Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNAseq analysis of NGATHA loss and gain of function alleles

ABSTRACT: The four NGATHA genes (NGA) form a small subfamily within the large family of B3-domain transcription factors of Arabidopsis thaliana. NGA genes act redundantly to direct the development of the apical tissues of the gynoecium, the style and the stigma. Previous studies indicate that NGA genes could exert this function at least partially by directing the synthesis of auxin at the distal end of the developing gynoecium through the upregulation of two different YUCCA genes, which encode flavin monooxygenases involved in auxin biosynthesis. We have compared three developing pistil transcriptome data sets from wildtype, nga quadruple mutants and a 35S::NGA3 line. The differentially expressed genes showed a significant enrichment for auxin-related genes, supporting the idea of NGA genes as major regulators of auxin accumulation and distribution within the developing gynoecium. Expression profile comparation of wild type, nga mutant and NGA overexpression

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Vicente Balanza

PROVIDER: E-GEOD-56326 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

The effect of NGATHA altered activity on auxin signaling pathways within the Arabidopsis gynoecium.

Martínez-Fernández Irene I Sanchís Sofía S Marini Naciele N Balanzá Vicente V Ballester Patricia P Navarrete-Gómez Marisa M Oliveira Antonio C AC Colombo Lucia L Ferrándiz Cristina C

Frontiers in plant science 20140521

The four NGATHA genes (NGA) form a small subfamily within the large family of B3-domain transcription factors of Arabidopsis thaliana. NGA genes act redundantly to direct the development of the apical tissues of the gynoecium, the style, and the stigma. Previous studies indicate that NGA genes could exert this function at least partially by directing the synthesis of auxin at the distal end of the developing gynoecium through the upregulation of two different YUCCA genes, which encode flavin mon ...[more]

PMID: 24904608

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Project description:Background: The carpel margin meristem is a vital multi-potent structure located in the medial domain of the Arabidopsis thaliana gynoecium, the female floral reproductive organ. The carpel margin meristem generates ovules that upon fertilization become seeds. The molecular mechanisms that specify this meristematic region and regulate its organogenic potential are poorly understood. Here, we present an analysis of the transcriptional profile of the medial domain of the Arabidopsis gynoecium highlighting the developmental stages that immediately proceed ovule initiation, the earliest stages of seed development. Results: Using a floral synchronization system and a SHATTERPROOF2 domain-specific reporter construct, paired with fluorescence-activated cell sorting, we assayed the transcriptome of the gynoecial medial domain with temporal and spatial precision. Our analysis reveals a set of genes that are differentially-expressed within the SHATTERPROOF2 expression domain that marks portions of the developing medial domain. Many members of this gene set have been shown previously to function during the development of medial domain-derived structures, including the ovules, thus validating our approach. Other uncharacterized members of this gene set, including a set of differentially-expressed cis-natural antisense transcripts, are potential novel regulators of medial domain development and candidates for future functional studies. Several members of the REM family of transcriptional regulators were enriched in the SHP2-expressing cell population including a previously unrecognized REM family member (At5g60142). Analysis of the abundance of specific transcriptional isoforms identified genes that may exhibit âisoform switchingâ behavior during gynoecial development. Conclusions: This data set provides genome-wide transcriptional insight into the development of the gynoecial medial domain that contains the carpel margin meristem, an important reproductive structure that gives rise to the ovules in Arabidopsis thaliana. Four samples (YFP-positive, YFP-negative, all-sorted, and non-sorted). Four biological replicates of each sample (except YFP-positive, collected in triplicated). Strand-specific libraries were sequenced (single-end) in two lanes of a HiSeq 2500 Illumina flow cell (each lane was later analyzed as a technical replicate).

Project description:Floral organ identities are specified by few transcription factors which act as master regulators. Subsequently, specification of organ axes programs the distribution of distinct tissue types within the organs that themselves develop unique identities. The C-class, AGAMOUS-clade MADS box genes are primary promoters of the gynoecium which is divided into a distal style and a subtending ovary along the apical-basal axis. We show that members of a clade of B3-domain transcription factors, NGATHA1 to NGA4 (NGA1-4), are expressed distally in all lateral organs, and all four have a redundant and essential role in style development. Loss of all four genes results in gynoecia where style is replaced by valve-like projections and a reduction in style-specific SHATTERPROOF1 (SHP1) expression. In agreement, floral misexpression of NGA1 promotes ectopic style and SHP1 expression. STYLISH1, an auxin biosynthesis inducer, conditionally activated NGA genes, which in turn, promoted distal expression of other STY genes in a putative positive feed back loop. Inhibited auxin transport or lack of YABBY1 gene activities resulted in a basally expanded style domain and broader expression of NGA genes. We speculate that early gynoecium factors delimit NGA gene response to an auxin-based signal, elicited by STY gene activity, to restrict the activation of style program to a late and distal carpel domain. RNA was extracted from inflorescences of 30 day old plants using Qiagen RNAEasy kit. cRNA was synthesized and hybridized to Affymetrix ATH1 array according to manufacture recommendation. Seven repeats of wild type, two repeats of nga quadruple mutants and two repeats of 35S:amiR-NGA164a were collected. Signal values were obtained and normalized using the GC-RMA protocol, using R 2.7.2 (www.r-project.org) and Bioconductor 2.2 (www.bioconductor.org/). Average correlation values between repeats was 0.985, while the average correlation between wild type and mutant samples was only 0.972. As the average correlation between samples the nga quadruple mutants and 35S:amiR-NGA164a plants was 0.984, and given the identical phenotype, we grouped the two genotypes together.

Dataset Information

RNAseq analysis of NGATHA loss and gain of function alleles

Publications

The effect of NGATHA altered activity on auxin signaling pathways within the Arabidopsis gynoecium.

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