ArticleNucleic acids research2003
Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information.
Article in Nucleic acids research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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43 citing papers in PubMed.
- Unlocking the Regulatory Genome: Interpreting the Clinical Impact of Noncoding Variants in Genetic Cardiomyopathies.Circulation. Genomic and precision medicine · 2026Review
- Integrated RNA-seq and DNase-seq analyses identify phenotype-specific BMP4 signaling in breast cancer.BMC genomics · 2017Article
- Differential Nucleosome Occupancies across Oct4-Sox2 Binding Sites in Murine Embryonic Stem Cells.PloS one · 2015Article
- Computational analysis of auxin responsive elements in the Arabidopsis thaliana L. genome.BMC genomics · 2014Article
- Functional Brachyury binding sites establish a temporal read-out of gene expression in the Ciona notochord.PLoS biology · 2013Article
- Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development.Nucleic acids research · 2013Article
- Transcription factors in late megakaryopoiesis and related platelet disorders.Journal of thrombosis and haemostasis : JTH · 2013Review
- A robust and sensitive synthetic sensor to monitor the transcriptional output of the cytokinin signaling network in planta.Plant physiology · 2013Article
- Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy.PLoS genetics · 2013Article
- The cis-regulatory code of Hox function in Drosophila.The EMBO journal · 2012Article
- CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation.Nucleic acids research · 2012Article
- Identification of co-occurring transcription factor binding sites from DNA sequence using clustered position weight matrices.Nucleic acids research · 2012Article
- Functional analysis of the Arabidopsis PLDZ2 promoter reveals an evolutionarily conserved low-Pi-responsive transcriptional enhancer element.Journal of experimental botany · 2012Article
- A novel candidate cis-regulatory motif pair in the promoters of germline and oogenesis genes in C. elegans.Genome research · 2012Article
- COPS: detecting co-occurrence and spatial arrangement of transcription factor binding motifs in genome-wide datasets.PloS one · 2012Article
- Enhancers regulate progression of development in mammalian cells.Nucleic acids research · 2011Article
- Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development.PLoS genetics · 2011Article
- WordCluster: detecting clusters of DNA words and genomic elements.Algorithms for molecular biology : AMB · 2011Article
- CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors.Genome research · 2010Article
- Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression.PLoS computational biology · 2010Article
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4 authors.
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Abstract
We explored distance preferences in the arrangement of binding motifs for five transcription factors (Bicoid, Krüppel, Hunchback, Knirps and Caudal) in a large set of Drosophila cis-regulatory modules (CRMs). Analysis of non-overlapping binding motifs revealed the presence of periodic signals specific to particular combinations of binding motifs. The most striking periodic signals (10 bp for Bicoid and 11 bp for Hunchback) suggest preferential positioning of some binding site combinations on the same side of the DNA helix. We also analyzed distance preferences in arrangements of highly correlated overlapping binding motifs, such as Bicoid and Krüppel. Based on the distance analysis, we extracted preferential binding site arrangements and proposed models for potential composite elements (CEs) and antagonistic motif pairs involved in the function of developmental CRMs. Our results suggest that there are distinct hierarchical levels in the organization of transcription regulatory information. We discuss the role of the hierarchy in understanding transcriptional regulation and in detection of transcription regulatory regions in genomes.
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