ArticleBMC genomics2008
Genome-wide analysis of alternative promoters of human genes using a custom promoter tiling array.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
42 citing papers in PubMed, 64 citations in OpenAlex.
- Trial
- SpliceImpactR maps alternative RNA processing events driving protein functional diversity.Nucleic acids research · 2026Article
- RBM20 isoform regulation by independent transcription start sites adapts alternative splicing in development and disease.Nature communications · 2026Article
- Novel non-coding FOXP3 transcript isoform associated to potential transcriptional interference in human regulatory T cells.RNA biology · 2025Article
- G-quadruplex structures as modulators of alternative promoter usage.NAR genomics and bioinformatics · 2025Article
- Alternative Promoters Drive Transcriptomic Reprogramming and Prognostic Stratification in TNBC.NPJ systems biology and applications · 2025Article
- U1 snRNP regulates alternative promoter activity by inhibiting premature polyadenylation.Molecular cell · 2025Article
- Quantification of single cell-type-specific alternative transcript initiation.bioRxiv : the preprint server for biology · 2025Article
- G-quadruplex forming regions in GCK and TM6SF2 are targets for differential DNA methylation in metabolic disease and hepatocellular carcinoma patients.Scientific reports · 2024Article
- Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes.Nature communications · 2023Article
- Integrative analysis of Iso-Seq and RNA-seq reveals dynamic changes of alternative promoter, alternative splicing and alternative polyadenylation during Angiotensin II-induced senescence in rat primary aortic endothelial cells.Frontiers in genetics · 2023Article
- Super-enhanced MARCO variant drives triple-negative breast cancer progression.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- A large deletion at the cortex locus eliminates butterfly wing patterning.G3 (Bethesda, Md.) · 2022Article
- Hippocampal ceRNA networks from chronic intermittent ethanol vapor-exposed male mice and functional analysis of top-ranked lncRNA genes for ethanol drinking phenotypes.Advances in drug and alcohol research · 2022Article
- Article
- Promoter switching in response to changing environment and elevated expression of protein-coding genes overlapping at their 5' ends.Scientific reports · 2021Article
- Cancer Epigenomics and Beyond: Advancing the Precision Oncology Paradigm.Journal of immunotherapy and precision oncology · 2020Review
- Tumor-Based Genetic Testing and Familial Cancer Risk.Cold Spring Harbor perspectives in medicine · 2020Review
- Article
- Expressional activation and functional roles of human endogenous retroviruses in cancers.Reviews in medical virology · 2019Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundIndependent lines of evidence suggested that a large fraction of human genes possess multiple promoters driving gene expression from distinct transcription start sites. Understanding which promoter is employed in which cellular context is required to unravel gene regulatory networks within the cell.
resultsWe have developed a custom microarray platform that tiles roughly 35,000 alternative putative promoters from nearly 7,000 genes in the human genome. To demonstrate the utility of this array platform, we have analyzed the patterns of promoter usage in 17beta-estradiol (E2)-treated and untreated MCF7 cells and show widespread usage of alternative promoters. Most intriguingly, we show that the downstream promoter in E2-sensitive multiple promoter genes tends to be very close to the 3'-terminus of the gene, suggesting exotic mechanisms of expression regulation in these genes.
conclusionThe usage of alternative promoters greatly multiplies the transcriptional complexity available within the human genome. The fact that many of these promoters are incapable of driving the synthesis of a meaningful protein-encoding transcript further complicates the story.
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Registered trials
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.