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Changing the transcriptome by altering ZmPIN1a expression

ABSTRACT: A genome-wide transcriptome analysis showed that altering ZmPIN1a expression led to wide-ranging gene expression changes. When comparing overexpression lines A17 with the WT, 2975 genes were differentially expressed with 793 up-regulated and 2182 down-regulated in the leaves, and 2129 genes were differentially expressed with 938 up-regulated and 1191 down-regulated in the roots. GO analysis indicated that these differentially expressed genes participate in multiple biological processes from hormone signaling to metabolism. The local biosynthesis, PAT and signaling of auxin were altered; some was directly employed in plant developments such as AUX/IAA, ARFs and genes related to PAT. The genes involved in ethylene, GA, BR CK and ABA metabolism and signaling were altered as well. These phytohormones were also confirmed as key regulators in plant development and abiotic stress responses. Some of the differentially expressed genes between A17 and WT were identified as Arabidopsis root morphology and development mutant genes. These mutants were abnormal in their plant hormone synthesis and signaling, calcium-mediated signaling, MAP kinase signaling, transcription factors, membrane transporters etc. This finding suggested that ZmPIN1a overexpression led to a change of the auxin signaling transduction and even the metabolism of auxin and the metabolism and signaling of other hormones. These events led to changes in the expression of numerous genes and resulted in the modification of plant morphology, especially the root architecture.

ORGANISM(S): Zea mays

PROVIDER: GSE57291 | GEO | 2014/05/06

SECONDARY ACCESSION(S): PRJNA246196

REPOSITORIES: GEO

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Changing the transcriptome by altering ZmPIN1a expression

Project description:A genome-wide transcriptome analysis showed that altering ZmPIN1a expression led to wide-ranging gene expression changes. When comparing overexpression lines A17 with the WT, 2975 genes were differentially expressed with 793 up-regulated and 2182 down-regulated in the leaves, and 2129 genes were differentially expressed with 938 up-regulated and 1191 down-regulated in the roots. GO analysis indicated that these differentially expressed genes participate in multiple biological processes from hormone signaling to metabolism. The local biosynthesis, PAT and signaling of auxin were altered; some was directly employed in plant developments such as AUX/IAA, ARFs and genes related to PAT. The genes involved in ethylene, GA, BR CK and ABA metabolism and signaling were altered as well. These phytohormones were also confirmed as key regulators in plant development and abiotic stress responses. Some of the differentially expressed genes between A17 and WT were identified as Arabidopsis root morphology and development mutant genes. These mutants were abnormal in their plant hormone synthesis and signaling, calcium-mediated signaling, MAP kinase signaling, transcription factors, membrane transporters etc. This finding suggested that ZmPIN1a overexpression led to a change of the auxin signaling transduction and even the metabolism of auxin and the metabolism and signaling of other hormones. These events led to changes in the expression of numerous genes and resulted in the modification of plant morphology, especially the root architecture. Maize (Zea mays L.) inbred line DH4866, its ZmPIN1a sense transgenic lines A17 and antisense transgenic lines a55 were used in this study. The transcriptome by altering ZmPIN1a expression was done by comparing the transcriptome of WT and transgenic lines both in root and leaf of V3 stage plants.

2014-05-06 | E-GEOD-57291 | biostudies-arrayexpress

Expression data from Medicago truncatula roots treated with S. meliloti wild-type or exoA mutant bacteria, or auxin transport inhibitors

Project description:Publication title: Pseudonodule formation by wild type and symbiotic mutant Medicago truncatula in response to auxin transport inhibitors This SuperSeries is composed of the following subset Series: GSE27991: Expression data of Medicago truncatula Jemalong A17 roots treated with auxin transport inhibitors GSE28171: Expression data of Medicago truncatula Jemalong A17 roots treated with S. meliloti exoA mutant or auxin transport inhibitors GSE28172: Expression data of Medicago truncatula skl1-1 roots treated with S. meliloti wild-type or auxin transport inhibitors GSE28173: Genes differentially expressed in wild-type Medicago truncatula plants during nodulation Refer to individual Series

2011-03-25 | E-GEOD-28174 | biostudies-arrayexpress

Expression data from Arabidopsis thaliana seedings treated with scutellarin

Project description:Maintenance of the root-meristem is determined by polar auxin transport (PAT) and asymmetric cell division (ACD). We find that flavonoids scutellarin and scutellarein, which both have 6-hydroxyl group that differs in its structure from all known-flavonoid PAT inhibitors, promote PAT and ACD in Arabidopsis thaliana root tip, and increase root length. We used microarrays to detail the global programme of gene expression under scutellarin and mock (DMSO) treatment and identified distinct classes of genes regulated by scutellarin.

2020-12-31 | GSE127830 | GEO

Expression profiling of genes involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton

Project description:We used a next-generation sequencing approach, Illumina Digital Gene Expression (DGE) technology, to Genome-wide profiling of gene expression during cotton SE. As a result, 5,076 differentially expressed genes were identified during cotton SE. Expression profile and functional assignments of these genes indicated significant transcriptional complexity during this process. Transcription factor-encoding genes were found to be differentially regulated during SE. The complex pathways of auxin abundance, transport and response with differentially regulated genes revealed that the auxin-related transcripts belonged to IAA biosynthesis, indole-3-butyric acid (IBA) metabolism, IAA conjugate metabolism, auxin transport, auxin-responsive protein / indoleacetic acid-induced protein (Aux/IAA), auxin response factor (ARF), small auxin-up RNA (SAUR), Aux/IAA degradation, and other auxin-related proteins, which allow an intricate system of auxin utilization to achieve multiple purposes in SE. Quantitative real-time PCR (qRT-PCR) was performed on selected genes with different expression patterns and functional assignments were made to demonstrate the utility of RNA-Seq for gene expression profiles during cotton SE. We report here the first comprehensive analysis of transcriptome dynamics that may serve as a gene expression profile blueprint in cotton SE. Our main goal was to adapt the RNA-Seq technology to this notable development process and to analyse the gene expression profile. Complex auxin signalling pathway and transcription regulation were highlighted. Together with biochemical and histological approaches, this study provides comprehensive gene expression data sets for cotton SE that serve as an important platform resource for further functional studies in plant embryogenesis. differential gene expression analysis at 9 time-points/stages during somatic embryogenesis in cotton by deep sequencing, using Illumina GAIIx.

2012-05-31 | E-GEOD-38209 | biostudies-arrayexpress

Expression profiling of genes involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton

2012-05-31 | GSE38209 | GEO

RNA-sequencing of WT and P2Y4 KO pericardial adipose tissue (PAT) 24 hours after left anterior descending artery (LAD) ligation

Project description:We identified differentially regulated genes in the pericardial adipose tissue of wild type (WT) and P2Y4 KO mice, 24 hours after left anterior descending artery (LAD) ligation as a model of myocardial infarction (MI). Differentially regulated genes were involved in metabolism, brown fat cell differentiation, immune response and inflammation. P2Y4 KO mice displayed adipocyte beiging with increased PD-L1 expression and a higher number of regulatory leukocytes in their PAT 24 hours after LAD ligation. Up-regulated genes linked to adipocyte beiging included Ucp1, Cited1 and Prdm16.

2022-08-25 | GSE211768 | GEO

Key genes during ethylene-induced adventitious root development in cucumber (Cucumis sativus L.)

Project description:Our previous studies have shown that exogenous ethylene (ETH) may induce plant adventitious root development in cucumber. In this study, transcriptome technique was used to explore the key genes in ETH-induced rooting. The results revealed that ETH regulated 1415 diferentially expressed genes (DEGs) during rooting, among which 687 DEGs were up-regulated and 728 DEGs were down-regulated. According to Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis, the critical pathways involved in ETH-induced adventitious root development were selected for further study, including carbon metabolism [starch and sucrose metabolism, glycolysis / gluconeogenesis, citrate cycle (TCA cycle), oxidative phosphorylation, fatty acid biosynthesis and fatty acid degradation], secondary metabolite biosynthesis (phenylalanine metabolism and flavonoid biosynthesis) and plant hormone signal transduction. In carbon metabolism, ETH reduced t the expression of CsHK2, CsPK2 and CsCYP86A1, whereas enhanced the expression of CsBAM1 and CsBAM3. Moreover, ETH negatively regulated the transcript level of CsPAL and CsF3’M and positively mediated that of CsPAO in secondary metabolite biosynthesis pathway. Additionally, ETH could induce adventitious rooting by negatively regulating auxin and ETH signal transduction-related genes (CsLAX5, CsGH3.17, CsSUAR50 and CsERS) and positively regulating ABA and BR signaling transduction-related genes (CsPYL1, CsPYL5, CsPYL8, CsBAK1 and CsXTH3) . Furthermore, the results of real-time PCR about the mRNA levels of these genes were consistent with transcriptome results. Therefore, ETH may induce adventitious root development by regulating carbon metabolism-related genes, secondary metabolite biosynthesis-related genes and plant hormone signal transduction-related genes.

2021-11-30 | GSE189315 | GEO

Transcriptomical study on multipul pat mutants

Project description:The Arabidopsis genome encodes 3 PAT mRNA decapping factors: PAT1(AT1g79090), PATH1 (AT3g22270) and PATH2 (AT4g14990). We generated single, double and triple knockouts (KOs) of the three PATs by CRISPR/CAS9-mediated genome editing in the summ2-8 background to avoid immune activation. The 6 weeks-old soil-grown pat triple mutants exhibited markedly stunted growth compared to the other pat single or double mutants indicating functional redundancy of PATs in regulating plant development. To identify genes which affect different developmental programs regulated by PATs, we performed RNA-seq from plants of pat1-1path1-4path2-1summ2-8 and all single and double mutant combinations.

2024-01-26 | GSE253757 | GEO

Transcriptional responses analysis of the inflorescence meristems in Jatropha curcas following gibberellin treatment

Project description:Our results showed that 951 differentially expressed genes (DEGs) were obtained to response to gibberellin treatment. The 6-h time point was an important phase in the response to exogenous gibberellin. Furthermore, the plant endogenous gibberellin, auxin, ethylene, abscisic acid, and brassinolide signaling transduction pathways were repressed after exogenous GA3 treatment. However, the DEGs (JcAHP1, JcHK3, and JcMYC2, JcMYC4) which were respectively associated with cytokinin and jasmonic acid signaling were up-regulation for 24-h time point following GA3 treatment. In addition, the floral meristem determinacy genes (JcLFY and JcSOC1) and floral organ identity genes (JcAP3, JcPI, and JcSEP1-3) were significantly up-regulated, but their negative factor (JcSVP) was down-regulated after GA3 treatment.

2021-12-31 | GSE107561 | GEO

Auxin stimulates brassinosteroid biosynthesis in Arabidopsis roots

Project description:We found that auxin stimulates gene expression of DWF4, which encodes a rate-dertermining step in brassinosteroid biosynthesis pathways. This increased gene expressioin subsequently led to elevation of the biosynthetic flux in Arabidopsis roots. To determine the list of genes that are regulated by auxin-synthesizing brassinosteroids, we challenged Arabidopsis seedlings with either auxin only or auxin plus brassinosteroid biosynthetic inhibitor brassinazole. Keywords: Hormone treatment Arabidopsis seedlings (Columbia ecotype) were grown for 10 d on 1× MS agar-solidified media under long-day conditions (16:8, white light and dark cycle). The seedlings were then transferred to 2 different liquid media containing either 10–7 M 2,4-D or 10–7 M 2,4-D plus 10–6 M brassinazole. After 8 h of treatment, the seedlings were blotted with paper towels to remove excess media and subject to total RNA isolation. Total RNAs isolated from each batch were prepared from 3 replicate seedlings using an RNeasy plant mini kit (Qiagen, Germany).

2011-02-15 | E-GEOD-12964 | biostudies-arrayexpress

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