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ArabidopsisArabidopsis ProteinsGene Expression Regulation, PlantGenes, PlantPlants, Genetically ModifiedPlant RootsPlant ProteinsRNA, PlantPlant LeavesSeedlingFlowersMolecular Sequence DataDNA, PlantMutationSeedsAmino Acid SequenceIndoleacetic AcidsGenome, PlantGerminationPlant Growth RegulatorsPlant ShootsAbscisic AcidMeristemPhenotypeOxylipinsPlant DiseasesSequence Homology, Amino AcidPlant EpidermisSalicylic AcidEthylenesCyclopentanesBase SequencePhylogenyGenetic Complementation TestCotyledonChloroplastsLightCloning, MolecularSequence AlignmentMutagenesis, InsertionalPlastidsHypocotylPseudomonas syringaePlant StomataGlucosinolatesBrassicaceaeChromosomes, PlantMADS Domain ProteinsDNA, ComplementaryCytokininsPollenMultigene FamilyGibberellinsOryza sativaPlant StemsTranscription FactorsTobaccoGene Expression ProfilingPlant ImmunityEcotypePlant Vascular BundlePhotoperiodSignal TransductionPlant StructuresBrassicaChlorophyllPhytochromeGlucuronidasePhototropismChromosome MappingProtoplastsStress, PhysiologicalThylakoidsPhytochrome BGravitropismDarknessPlantsSalt-ToleranceDNA PrimersDisease ResistancePhotosynthesisAGAMOUS Protein, ArabidopsisPollen TubeOvuleRNA, MessengerPromoter Regions, GeneticPhytochrome AReverse Transcriptase Polymerase Chain ReactionInflorescenceTranscription, GeneticAnthocyaninsTwo-Hybrid System TechniquesSequence Analysis, DNABrassinosteroidsRecombinant Fusion ProteinsDroughtsEvolution, MolecularConserved SequenceOomycetesAcclimatization
Flowering plant Arabidopsis thalianaGenesMethylationPutativeCDNAGene expressionEukaryoticTranscriptionalProteasomeExpressionMeristemMiRNADifferentiallySequencesAccessionsDrosophilaAuxinBiologyProteinsSpliceosomeCharacterizeRegulatorProcessesPolyadenylation siteConservationLeafTranscriptsTranscriptionGenomesDevelopmentBacterialRiceAnnotationVectorAnalysisIdentificationTranslationComplete cdsGrowthSmallReferenceTreatmentsTargetFound
Flowering plant Arabidopsis thaliana1
  • The flowering plant Arabidopsis thaliana is a dicot model organism for research in many aspects of plant biology. (jcvi.org)
Genes13
  • The genome-wide abundance of two histone modifications, H3K4me3 and H3K9ac, both associated with actively expressed genes, was monitored in Arabidopsis thaliana leaves at different time points during developmental senescence, along with expression in the form of RNA-seq data. (nih.gov)
  • However, for a subset of genes showing increased or decreased expression, the respective gain or loss of H3K4me3 marks were found to closely match the temporal changes in mRNA abundance. (nih.gov)
  • A cell type-specific view on the translation of mRNAs from ROS-responsive genes upon paraquat treatment of Arabidopsis thaliana leaves. (mpg.de)
  • We found 1,720 animal-like target sites in the 3'UTRs of 12,858 mRNAs and 19 plant-like target sites in 51,917 genes. (biomedcentral.com)
  • We measured Arabidopsis aerial growth at early and late life stages, seed production, and used mRNA sequencing to characterize differentially expressed plant genes in response to fungal inoculation with and without bacterial endosymbionts. (duke.edu)
  • Notably, the presence of Mollicutes- or Burkholderia-related endosymbionts in Linnemannia did not impact the expression of genes in Arabidopsis or overall growth rates. (duke.edu)
  • Further demonstrating that expressed CRP genes lack gene body methylation, a CRP4-GFP fusion gene under the control of the constitutive 35 S promoter remains unmethylated in leaves and is transcribed to produce a translatable mRNA. (biomedcentral.com)
  • AtRTD3 contains over 169,000 transcripts-twice that of the best current Arabidopsis transcriptome and including over 1500 novel genes. (dundee.ac.uk)
  • Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. (gao-lab.org)
  • 2005) Expression of Arabidopsis MIRNA Genes. (ttu.edu)
  • 2004) Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana . (ttu.edu)
  • 17. Yanofsky M F. Floral meristems to floral organs:genes controlling early events in Arabidopsis flower development[J].Annu Rev Plant Physiol Plant Mol Biol,1995,46:167-188. (nefu.edu.cn)
  • 19. Mara C D,Huang T,Irish V F. The Arabidopsis floral homeotic proteins APETALA3 and PISTILLATA negatively regulate the BANQUO genes implicated in light signaling[J].Plant Cell,2010,22(3):690-702. (nefu.edu.cn)
Methylation3
  • Here we present the first genome-wide 1-bp resolution maps of histone acetylation, histone methylation and core histone in Arabidopsis thaliana and a comprehensive analysis of these maps and gene expression data in A. thaliana, A. arenosa and allotetraploids. (nih.gov)
  • We performed a methylation-sensitive amplification polymorphism analysis to search for targets of RNA-directed DNA methylation in Arabidopsis thaliana and identified several members of a gene family encoding cysteine-rich peptides (CRPs). (biomedcentral.com)
  • 2004) Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. (ttu.edu)
Putative3
  • At least 20 type of putative ionotropic glutamate receptor (iGluR)-like channels have been identified in Arabidopsis thaliana. (intechopen.com)
  • Taken together, these results suggest a correlation between the putative iGluR-like channel function and the alteration of root growth and development in the Arabidopsis roots. (intechopen.com)
  • BT002017.1 Arabidopsis thaliana putative protein (At5g11270) mRNA, complete cds. (gao-lab.org)
CDNA2
  • However, accuracy is significantly affected by sequencing errors, mRNA degradation, or incomplete cDNA synthesis. (dundee.ac.uk)
  • In order to explore the function of PI gene in the development of petals and stamens, the PI gene in Arabidopsis thaliana was used as the research object, and the AtPI gene was amplified from cDNA by PCR, and the plant expression vector(pROKⅡ- AtPI ) was constructed and transformed into tobacco. (nefu.edu.cn)
Gene expression4
  • The 3' regulatory regions have a great diversity of cis -regulatory elements directly involved in polyadenylation, stability, transport and mRNA translation, essential to achieve the desired levels of gene expression. (frontiersin.org)
  • We analyzed gene expression during Arabidopsis thaliana meristem development under long day conditions from day 7 to 16 after germination in one-day increments. (biomedcentral.com)
  • Integration of smRNA and mRNA expression profiling identified a variety of processes that could be under microRNA control, e.g. protein modification, signaling, gene expression, and response to DNA damage. (biomedcentral.com)
  • However, we lack an understanding of how the spatial microbial networks and hotspots are distributed on a leaf and how these factors affect the host tissues' gene expression per location.To fill this gap, we applied an innovative, high-throughput technology originally developed for mammalian tissues, Spatial Transcriptomics (ST), to outdoor-grown Arabidopsis thaliana leaves. (mpg.de)
Eukaryotic2
  • In addition, after transcription, a wide array of RNA-binding proteins interacts with cis -acting elements located mainly in the 3' untranslated region, determining the fate of mRNAs in eukaryotic cells. (frontiersin.org)
  • Moreover, recent global ribosome-sequencing (Ribo-seq, sequencing of ribosome-protected RNA fragments) studies have shown that uORFs are a prevalent feature in eukaryotic mRNAs, not limited to these few well-studied examples 19 - 21 . (biorxiv.org)
Transcriptional2
  • Promotion of growth by elevated carbon dioxide is coordinated through a flexible transcriptional network in Arabidopsis. (mpg.de)
  • Together, these results indicate that beneficial plant growth promotion and seed mass impacts of L. elongata on Arabidopsis are likely driven by plant hormone and defense transcription responses after plant-fungal contact, and that plant phenotypic and transcriptional responses are independent of whether the fungal symbiont is colonized by Mollicutes or Burkholderia-related endohyphal bacteria. (duke.edu)
Proteasome3
  • Prefoldins negatively regulate cold acclimation in Arabidopsis thaliana by promoting nuclear proteasome-mediated HY5 degradation. (bu.edu)
  • An upstream regulator of the 26S proteasome modulates organ size in Arabidopsis thaliana. (mpg.de)
  • Arabidopsis thaliana proteasome alpha subunit D2 (PAD2), mRNA. (genscript.com)
Expression4
  • In order to characterize the repertoire of endogenous smRNAs and potential gene targets in dinoflagellates, we conducted smRNA and mRNA expression profiling over 9 experimental treatments of cultures from Symbiodinium microadriaticum , a photosynthetic symbiont of scleractinian corals. (biomedcentral.com)
  • The expression pattern of the Picea glauca Defensin 1 promoter is maintained in Arabidopsis thaliana, indicating the conservation of signalling pathways between angiosperms and gymnosperms. (uquebec.ca)
  • Liu X, Huang J, Wang Y, Khanna K, Xie Z , Owen HA, Zhao D. (2010) The role of floral organs in carpels , an Arabidopsis loss-of-function mutation in MicroRNA160a , in organogenesis and the mechanism regulating its expression. (ttu.edu)
  • Construction of Plant Expression Vector and Genetic Transformation Analysis of Arabidopsis thaliana AtPI Gene in Nicotiana tabacum [J]. Bulletin of Botanical Research, 2016, 36(3): 388-394. (nefu.edu.cn)
Meristem1
MiRNA2
  • isolated the lin-4 miRNA, they found that instead of producing an mRNA encoding a protein, it produced short non-coding RNAs, one of which was a ~22-nucleotide RNA that contained sequences partially complementary to multiple sequences in the 3' UTR of the lin-14 mRNA. (wikipedia.org)
  • Xie Z . (2010) Piecing the Puzzle Together: Genetic Requirements for miRNA Biogenesis in Arabidopsis thaliana . (ttu.edu)
Differentially1
  • The LSM1-7 complex differentially regulates Arabidopsis thaliana tolerance to abiotic stress conditions by promoting selective mRNA decapping. (bu.edu)
Sequences2
  • miRNAs base-pair to complementary sequences in mRNA molecules, then gene silence said mRNA molecules by one or more of the following processes: Cleavage of mRNA strand into two pieces, Destabilization of mRNA by shortening its poly(A) tail, or Translation of mRNA into proteins. (wikipedia.org)
  • The mechanisms involved in the stress-induced translation have been investigated for a small number of key transcription factors (for example, yeast general control nondepressible 4 (GCN4) 12 and mammalian activating transcription factor 4 (ATF4) 13 ), whose translation is normally inhibited by the uORFs in the 5' leader sequences of their mRNAs. (biorxiv.org)
Accessions1
  • Positional Information Resolves Structural Variations and Uncovers an Evolutionarily Divergent Genetic Locus in Accessions of Arabidopsis thaliana. (mpg.de)
Drosophila1
Auxin1
  • Linnemannia elongata (Mortierellaceae) stimulates Arabidopsis thaliana aerial growth and responses to auxin, ethylene, and reactive oxygen species. (duke.edu)
Biology1
  • Lucky to have the chance on working on RNA biology during my PhD training in the lab of Dr Julio Salinas using Arabidopsis as a model to understand how plants respond and adapt to environmental challenges. (bu.edu)
Proteins2
  • LSM proteins provide accurate splicing and decay of selected transcripts to ensure normal Arabidopsis development. (bu.edu)
  • Like the other six RAP2.4 proteins, Rap2.4 h promotes APx mRNA accumulation. (fu-berlin.de)
Spliceosome1
  • Prefoldins contribute to maintaining the levels of the spliceosome LSM2-8 complex through Hsp90 in Arabidopsis. (bu.edu)
Characterize1
  • In a just published Nature Genetics paper, Wolfgang Busch and his research group at the Gregor Mendel Institute use genome-wide association studies on cellular traits to identify and characterize a new regulator of root development in Arabidopsis. (oeaw.ac.at)
Regulator1
  • miR396a-Mediated basic helix-loop-helix transcription factor bHLH74 repression acts as a regulator for root growth in Arabidopsis seedlings. (chinbullbotany.com)
Processes2
  • This updated Arabidopsis genome annotation with a substantially increased resolution of gene models will not only further our understanding of the biological processes of this plant model but also of other species. (jcvi.org)
  • We applied several advancements to the original method to study the concerted, multimodal microbial infection processes and host's response in A. thaliana leaves. (mpg.de)
Polyadenylation site1
  • The polyadenylation site (PAS), point from which the pre-mRNA is cleaved and polyadenylated, is defined by surrounding cis- elements ( Tian and Manley, 2016 ). (frontiersin.org)
Conservation1
  • Conservation of the RNA helicases suggests that mRNA structurome remodelling is a general mechanism for stress-induced translation across kingdoms. (biorxiv.org)
Leaf4
  • Overall design: ChIP-Seq: Identification of distribution of H3K9ac, H3K4me3 and H3 in Arabidopsis thaliana leaf. (nih.gov)
  • mRNA expressions in leaf and flower of the AtHD1 mutant were compared with those of the wild type plants. (nih.gov)
  • The Arabidopsis onset of leaf death5 Mutation of Quinolinate Synthase Affects Nicotinamide Adenine Dinucleotide Biosynthesis and Causes Early Ageing. (mpg.de)
  • Ectopic of miR396 suppresses GRF target gene and alters leaf growth in Arabidopsis. (chinbullbotany.com)
Transcripts3
  • A comprehensive annotation of its genome paves the way for understanding the functions and activities of all types of transcripts, including mRNA, the various classes of non-coding RNA, and small RNA. (jcvi.org)
  • To identify common features shared by transcripts with stress-upregulated translation efficiency (TE-up), we first performed high-resolution ribosome-sequencing in Arabidopsis during pattern-triggered immunity and found that TE-up transcripts are enriched with upstream open reading frames (uORFs). (biorxiv.org)
  • Using in planta nucleotide-resolution mRNA structurome probing, we discovered that this stress-induced switch in translation is mediated by highly structured regions detected downstream of uAUGs in TE-up transcripts. (biorxiv.org)
Transcription1
  • The Arabidopsis ERFIb / RAP2.4 transcription factor family consists of eight members with highly conserved DNA binding domains. (fu-berlin.de)
Genomes1
  • In this study, we focused on the symbiosis between soil fungus Linnemannia elongata (Mortierellaceae) and Arabidopsis thaliana (Brassicaceae), as both organisms have high-quality reference genomes and transcriptomes available, and their lifestyles and growth requirements are conducive to research conditions. (duke.edu)
Development3
  • For annual plants, such as Arabidopsis thaliana , proper determination of the flowering time is critical for plant reproductive success because a switch from vegetative to reproductive development is irreversible. (biomedcentral.com)
  • Molecular mechanism of microRNA396 mediating pistil development in Arabidopsis. (chinbullbotany.com)
  • The present review documents recent advances in our understanding of how these various factors modulate the development of both simple leaves (focusing mainly on the model plant Arabidopsis thaliana ) and compound leaves (focusing mainly on the model legume species Medicago truncatula ). (jipb.net)
Bacterial2
  • The effect of PAD2 mutations on the susceptibility of A. thaliana to bacterial diseases is reported. (genscript.com)
  • Second, we demonstrated the capture of bacterial and fungal diversity from outdoor grown A. thaliana leaves. (mpg.de)
Rice1
  • Public data sets used in this study include PRJNA298638 (rice TRAP-seq) 13 , SRP043448 (rice small RNA-seq) 15 and GSE52952 ( Arabidopsis small RNA-seq and degradome-seq) 17 . (nature.com)
Annotation1
  • The TAIR10 annotation update had a profound impact on Arabidopsis research but was released more than 5 years ago. (jcvi.org)
Vector1
  • In this study, we focused on the deregulations induced in Arabidopsis thaliana by an aphid vector that were alleviated when the plants were infected with turnip yellows virus (TuYV), a polerovirus strictly transmitted by aphids in a circulative and nonpropagative mode. (bvsalud.org)
Analysis3
Identification2
  • Characterization and Identification of cis-Regulatory Elements in Arabidopsis Based on Single-Nucleotide Polymorphism Information. (mpg.de)
  • Title: Identification of PAD2 as a gamma-glutamylcysteine synthetase highlights the importance of glutathione in disease resistance of Arabidopsis. (genscript.com)
Translation4
  • This complementarity was proposed to inhibit the translation of the lin-14 mRNA into the LIN-14 protein. (wikipedia.org)
  • The m 7 G-cap of the mRNA is recognized by the 43S translation preinitiation complex comprised of the 40S ribosomal subunit and the eIF2-GTP-Met-tRNAi ternary complex. (biorxiv.org)
  • The preinitiation complex then scans along the 5' leader sequence of the mRNA to initiate translation at a start codon 1 - 3 . (biorxiv.org)
  • This raises questions: How is translation of these uORF-containing mRNAs regulated if not by phosphorylation of eIF2α? (biorxiv.org)
Complete cds3
Growth3
Small1
  • Qi X, Bao FS, and Xie Z. (2009) Small RNA Deep Sequencing Reveals Role for Arabidopsis thaliana RNA-Dependent RNA Polymerases in Viral siRNA Biogenesis. (ttu.edu)
Reference2
Treatments1
  • First, we showed that the introduction of tissue treatments facilitate spatial capture of plant mRNAs while preserving the complete morphology of the plant tissue. (mpg.de)
Target1
  • Polyadenylation is essential for the stability of the transcript, preventing the mRNA from being the target of posttranscriptional gene silencing (PTGS) via RNA-dependent RNA polymerase 6 (RDR6) in plants ( Luo and Chen, 2007 ). (frontiersin.org)
Found1