ArticleBMC genomics2014
Computational analysis of auxin responsive elements in the Arabidopsis thaliana L. genome.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
28 citing papers in PubMed, 1 synthesis or guideline pooled it, 78 citations in OpenAlex.
- Pooled it
- Co-transformation using T-DNA genes from Agrobacterium strain 82.139 enhances regeneration of transgenic shoots in Populus.Plant biotechnology journal · 2025Article
- Stochastic gene expression in auxin signaling in the floral meristem of Arabidopsis thaliana.Nature communications · 2025Article
- Spatial transcriptome analysis reveals de novo regeneration of poplar roots.Horticulture research · 2024Article
- OsMYB7 determines leaf angle at the late developmental stage of lamina joints in rice.Frontiers in plant science · 2023Article
- An Evidence Theory and Fuzzy Logic Combined Approach for the Prediction of Potential ARF-Regulated Genes in Quinoa.Plants (Basel, Switzerland) · 2022Article
- On the trail of auxin: Reporters and sensors.The Plant cell · 2022Review
- Methyl Jasmonate Activates theMolecules (Basel, Switzerland) · 2022Article
- Microtubule-based perception of mechanical conflicts controls plant organ morphogenesis.Science advances · 2022Article
- Characterization of Transcription Regulatory Domains of OsMADS29: Identification of Proximal Auxin-Responsive Domains and a Strong Distal Negative Element.Frontiers in plant science · 2022Article
- An Essential Function for Auxin in Embryo Development.Cold Spring Harbor perspectives in biology · 2021Review
- It's Morphin' time: how multiple signals converge on ARF transcription factors to direct development.Current opinion in plant biology · 2020Review
- Architecture of DNA elements mediating ARF transcription factor binding and auxin-responsive gene expression inProceedings of the National Academy of Sciences of the United States of America · 2020Article
- The HD-ZIP II Transcription Factors Regulate Plant Architecture through the Auxin Pathway.International journal of molecular sciences · 2020Article
- Specificity in Auxin Responses Is Not Explained by the Promoter Preferences of Activator ARFs.Plant physiology · 2020Article
- Functional dissection of the DORNRÖSCHEN-LIKE enhancer 2 during embryonic and phyllotactic patterning.Planta · 2020Article
- Deep Conservation ofThe Plant cell · 2019Article
- Article
- Article
- The DNA binding landscape of the maize AUXIN RESPONSE FACTOR family.Nature communications · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Auxin responsive elements (AuxRE) were found in upstream regions of target genes for ARFs (Auxin response factors). While Chip-seq data for most of ARFs are still unavailable, prediction of potential AuxRE is restricted by consensus models that detect too many false positive sites. Using sequence analysis of experimentally proven AuxREs, we revealed both an extended nucleotide context pattern for AuxRE itself and three distinct types of its coupling motifs (Y-patch, AuxRE-like, and ABRE-like), which together with AuxRE may form the composite elements. Computational analysis of the genome-wide distribution of the predicted AuxREs and their impact on auxin responsive gene expression allowed us to conclude that: (1) AuxREs are enriched around the transcription start site with the maximum density in 5'UTR; (2) AuxREs mediate auxin responsive up-regulation, not down-regulation. (3) Directly oriented single AuxREs and reverse multiple AuxREs are mostly associated with auxin responsiveness. In the composite AuxRE elements associated with auxin response, ABRE-like and Y-patch are 5'-flanking or overlapping AuxRE, whereas AuxRE-like motif is 3'-flanking. The specificity in location and orientation of the coupling elements suggests them as potential binding sites for ARFs partners.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.