ArticlePlant physiology2003
Identification of promoter motifs involved in the network of phytochrome A-regulated gene expression by combined analysis of genomic sequence and microarray data.
Article in Plant physiology, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 111 papers, 2 of them syntheses that pooled it.
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Who cites it
111 citing papers in PubMed, 2 syntheses or guidelines pooled it, 261 citations in OpenAlex.
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- IGT/LAZY genes are differentially influenced by light and required for light-induced change to organ angle.BMC biology · 2024Article
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- Evolutionary insights and expression dynamics of the CaNFYB transcription factor gene family in pepper (Frontiers in genetics · 2023Article
- Genome-scale analysis of Arabidopsis splicing-related protein kinase families reveals roles in abiotic stress adaptation.BMC plant biology · 2022Article
- Molecular Cloning and Functional Characterization of a β-Glucosidase Gene to Produce Platycodin D inFrontiers in plant science · 2022Article
- In silico analysis of promoter region and regulatory elements of mitogenome co-expressed trn gene clusters encoding for bio-pesticide in entomopathogenic fungus, Metarhizium anisopliae: strain ME1.Journal, genetic engineering & biotechnology · 2021Article
- The gene expression profiles of mitochondrial respiratory components in Arabidopsis plants with differing amounts ofPlant signaling & behavior · 2021Article
- Characterizing Promoter and Enhancer Sequences by a Deep Learning Method.Frontiers in genetics · 2021Article
- Chloroplasts in C3 grasses move in response to blue-light.Plant cell reports · 2020Article
- Interspecific analysis of diurnal gene regulation in panicoid grasses identifies known and novel regulatory motifs.BMC genomics · 2020Article
- The SWI/SNF ATP-Dependent Chromatin Remodeling Complex in Arabidopsis Responds to Environmental Changes in Temperature-Dependent Manner.International journal of molecular sciences · 2020Article
- Identification and Functional Characterization of a Soybean (Plants (Basel, Switzerland) · 2019Article
- Different copies of SENSITIVITY TO RED LIGHT REDUCED 1 show strong subfunctionalization in Brassica napus.BMC plant biology · 2019Article
- CALMODULIN-BINDING TRANSCRIPTION ACTIVATOR 6: A Key Regulator of NaPlant physiology · 2019Article
51 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Several hundred Arabidopsis genes, transcriptionally regulated by phytochrome A (phyA), were previously identified using an oligonucleotide microarray. We have now identified, in silico, conserved sequence motifs in the promoters of these genes by comparing the promoter sequences to those of all the genes present on the microarray from which they were sampled. This was done using a Perl script (called Sift) that identifies over-represented motifs using an enumerative approach. The utility of Sift was verified by analysis of circadian-regulated promoters known to contain a biologically significant motif. Several elements were then identified in phyA-responsive promoters by their over-representation. Five previously undescribed motifs were detected in the promoters of phyA-induced genes. Four novel motifs were found in phyA-repressed promoters, plus a motif that strongly resembles the DE1 element. The G-box, CACGTG, was a prominent hit in both induced and repressed phyA-responsive promoters. Intriguingly, two distinct flanking consensus sequences were observed adjacent to the G-box core sequence: one predominating in phyA-induced promoters, the other in phyA-repressed promoters. Such different conserved flanking nucleotides around the core motif in these two sets of promoters may indicate that different members of the same family of DNA-binding proteins mediate phyA induction and repression. An increased abundance of G-box sequences was observed in the most rapidly phyA-responsive genes and in the promoters of phyA-regulated transcription factors, indicating that G-box-binding transcription factors are upstream components in a transcriptional cascade that mediates phyA-regulated development.
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