ArticlePloS one2011
Speeding cis-trans regulation discovery by phylogenomic analyses coupled with screenings of an arrayed library of Arabidopsis transcription factors.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 83 citations in OpenAlex.
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- Membrane-associated DELLA degradation modulates growth under carbon/nitrogen imbalance.The Plant cell · 2026Article
- TCP3 is a substrate of the COP1/SPA ubiquitin ligase to regulate anthocyanin accumulation and flowering time inProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Workflow to Select Functional Promoter DNA Baits and Screen Arrayed Gene Libraries in Yeast.Current protocols · 2024Article
- A quantitative gibberellin signaling biosensor reveals a role for gibberellins in internode specification at the shoot apical meristem.Nature communications · 2024Article
- Expression of the Arabidopsis redox-related LEA protein, SAG21 is regulated by ERF, NAC and WRKY transcription factors.Scientific reports · 2024Article
- Identification, evolution, and expression of GDSL-type Esterase/Lipase (GELP) gene family in three cotton species: a bioinformatic analysis.BMC genomics · 2023Article
- Heat shock factor HSFA2 fine-tunes resetting of thermomemory via plastidic metalloprotease FtsH6.Journal of experimental botany · 2022Article
- The Seed Development FactorsGenes · 2021Article
- A Molecular Signal Integration Network Underpinning Arabidopsis Seed Germination.Current biology : CB · 2020Article
- UV-B photoreceptor UVR8 interacts with MYB73/MYB77 to regulate auxin responses and lateral root development.The EMBO journal · 2020Article
- PDIL1-2 can indirectly and negatively regulate expression of the AGPL1 gene in bread wheat.Biological research · 2019Article
- A Regulatory Module Controlling GA-Mediated Endosperm Cell Expansion Is Critical for Seed Germination in Arabidopsis.Molecular plant · 2019Article
- An Integrative Approach to Analyze Seed Germination inFrontiers in plant science · 2019Article
- Molecular and epigenetic regulations and functions of the LAFL transcriptional regulators that control seed development.Plant reproduction · 2018Review
- Cis and trans determinants of epigenetic silencing by Polycomb repressive complex 2 in Arabidopsis.Nature genetics · 2017Article
- Mitochondrial AtTrxo1 is transcriptionally regulated by AtbZIP9 and AtAZF2 and affects seed germination under saline conditions.Journal of experimental botany · 2017Article
- JUNGBRUNNEN1 Confers Drought Tolerance Downstream of the HD-Zip I Transcription Factor AtHB13.Frontiers in plant science · 2017Article
- Cytokinin response factors regulate PIN-FORMED auxin transporters.Nature communications · 2015Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcriptional regulation is an important mechanism underlying gene expression and has played a crucial role in evolution. The number, position and interactions between cis-elements and transcription factors (TFs) determine the expression pattern of a gene. To identify functionally relevant cis-elements in gene promoters, a phylogenetic shadowing approach with a lipase gene (LIP1) was used. As a proof of concept, in silico analyses of several Brassicaceae LIP1 promoters identified a highly conserved sequence (LIP1 element) that is sufficient to drive strong expression of a reporter gene in planta. A collection of ca. 1,200 Arabidopsis thaliana TF open reading frames (ORFs) was arrayed in a 96-well format (RR library) and a convenient mating based yeast one hybrid (Y1H) screening procedure was established. We constructed an episomal plasmid (pTUY1H) to clone the LIP1 element and used it as bait for Y1H screenings. A novel interaction with an HD-ZIP (AtML1) TF was identified and abolished by a 2 bp mutation in the LIP1 element. A role of this interaction in transcriptional regulation was confirmed in planta. In addition, we validated our strategy by reproducing the previously reported interaction between a MYB-CC (PHR1) TF, a central regulator of phosphate starvation responses, with a conserved promoter fragment (IPS1 element) containing its cognate binding sequence. Finally, we established that the LIP1 and IPS1 elements were differentially bound by HD-ZIP and MYB-CC family members in agreement with their genetic redundancy in planta. In conclusion, combining in silico analyses of orthologous gene promoters with Y1H screening of the RR library represents a powerful approach to decipher cis- and trans-regulatory codes.
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