ArticleBMC genomics2007
Positional bias of general and tissue-specific regulatory motifs in mouse gene promoters.
Article in BMC genomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 24 citations in OpenAlex.
- Article
- Assessment of DDAH1 and DDAH2 Contributions to Psychiatric Disorders via In Silico Methods.International journal of molecular sciences · 2022Article
- Characterization of gene promoters in pig: conservative elements, regulatory motifs and evolutionary trend.PeerJ · 2019Article
- Article
- An integrated transcriptomics-guided genome-wide promoter analysis and next-generation proteomics approach to mine factor(s) regulating cellular differentiation.DNA research : an international journal for rapid publication of reports on genes and genomes · 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
- Transcription Factor RFX2 Is a Key Regulator of Mouse Spermiogenesis.Scientific reports · 2016Article
- Enhancers: holding out for the right promoter.Current biology : CB · 2015Article
- Juvenile hormone and its receptor, methoprene-tolerant, control the dynamics of mosquito gene expression.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Genome-wide prediction and functional validation of promoter motifs regulating gene expression in spore and infection stages of Phytophthora infestans.PLoS pathogens · 2013Article
- A Parzen window-based approach for the detection of locally enriched transcription factor binding sites.BMC bioinformatics · 2013Article
- Cell-specific occupancy of an extended repertoire of CREM and CREB binding loci in male germ cells.BMC genomics · 2010Article
- PriorsEditor: a tool for the creation and use of positional priors in motif discovery.Bioinformatics (Oxford, England) · 2010Article
- TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation.BMC genomics · 2010Article
- RFX2 is a candidate downstream amplifier of A-MYB regulation in mouse spermatogenesis.BMC developmental biology · 2009Article
- Interferon-gamma is a critical modulator of CB(2) cannabinoid receptor signaling during neuropathic pain.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2008Article
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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
backgroundThe arrangement of regulatory motifs in gene promoters, or promoter architecture, is the result of mutation and selection processes that have operated over many millions of years. In mammals, tissue-specific transcriptional regulation is related to the presence of specific protein-interacting DNA motifs in gene promoters. However, little is known about the relative location and spacing of these motifs. To fill this gap, we have performed a systematic search for motifs that show significant bias at specific promoter locations in a large collection of housekeeping and tissue-specific genes.
resultsWe observe that promoters driving housekeeping gene expression are enriched in particular motifs with strong positional bias, such as YY1, which are of little relevance in promoters driving tissue-specific expression. We also identify a large number of motifs that show positional bias in genes expressed in a highly tissue-specific manner. They include well-known tissue-specific motifs, such as HNF1 and HNF4 motifs in liver, kidney and small intestine, or RFX motifs in testis, as well as many potentially novel regulatory motifs. Based on this analysis, we provide predictions for 559 tissue-specific motifs in mouse gene promoters.
conclusionThe study shows that motif positional bias is an important feature of mammalian proximal promoters and that it affects both general and tissue-specific motifs. Motif positional constraints define very distinct promoter architectures depending on breadth of expression and type of tissue.
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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.