ArticleNucleic acids research2009
CpG-depleted promoters harbor tissue-specific transcription factor binding signals--implications for motif overrepresentation analyses.
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 28 papers.
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Who cites it
28 citing papers in PubMed.
- Mechanisms and functional implications of long-range enhancer-dependent gene regulation.Nature genetics · 2026Review
- Loss of Kmt2c or Kmt2d primes urothelium for tumorigenesis and redistributes KMT2A-menin to bivalent promoters.Nature genetics · 2025Article
- Cooperative insulation of regulatory domains by CTCF-dependent physical insulation and promoter competition.Nature communications · 2024Article
- Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation.PLoS computational biology · 2023Article
- Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes.Nature communications · 2023Article
- Expression regulation of genes is linked to their CpG density distributions around transcription start sites.Life science alliance · 2022Article
- Enhancer-gene specificity in development and disease.Development (Cambridge, England) · 2022Review
- Quantifying the tissue-specific regulatory information within enhancer DNA sequences.NAR genomics and bioinformatics · 2021Article
- TATA and paused promoters active in differentiated tissues have distinct expression characteristics.Molecular systems biology · 2021Article
- CpG content-dependent associations between transcription factors and histone modifications.PloS one · 2021Article
- Sequence Characteristics Distinguish Transcribed Enhancers from Promoters and Predict Their Breadth of Activity.Genetics · 2019Article
- Eukaryotic core promoters and the functional basis of transcription initiation.Nature reviews. Molecular cell biology · 2018Review
- Functional conservation of sequence determinants at rapidly evolving regulatory regions across mammals.PLoS computational biology · 2018Article
- Developmental alterations in Huntington's disease neural cells and pharmacological rescue in cells and mice.Nature neuroscience · 2017Article
- Hyper- and hypo- nutrition studies of the hepatic transcriptome and epigenome suggest that PPARα regulates anaerobic glycolysis.Scientific reports · 2017Article
- Article
- CpG island-mediated global gene regulatory modes in mouse embryonic stem cells.Nature communications · 2014Article
- Chromatin and epigenetic features of long-range gene regulation.Nucleic acids research · 2013Review
- A Parzen window-based approach for the detection of locally enriched transcription factor binding sites.BMC bioinformatics · 2013Article
- Sequence signatures extracted from proximal promoters can be used to predict distal enhancers.Genome biology · 2013Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motif overrepresentation analysis of proximal promoters is a common approach to characterize the regulatory properties of co-expressed sets of genes. Here we show that these approaches perform well on mammalian CpG-depleted promoter sets that regulate expression in terminally differentiated tissues such as liver and heart. In contrast, CpG-rich promoters show very little overrepresentation signal, even when associated with genes that display highly constrained spatiotemporal expression. For instance, while approximately 50% of heart specific genes possess CpG-rich promoters we find that the frequently observed enrichment of MEF2-binding sites upstream of heart-specific genes is solely due to contributions from CpG-depleted promoters. Similar results are obtained for all sets of tissue-specific genes indicating that CpG-rich and CpG-depleted promoters differ fundamentally in their distribution of regulatory inputs around the transcription start site. In order not to dilute the respective transcription factor binding signals, the two promoter types should thus be treated as separate sets in any motif overrepresentation analysis.
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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.