ArticlePlant physiology2014
Characterization and identification of cis-regulatory elements in Arabidopsis based on single-nucleotide polymorphism information.
Article in Plant physiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 78 citations in OpenAlex.
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- MYB transcription factors, their regulation and interactions with non-coding RNAs during drought stress in Brassica juncea.BMC plant biology · 2024Article
- Deep learning the cis-regulatory code for gene expression in selected model plants.Nature communications · 2024Article
- Dissection of the IDA promoter identifies WRKY transcription factors as abscission regulators in Arabidopsis.Journal of experimental botany · 2024Article
- AtSNP_TATAdb: Candidate Molecular Markers of Plant Advantages Related to Single Nucleotide Polymorphisms within Proximal Promoters ofInternational journal of molecular sciences · 2024Article
- Circadian gene transcription plays a role in cellular metabolism in hibernating brown bears, Ursus arctos.Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology · 2023Article
- Differentially Expressed Genes and Molecular Susceptibility to Human Age-Related Diseases.International journal of molecular sciences · 2023Article
- Distinct composition and amplification dynamics of transposable elements in sacred lotus (Nelumbo nucifera Gaertn.).The Plant journal : for cell and molecular biology · 2022Article
- Plant_SNP_TATA_Z-Tester: A Web Service That Unequivocally Estimates the Impact of Proximal Promoter Mutations on Plant Gene Expression.International journal of molecular sciences · 2022Article
- Comprehensive Expression Analyses of Plastidial Thioredoxins ofAntioxidants (Basel, Switzerland) · 2022Article
- Arabidopsis nitrate-induced aspartate oxidase gene expression is necessary to maintain metabolic balance under nitrogen nutrient fluctuation.Communications biology · 2022Article
- Characterization of APX and APX-R gene family in Brassica juncea and B. rapa for tolerance against abiotic stresses.Plant cell reports · 2022Article
- Genome-wide analysis of WRKY transcription factor genes inFrontiers in plant science · 2022Article
- The MYB family transcription factor TuODORANT1 from Triticum urartu and the homolog TaODORANT1 from Triticum aestivum inhibit seed storage protein synthesis in wheat.Plant biotechnology journal · 2021Article
- Identification of cis-regulatory motifs in first introns and the prediction of intron-mediated enhancement of gene expression in Arabidopsis thaliana.BMC genomics · 2021Article
- A novel NAC family transcription factor SPR suppresses seed storage protein synthesis in wheat.Plant biotechnology journal · 2021Article
- Tuning promoter boundaries improves regulatory motif discovery in nonmodel plants: the peach example.Plant physiology · 2021Article
- In silico analysis of promoter regions and regulatory elements (motifs and CpG islands) of the genes encoding for alcohol production in Saccharomyces cerevisiaea S288C and Schizosaccharomyces pombe 972h.Journal, genetic engineering & biotechnology · 2021Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Identifying regulatory elements and revealing their role in gene expression regulation remains a central goal of plant genome research. We exploited the detailed genomic sequencing information of a large number of Arabidopsis (Arabidopsis thaliana) accessions to characterize known and to identify novel cis-regulatory elements in gene promoter regions of Arabidopsis by relying on conservation as the hallmark signal of functional relevance. Based on the genomic layout and the obtained density profiles of single-nucleotide polymorphisms (SNPs) in sequence regions upstream of transcription start sites, the average length of promoter regions in Arabidopsis could be established at 500 bp. Genes associated with high degrees of variability of their respective upstream regions are preferentially involved in environmental response and signaling processes, while low levels of promoter SNP density are common among housekeeping genes. Known cis-elements were found to exhibit a decreased SNP density than sequence regions not associated with known motifs. For 15 known cis-element motifs, strong positional preferences relative to the transcription start site were detected based on their promoter SNP density profiles. Five novel candidate cis-element motifs were identified as consensus motifs of 17 sequence hexamers exhibiting increased sequence conservation combined with evidence of positional preferences, annotation information, and functional relevance for inducing correlated gene expression. Our study demonstrates that the currently available resolution of SNP data offers novel ways for the identification of functional genomic elements and the characterization of gene promoter sequences.
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