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Genome-wide binding of Arabidopsis growth regulating factors uncovers their broad regulatory functions in plant growth, development and stress response [ChIP-Seq]

ABSTRACT: The goal of this study is to identify direct target of GRF1 and GRF3.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE128168 | GEO | 2020/02/26

REPOSITORIES: GEO

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Genome-wide binding of Arabidopsis growth regulating factors uncovers their broad regulatory functions in plant growth, development and stress response [RNA-Seq]

Project description:The goal of this study is to identify genes regulated by GRF1 and GRF3. Results: 2,596 and 2,212 differentially expressed genes were identified in the 35S:GRF1 and 35S:GRF3 plants, respectively, when compared with the grf1/grf2/grf3 triple mutant at a false discovery rate (FDR) of 0.05. Similarly, a set of 826 genes was identified as differentially expressed in the grf1/grf2/grf3 mutant when compared with the wild-type WS plants.

2020-02-26 | GSE128170 | GEO

Genes regulated by GRF1 and GRF3 in Arabidopsis roots

Project description:Arabidopsis Affymetrix ATH1 GeneChips were used to compare the mRNA profiles of root tissues of the grf1/grf2/grf3 triple mutant and transgenic plants overexpressing miR396-resistant variants of GRF1 (P35S:rGRF1) or GRF3 (P35S:rGRF3) with those of the corresponding wild-type (Col-0 or WS). Wild-type (Arabidopsis thaliana ecotypes Col-0 and Ws), the triple mutant grf1/grf2/grf3, and transgenic plants overexpressing rGRF1 or rGRF3 were grown in vertical culture dishes on modified KnopM-bM-^@M-^Ys medium for 2 weeks and then root tissues were collected for RNA extraction. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Tarek Hewezi. The equivalent experiment is AT109 at PLEXdb.] genotype: Arabidopsis thaliana ecotypes Col-0(3-replications); genotype: Arabidopsis thaliana ecotypes WS(3-replications); genotype: Triple mutant grf1/grf2/grf3(3-replications); genotype: P35S:rGRF1 overexpression(3-replications); genotype: P35S:rGRF3 overexpression(3-replications)

2012-03-13 | E-GEOD-31593 | biostudies-arrayexpress

Genes regulated by GRF1 and GRF3 in Arabidopsis roots

Project description:Arabidopsis Affymetrix ATH1 GeneChips were used to compare the mRNA profiles of root tissues of the grf1/grf2/grf3 triple mutant and transgenic plants overexpressing miR396-resistant variants of GRF1 (P35S:rGRF1) or GRF3 (P35S:rGRF3) with those of the corresponding wild-type (Col-0 or WS). Wild-type (Arabidopsis thaliana ecotypes Col-0 and Ws), the triple mutant grf1/grf2/grf3, and transgenic plants overexpressing rGRF1 or rGRF3 were grown in vertical culture dishes on modified Knop’s medium for 2 weeks and then root tissues were collected for RNA extraction. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Tarek Hewezi. The equivalent experiment is AT109 at PLEXdb.]

2012-03-13 | GSE31593 | GEO

Genome-wide binding of Arabidopsis growth regulating factors uncovers their broad regulatory functions in plant growth, development and stress response

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-02-26 | GSE128171 | GEO

Arabidopsis thaliana

Project description:Genes regulated by GRF1 and GRF3 in Arabidopsis roots

| PRJNA145565 | ENA

Genome-wide binding of Arabidopsis growth regulating factors uncovers their broad regulatory functions in plant growth, development and stress response

Project description:Genome-wide binding of Arabidopsis growth regulating factors uncovers their broad regulatory functions in plant growth, development and stress response

| PRJNA526666 | ENA

Genome-wide binding of Arabidopsis growth regulating factors uncovers their broad regulatory functions in plant growth, development and stress response [ChIP-Seq]

Project description:Genome-wide binding of Arabidopsis growth regulating factors uncovers their broad regulatory functions in plant growth, development and stress response [ChIP-Seq]

| PRJNA526668 | ENA

Genome-wide binding of Arabidopsis growth regulating factors uncovers their broad regulatory functions in plant growth, development and stress response [RNA-Seq]

Project description:Genome-wide binding of Arabidopsis growth regulating factors uncovers their broad regulatory functions in plant growth, development and stress response [RNA-Seq]

| PRJNA526669 | ENA

A role for Arabidopsis growth-regulating factors 1 and 3 in growth-stress antagonism.

Project description:Growth-regulating factors (GRFs) belong to a small family of transcription factors that are highly conserved in plants. GRFs regulate many developmental processes and plant responses to biotic and abiotic stimuli. Despite the importance of GRFs, a detailed mechanistic understanding of their regulatory functions is still lacking. In this study, we used ChIP sequencing (ChIP-seq) to identify genome-wide binding sites of Arabidopsis GRF1 and GRF3, and correspondingly their direct downstream target genes. RNA-sequencing (RNA-seq) analysis revealed that GRF1 and GRF3 regulate the expression of a significant number of the identified direct targets. The target genes unveiled broad regulatory functions of GRF1 and GRF3 in plant growth and development, phytohormone biosynthesis and signaling, and the cell cycle. Our analyses also revealed that clock core genes and genes with stress- and defense-related functions are most predominant among the GRF1- and GRF3-bound targets, providing insights into a possible role for these transcription factors in mediating growth-defense antagonism and integrating environmental stimuli into developmental programs. Additionally, GRF1 and GRF3 target molecular nodes of growth-defense antagonism and modulate the levels of defense- and development-related hormones in opposite directions. Taken together, our results point to GRF1 and GRF3 as potential key determinants of plant fitness under stress conditions.

| S-EPMC7031083 | biostudies-literature

Higher plant calreticulins have acquired specialized functions in Arabidopsis.

Project description:Calreticulin (CRT) is a ubiquitous ER protein involved in multiple cellular processes in animals, such as protein folding and calcium homeostasis. Like in animals, plants have evolved divergent CRTs, but their physiological functions are less understood. Arabidopsis contains three CRT proteins, where the two CRTs AtCRT1a and CRT1b represent one subgroup, and AtCRT3 a divergent member.Through expression of single Arabidopsis family members in CRT-deficient mouse fibroblasts we show that both subgroups have retained basic CRT functions, including ER Ca2+-holding potential and putative chaperone capabilities. However, other more general cellular defects due to the absence of CRT in the fibroblasts, such as cell adhesion deficiencies, were not fully restored. Furthermore, in planta expression, protein localization and mutant analyses revealed that the three Arabidopsis CRTs have acquired specialized functions. The AtCRT1a and CRT1b family members appear to be components of a general ER chaperone network. In contrast, and as recently shown, AtCRT3 is associated with immune responses, and is essential for responsiveness to the bacterial Pathogen-Associated Molecular Pattern (PAMP) elf18, derived from elongation factor (EF)-Tu. Whereas constitutively expressed AtCRT1a fully complemented Atcrt1b mutants, AtCRT3 did not.We conclude that the physiological functions of the two CRT subgroups in Arabidopsis have diverged, resulting in a role for AtCRT3 in PAMP associated responses, and possibly more general chaperone functions for AtCRT1a and CRT1b.

| S-EPMC2893204 | biostudies-literature

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