated by both DNA methylation and histone modifications through bisulfite sequencing and chromatin immunoprecipitation. Third, DNA methylation in the regulatory regions of WUS was lost in the met1 mutant, thus leading to increased WUS expression and its localization. Fourth, we did a genome-wide transcriptional analysis and found out that some of differentially expressed genes between wild type and met1 were involved in signal transduction of the phytohormone auxin. We verified that the increased expression of AUXIN RESPONSE FACTOR3 (ARF3) in met1 indeed was due to DNA demethylation, suggesting DNA methylation regulates de novo shoot regeneration by modulating auxin signaling. We propose that DNA methylation and histone modifications regulate de novo shoot regeneration by modulating WUS expression and auxin signaling. The study demonstrates that, although molecular components involved in organogenesis are divergently evolved in plants and animals, epigenetic modifications play an evolutionarily convergent role in this process.
| S-EPMC3158056 | biostudies-literature
Project description:Plants can regenerate from a variety of tissues on culturing in appropriate media. However, the metabolic shifts involved in callus formation and shoot regeneration are largely unknown. The metabolic profiles of callus generated from tomato (Solanum lycopersicum) cotyledons and that of shoot regenerated from callus were compared with the pct1-2 mutant that exhibits enhanced polar auxin transport and the shr mutant that exhibits elevated nitric oxide levels. The transformation from cotyledon to callus involved a major shift in metabolite profiles with denser metabolic networks in the callus. In contrast, the transformation from callus to shoot involved minor changes in the networks. The metabolic networks in pct1-2 and shr mutants were distinct from wild type and were rewired with shifts in endogenous hormones and metabolite interactions. The callus formation was accompanied by a reduction in the levels of metabolites involved in cell wall lignification and cellular immunity. On the contrary, the levels of monoamines were upregulated in the callus and regenerated shoot. The callus formation and shoot regeneration were accompanied by an increase in salicylic acid in wild type and mutants. The transformation to the callus and also to the shoot downregulated LST8 and upregulated TOR transcript levels indicating a putative linkage between metabolic shift and TOR signalling pathway. The network analysis indicates that shift in metabolite profiles during callus formation and shoot regeneration is governed by a complex interaction between metabolites and endogenous hormones.
2018-06-29 | MTBLS447 | MetaboLights
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
Project description:Iodine treatments specifically regulated the expression of several genes in shoot and root tissues, mostly involved in the plant defence response, suggesting the protective role of iodine against both biotic and abiotic stresses.
2021-01-01 | GSE157643 | GEO
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
Project description:Protein arginine methylation plays essential roles in diverse biological processes, but its role in regulating shoot regeneration remains elusive. In this study, we analyzed the function of the protein arginine methyltransferase AtPRMT5 during de novo shoot regeneration in Arabidopsis. AtPRMT5 encodes a type II PRMT that methylates proteins, including histones and RNA splicing factors. Mutation of AtPMRT5 decreased the frequency of shoot regeneration and number of shoots per callus in the atprmt5 mutant compared with those of the wild type. To understand the mechanism of AtPRMT5 regulation of shoot regeneration, we analyzed the transcript levels of wild type and the mutant atprmt5 calli during shoot regeneration by RNA-seq. Three biological repeats of wild type and the mutant atprmt5-1 calli were used for RNA sequencing. Total RNAs were isolated from the calli of wild type Col and the mutant atprmt5-1 cultured on cultured on shoot-induction medium. The RNA-seq llibraries were constructed with TruSeq Stranded mRNA Library Prep Kit and sequenced using the Illumina Hiseq 2500. The raw reads were aligned to the genome sequences of TAIR10 using Tophat software. The gene expression levels were measured in RPKM, and many critical genes regulated by AtPRMT5 were identified to be involved in shoot regeneration.
2017-06-18 | E-MTAB-5044 | biostudies-arrayexpress