Project description:Transcriptional profiling of root part comparing wild type with scl3 mutant and SCL3 OE. We used Affymetrix ATH1 microarrays to determine the effect of GRAS transcription factor SCL3 on growth and development of Arabidopsis root system by global transcriptome analysis and to identify new regulators in the regulatory pathway.
Project description:Transcriptional profiling in the root between ga1, ga1 scl3 and ga1 SCL3 OE. We used Affymetrix ATH1 microarrays to determine the effect of GRAS transcription factor SCL3 and gibberellin on the growth and development of the Arabidopsis root system by global transcriptome analysis and to identify new regulators in the regulatory pathway.
Project description:Transcript profiling analysis of Hydraulic conductivity of Root 1 (HCR1) mutant compared to wild type (Col-0) using ARABIDOPSIS GENE1.1ST ARRAY STRIP (901793, Affymetrix, Santa Clara, USA).
Project description:The Arabidopsis SCARECROW-LIKE28 transcription factor promotes progression through G2/M, modulates division plane orientation and promotes post-mitotic cell expansion. To define the networks regulated by SCL28, we performed transcriptome profiling of wild-type and scl28-3 root tips.
Project description:Transcriptional profiling of hypocotyl comparing wild type with shr mutant. We used Affymetrix ATH1 microarrays to determine the effect of GRAS transcription factor SHORT-ROOT on growth and development of Arabidopsis shoot system (hypocotyl) by global transcriptome analysis and to identify the key players in the regulatory pathway.
Project description:The root cap surrounds the root meristem, protecting it from harsh environments and facilitating root movement through soil. In Arabidopsis, new root cap cells produced in the meristem displace older cells toward the root periphery, where they undergo programmed cell death and are released from the root. This rapid cell turnover is a unique feature of the root cap and is modulated in part by the combined action of four NAC transcription factors, as well as cell wall modification enzymes. Here we show that the transcription factor NIN-LIKE PROTEIN 7 (NLP7) regulates root cap maturation in Arabidopsis by modulating expression of each of the NAC TFs as well as several cell wall modifying enzymes. NLP7 is a homolog of NIN, a transcription factor required for nodulation in Lotus japonicas, and is highly expressed in the columella root cap. Mutants have altered columella root cap development and decreased levels of homogalacturonan, a major component of pectin. Reverse genetic analysis of genes differentially expressed in nlp7 roots showed that two cell wall modifying enzymes, CELLULASE5 and XTH5, modulate root cap maturation likely downstream of NLP7. Plant cell wall modification is critical for nodulation, and we propose that this characteristic is also present in NLPs. We used microarrays to identify the differences in gene expression between whole roots of WT and nlp7-1 Arabidopsis plants Roots were cut at the root/hypocotyl junction and collected into RLT buffer in the RNeasy plant mini kit. Approximately 60 roots were collected per replicate, with two biological replicates. RNA was extracted using the RNeasy Micro Kit. Probes for array analysis were preparedfrom 1μg total RNA with the one-cycle amplification protocol by Affymetrix according to the manufacturer's instructions. Samples were submitted to Expression Analysis Inc. (Durham, NC) for hybridization to Arabidopsis Whole Genome ATH1 Affymetrix GeneChips.
Project description:We characterised mutants in the GRAS family transcription factor AtSCL26 in Arabidopsis thaliana using a combination of gene functional analysis, hormone treatments and expression profiling at the cell type level. This has enabled us to implicate AtSCL26 in the cell-specific control of nitrogen-giberellic acid response cross-talk to control root architecture.
Project description:The Arabidopsis basic leucine zipper transcription factor bZIP29 of the bZIP group I TF family, expressed mainly in proliferative tissues, is functionally characterized in this study. In roots, bZIP29 is highly expressed in the quiescent centre and the columella cells of the root apical meristem. Mutant analyses demonstrate that bZIP29 regulates root meristem cell number and root gravitropic responses. RNA-seq transcriptome profiling of the root meristem shows that bZIP29 target genes are linked to cell wall organization, and that gene regulatory networks controlling proper root meristem organization are intensively rewired upon its perturbation.
Project description:The cotyledons of etiolated seedlings from terrestrial flowering plants must emerge from the soil surface, while roots must penetrate the soil to ensure plant survival. We show here that the soil emergence related transcription factor PHYTOCHROME-INTERACTING FACTOR 3 (PIF3) regulates root penetration via transducing external signals perceived by the receptor kinase FERONIA (FER) in Arabidopsis thaliana. The loss of FER function in the fer-4 mutant resulted in a severe defect in root penetration into hard soil or medium. Single-cell RNA-seq profiling of roots revealed a distinct cell clustering pattern, especially for root cap cells, and revealed PIF3 as a putative FER-regulated transcription factor. Biochemical, imaging, and genetic experiments confirmed that PIF3 is required for root soil penetration. Moreover, FER interacted with and stabilized PIF3, which then modulated the expression of mechanosensitive ion channels and the sloughing of outer cells in the root cap. We propose a novel mechanism of soil penetration by plant roots.