THE DNA BINDING LANDSCAPE OF THE MAIZE AUXIN RESPONSE FACTOR FAMILY [RNA-seq]
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ABSTRACT:
PROVIDER: PRJNA438144 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6830130.fastq.gz | Fastqsanger.gz | |||
| SRR6830131.fastq.gz | Fastqsanger.gz | |||
| SRR6830132.fastq.gz | Fastqsanger.gz | |||
| SRR6830127.fastq.gz | Fastqsanger.gz | |||
| SRR6830128.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:THE DNA BINDING LANDSCAPE OF THE MAIZE AUXIN RESPONSE FACTOR FAMILY
| PRJNA438360 | ENA
Project description:THE DNA BINDING LANDSCAPE OF THE MAIZE AUXIN RESPONSE FACTOR FAMILY [DAP-seq]
| PRJNA438151 | ENA
Project description:DAP-seq was used to generate genome-wide DNA:TF interaction maps for fourteen maize ARFs from the evolutionarily conserved class A ‘activator’ and class B ‘repressor’ clades. Among the distinct binding sites that were identified, we observed a high degree of overlap for ARFs of the same class, but found substantial differences in motif sequence, spacing, site preference, and association with auxin induced genes among clade A and clade B ARFs.
2018-09-14 | GSE111795 | GEO
Project description:DAP-seq was used to generate genome-wide DNA:TF interaction maps for fourteen maize ARFs from the evolutionarily conserved class A ‘activator’ and class B ‘repressor’ clades. Among the distinct binding sites that were identified, we observed a high degree of overlap for ARFs of the same class, but found substantial differences in motif sequence, spacing, site preference, and association with auxin induced genes among clade A and clade B ARFs.
2018-09-14 | GSE111792 | GEO
Project description:AUXIN RESPONSE FACTORS (ARFs) are plant-specific transcription factors (TFs) that couple perception of the hormone auxin to gene expression programs essential to all land plants. As with many large TF families, a key question is whether individual members determine developmental specificity by binding distinct target genes. We use DAP-seq to generate genome-wide in vitro TF:DNA interaction maps for fourteen maize ARFs from the evolutionarily conserved A and B clades. Comparative analysis reveal a high degree of binding site overlap for ARFs of the same clade, but largely distinct clade A and B binding. Many sites are however co-occupied by ARFs from both clades, suggesting transcriptional coordination for many genes. Among these, we investigate known QTLs and use machine learning to predict the impact of cis-regulatory variation. Overall, large-scale comparative analysis of ARF binding suggests that auxin response specificity may be determined by factors other than individual ARF binding site selection.
| S-EPMC6207667 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2018-09-14 | GSE111857 | GEO
Project description:In order to elucidate the molecular mechanism of auxin-induced mesocotyl elongation, gene expression profiling analyses were performed in a deep-sowing tolerant maize inbred line 3681-4. Gene expression studies combing Affymetrix GeneChip analysis and Real-time PCR were employed to determine the molecular mechanism underlying IAA promotion of maize mesocotyl elongation. Under deep-sowing condition, IAA is transported by auxin transporter-like protein 1 and binds to auxin binding protein ABP20, which results in degradation of Aux/IAA and de-repressing of auxin-inducible genes. Then, transcriptional factor such as MYB, kinase such as LRR, fructose and mannose metabolism and so on are activated. Finally, genes involved in cell wall synthesis and modification are expressed so that mesocotyl elongation of 3681-4 is promoted. Furthermore, gene expression of a key enzyme ACO in ethylene biosynthesis and ethylene receptor ETR2 were up-regulated after the treatment with 10-4 M IAA, which suggested that mesocotyl elongation of 3681-4 inclined to be inhibited when the concentration of applied IAA was increased from 10-4 M to 10-3 M. In two independent experiments, we generate 10-day-old maize mesocotyl-specific gene expression profiles through comparing genome-wide expression patterns of IAA treatment and TIBA (an auxin transportation inhibitor) treatment under 20 cm deep-sowing condition in darkness by using 17,555 Affymetrix maize whole genome array.
2009-03-26 | E-GEOD-15371 | biostudies-arrayexpress
Project description:Directional transport of auxin is critical for inflorescence and floral development in flowering plants, but the role of auxin influx carriers (AUX1 proteins) has been largely overlooked. Taking advantage of available AUX1 mutants in Setaria viridis and maize, we uncover previously unreported aspects of plant development that are affected by auxin influx, including higher order branches in the inflorescence, stigma branch number, and glume (floral bract) development, and plant fertility. However, disruption of auxin flux does not affect all parts of the plant, with little obvious effect on inflorescence meristem size, time to flowering, and anther morphology. In double mutant studies in maize, disruptions of ZmAUX1 also affect vegetative development. A GFP-tagged construct of SvAUX1 under its native promoter showed that the AUX1 protein localizes to the plasma membrane of outer tissue layers in both roots and inflorescences, and accumulates specifically in inflorescence branch meristems, consistent with the mutant phenotype and expected auxin maxima. RNA-seq analysis finds that most gene expression modules are conserved between mutant and wildtype plants, with only a few hundred genes differentially expressed in spp1 inflorescences. Using CRISPR-Cas9 technology, we disrupted SPP1 and the other four AUX1 homologs in S. viridis. SvAUX1/SPP1 has a larger effect on inflorescence development than the others, although all contribute to plant height, tiller formation, leaf, and root development. The AUX1 importers are thus not fully redundant in S. viridis. Our detailed phenotypic characterization plus a stable GFP-tagged line offer tools for future dissection of the function of auxin influx proteins.
2022-01-13 | GSE193344 | GEO
Project description:In order to elucidate the molecular mechanism of auxin-induced mesocotyl elongation, gene expression profiling analyses were performed in a deep-sowing tolerant maize inbred line 3681-4. Gene expression studies combing Affymetrix GeneChip analysis and Real-time PCR were employed to determine the molecular mechanism underlying IAA promotion of maize mesocotyl elongation. Under deep-sowing condition, IAA is transported by auxin transporter-like protein 1 and binds to auxin binding protein ABP20, which results in degradation of Aux/IAA and de-repressing of auxin-inducible genes. Then, transcriptional factor such as MYB, kinase such as LRR, fructose and mannose metabolism and so on are activated. Finally, genes involved in cell wall synthesis and modification are expressed so that mesocotyl elongation of 3681-4 is promoted. Furthermore, gene expression of a key enzyme ACO in ethylene biosynthesis and ethylene receptor ETR2 were up-regulated after the treatment with 10-4 M IAA, which suggested that mesocotyl elongation of 3681-4 inclined to be inhibited when the concentration of applied IAA was increased from 10-4 M to 10-3 M.
2009-03-26 | GSE15371 | GEO
Project description:Understanding gene regulatory networks (GRNs) is essential for improving maize yield and quality through molecular breeding approaches. The lack of comprehensive transcription factor (TF)-DNA interaction data has hindered accurate GRN predictions, limiting our insight into the regulatory mechanisms. In this study, we performed large-scale profiling of maize TF binding sites. We obtained and collected reliable binding profiles for 513 TFs, identified 394,136 binding sites, and constructed an accuracy-enhanced maize GRN (mGRN+) by integrating chromatin accessibility and gene expression data. The mGRN+ comprises 397,699 regulatory relationships. We further divided the mGRN+ into multiple modules across six major tissues. Using machine-learning algorithms, we optimized the mGRN+ to improve the prediction accuracy of gene functions and key regulators. Through independent genetic validation experiments, we further confirmed the reliability of these predictions. This work provides the largest collection of experimental TF binding sites in maize and highly optimized regulatory networks, which serve as valuable resources for studying maize gene function and crop improvement.
2025-08-06 | GSE256146 | GEO