ArticleScientific reports2016
Positional distribution of transcription factor binding sites in Arabidopsis thaliana.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers, 1 of them a synthesis that pooled it.
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71 citing papers in PubMed, 1 synthesis or guideline pooled it, 132 citations in OpenAlex.
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- Positional grammar of transcription factor binding partitions developmental and stress-response regulation in plants.Nature communications · 2026Article
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- Synthetic promoter design in plants: integration of computational and experimental approaches.Frontiers in plant science · 2026Review
- Promoter Motif Profiling and Binding Site Distribution Analysis of Transcription Factors Predict Auto- and Cross-Regulatory Mechanisms inInternational journal of molecular sciences · 2025Article
- Episodic and Ongoing Mechanisms Drive Plastid-Derived Nuclear DNA Evolution in Angiosperms.Genome biology and evolution · 2025Article
- GOLEM: A tool for visualizing the distribution of Gene regulatOry eLEMents within the plant promoters with a focus on male gametophyte.The Plant journal : for cell and molecular biology · 2025Article
- Profiling conserved transcription factor binding motifs in Phaseolus vulgaris through comparative genomics.BMC genomics · 2025Article
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- CAX-INTERACTING PROTEIN4 depletion causes early lethality and pre-mRNA missplicing in Arabidopsis.Plant physiology · 2024Article
- Identification of a 301 bp promoter core region of the SrUGT91D2 gene from Stevia rebaudiana that contributes to hormone and abiotic stress inducibility.BMC plant biology · 2024Article
- A comparative analysis of ENCODE and Cistrome in the context of TF binding signal.BMC genomics · 2024Article
- CXIP4 depletion causes early lethality and pre-mRNA missplicing in Arabidopsis.bioRxiv : the preprint server for biology · 2024Article
- Deep learning the cis-regulatory code for gene expression in selected model plants.Nature communications · 2024Article
- Genomic analyses elucidateEcology and evolution · 2024Article
- Cacao pod transcriptome profiling of seven genotypes identifies features associated with post-penetration resistance to Phytophthora palmivora.Scientific reports · 2024Article
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- Sea-ATI unravels novel vocabularies of plant active cistrome.Nucleic acids research · 2023Article
11 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Binding of a transcription factor (TF) to its DNA binding sites (TFBSs) is a critical step to initiate the transcription of its target genes. It is therefore interesting to know where the TFBSs of a gene are likely to locate in the promoter region. Here we studied the positional distribution of TFBSs in Arabidopsis thaliana, for which many known TFBSs are now available. We developed a method to identify the locations of TFBSs in the promoter sequences of genes in A. thaliana. We found that the distribution is nearly bell-shaped with a peak at 50 base pairs (bp) upstream of the transcription start site (TSS) and 86% of the TFBSs are in the region from -1,000 bp to +200 bp with respect to the TSS. Our distribution was supported by chromatin immunoprecipitation sequencing and microarray data and DNase I hypersensitive site sequencing data. When TF families were considered separately, differences in positional preference were observed between TF families. Our study of the positional distribution of TFBSs seems to be the first in a plant.
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