Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Genome-wide transcriptome analysis bZIP29 dominant negative repressor line in root tips of Arabidopsis

ABSTRACT: 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.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Plant Systems Biology data submission

PROVIDER: E-MTAB-3755 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Functional characterization of the Arabidopsis transcription factor bZIP29 reveals its role in leaf and root development.

Van Leene Jelle J Blomme Jonas J Kulkarni Shubhada R SR Cannoot Bernard B De Winne Nancy N Eeckhout Dominique D Persiau Geert G Van De Slijke Eveline E Vercruysse Leen L Vanden Bossche Robin R Heyndrickx Ken S KS Vanneste Steffen S Goossens Alain A Gevaert Kris K Vandepoele Klaas K Gonzalez Nathalie N Inzé Dirk D De Jaeger Geert G

Journal of experimental botany 20160922 19

Plant bZIP group I transcription factors have been reported mainly for their role during vascular development and osmosensory responses. Interestingly, bZIP29 has been identified in a cell cycle interactome, indicating additional functions of bZIP29 in plant development. Here, bZIP29 was functionally characterized to study its role during plant development. It is not present in vascular tissue but is specifically expressed in proliferative tissues. Genome-wide mapping of bZIP29 target genes conf ...[more]

PMID: 27660483

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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:The mechanisms ensuring balanced growth remain a critical question in developmental biology. In plants, this balance relies on spatiotemporal integration of hormonal signaling pathways, but the understanding of the precise contribution of each hormone is just beginning to take form. Brassinosteroid (BR) hormone, is shown here to have opposing effects on root meristem size, depending on its site of action. BR is demonstrated to both delay and promote onset of stem cell daughter differentiation, when acting in the outer tissue of the root meristem, the epidermis, and the inner-most tissue, the stele, respectively. To understand the molecular basis of this phenomenon, a comprehensive spatiotemporal translatome mapping of Arabidopsis roots was performed. Analyses of wild type and mutants featuring different distributions of BR, revealed autonomous, tissue-specific gene responses to BR, implying its contrasting tissue-dependent impact on growth. BR-induced genes were primarily detected in epidermal cells of the basal meristem zone and were enriched by auxin-related genes. In contrast, repressed BR genes prevailed in the stele of the apical meristem zone. Furthermore, auxin was found to mediate the growth-promoting impact of BR signaling originating in the epidermis, while BR signaling in the stele buffered this effect. We propose that context-specific BR activity and responses are oppositely interpreted at the organ level, ensuring coherent growth. 24 samples of polyribosome-associated mRNA (following 0, 3, and 8 hours of BR treatment, in two biological repetitions), were collected. RNA samples were sequenced on an Illumina HiSeq 2500, to obtain 50 bp single-end reads. These reads were aligned to the TAIR10 assembly of the Arabidopsis thaliana genome, using Tophat2 v2.0.9. Transcript coordinates from the TAIR10 reference set were used to guide the alignment process. After alignment, the numbers of reads per transcript were estimated using HTSeq v0.5.3p3, and DESeq2 v1.2.8 was used to normalize read counts and call differentially expressed genes.

Dataset Information

Genome-wide transcriptome analysis bZIP29 dominant negative repressor line in root tips of Arabidopsis

Publications

Functional characterization of the Arabidopsis transcription factor bZIP29 reveals its role in leaf and root development.

Similar Datasets

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