ArticleBMC bioinformatics2008
Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 19 citations in OpenAlex.
- MEPP: more transparent motif enrichment by profiling positional correlations.NAR genomics and bioinformatics · 2022Article
- Deep neural networks identify sequence context features predictive of transcription factor binding.Nature machine intelligence · 2021Article
- Specific protein 1, c-Abl and ERK1/2 form a regulatory loop.Journal of cell science · 2019Article
- Beyond Transcription: Roles of Transcription Factors in Pre-mRNA Splicing.Chemical reviews · 2018Review
- Spatial promoter recognition signatures may enhance transcription factor specificity in yeast.PloS one · 2013Article
- Unbiased proteomic analysis of proteins interacting with the HIV-1 5'LTR sequence: role of the transcription factor Meis.Nucleic acids research · 2012Article
- Gis1 and Rph1 regulate glycerol and acetate metabolism in glucose depleted yeast cells.PloS one · 2012Article
- Identification of context-dependent motifs by contrasting ChIP binding data.Bioinformatics (Oxford, England) · 2010Article
- Many sequence-specific chromatin modifying protein-binding motifs show strong positional preferences for potential regulatory regions in the Saccharomyces cerevisiae genome.Nucleic acids research · 2010Article
- Nucleosomal context of binding sites influences transcription factor binding affinity and gene regulation.Genomics, proteomics & bioinformatics · 2009Article
- Mechanisms and evolution of control logic in prokaryotic transcriptional regulation.Microbiology and molecular biology reviews : MMBR · 2009Review
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe rate of mRNA transcription is controlled by transcription factors that bind to specific DNA motifs in promoter regions upstream of protein coding genes. Recent results indicate that not only the presence of a motif but also motif context (for example the orientation of a motif or its location relative to the coding sequence) is important for gene regulation.
resultsIn this study we present ContextFinder, a tool that is specifically aimed at identifying cases where motif context is likely to affect gene regulation. We used ContextFinder to examine the role of motif context in S. cerevisiae both for DNA binding by transcription factors and for effects on gene expression. For DNA binding we found significant patterns of motif location bias, whereas motif orientations did not seem to matter. Motif context appears to affect gene expression even more than it affects DNA binding, as biases in both motif location and orientation were more frequent in promoters of co-expressed genes. We validated our results against data on nucleosome positioning, and found a negative correlation between preferred motif locations and nucleosome occupancy.
conclusionWe conclude that the requirement for stable binding of transcription factors to DNA and their subsequent function in gene regulation can impose constraints on motif context.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.