ArticleNucleic acids research2009
Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- An analytical framework for decoding cell type-specific genetic variation of gene regulation.Nature communications · 2023Article
- Discovery of Novel Human Gene Regulatory Modules from Gene Co-expression and Promoter Motif Analysis.Scientific reports · 2017Article
- Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules.BMC bioinformatics · 2016Article
- A high definition look at the NF-Y regulome reveals genome-wide associations with selected transcription factors.Nucleic acids research · 2016Article
- A set of structural features defines the cis-regulatory modules of antenna-expressed genes in Drosophila melanogaster.PloS one · 2014Article
- Decoding a signature-based model of transcription cofactor recruitment dictated by cardinal cis-regulatory elements in proximal promoter regions.PLoS genetics · 2013Article
- Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development.Nucleic acids research · 2013Article
- A Parzen window-based approach for the detection of locally enriched transcription factor binding sites.BMC bioinformatics · 2013Article
- Incorporating motif analysis into gene co-expression networks reveals novel modular expression pattern and new signaling pathways.PLoS genetics · 2013Article
- The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding.BMC bioinformatics · 2012Article
- SP transcription factor paralogs and DNA-binding sites coevolve and adaptively converge in mammals and birds.Genome biology and evolution · 2012Article
- Article
- POWRS: position-sensitive motif discovery.PloS one · 2012Article
- Distance and helical phase dependence of synergistic transcription activation in cis-regulatory module.PloS one · 2012Article
- Enhancers regulate progression of development in mammalian cells.Nucleic acids research · 2011Article
- Inferring transcription factor complexes from ChIP-seq data.Nucleic acids research · 2011Article
- Nucleotide composition-linked divergence of vertebrate core promoter architecture.Genome research · 2011Article
- Coordinated genome-wide modifications within proximal promoter cis-regulatory elements during vertebrate evolution.Genome biology and evolution · 2011Article
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3 authors.
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Abstract
Transcriptional regulation is mediated by the collective binding of proteins called transcription factors to cis-regulatory elements. A handful of factors are known to function at particular distances from the transcription start site, although the extent to which this occurs is not well understood. Spatial dependencies can also exist between pairs of binding motifs, facilitating factor-pair interactions. We sought to determine to what extent spatial preferences measured at high-scale resolution could be utilized to predict cis-regulatory elements as well as motif-pairs binding interacting proteins. We introduce the 'motif positional function' model which predicts spatial biases using regression analysis, differentiating noise from true position-specific overrepresentation at single-nucleotide resolution. Our method predicts 48 consensus motifs exhibiting positional enrichment within human promoters, including fourteen motifs without known binding partners. We then extend the model to analyze distance preferences between pairs of motifs. We find that motif-pairs binding interacting factors often co-occur preferentially at multiple distances, with intervals between preferred distances often corresponding to the turn of the DNA double-helix. This offers a novel means by which to predict sequence elements with a collective role in gene regulation.
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