ArticleGenome research2007
Transcription factor binding and modified histones in human bidirectional promoters.
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers.
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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.
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Who cites it
82 citing papers in PubMed, 142 citations in OpenAlex.
- Lineage-associated Human Divergently-paired Genes Exhibit Structural and Regulatory Characteristics.Genomics, proteomics & bioinformatics · 2025Article
- Genomic Analysis and Functional Validation of Bidirectional Promoters in Medaka (International journal of molecular sciences · 2024Article
- Selection on synonymous codon usage in soybean (Glycine max) WRKY genes.Scientific reports · 2024Article
- Review
- Abundant binary promoter switches in lineage-determining transcription factors indicate a digital component of cell fate determination.Cell reports · 2023Article
- E-box binding transcription factors in cancer.Frontiers in oncology · 2023Review
- Cell cycle regulation of the psoriasis associated gene CCHCR1 by transcription factor E2F1.PloS one · 2023Article
- The fate of notch-1 transcript is linked to cell cycle dynamics by activity of a natural antisense transcript.Nucleic acids research · 2021Article
- Genetic and epigenetic features of promoters with ubiquitous chromatin accessibility support ubiquitous transcription of cell-essential genes.Nucleic acids research · 2021Article
- Co-regulation and function ofeLife · 2021Article
- Natural antisense transcripts in the biological hallmarks of cancer: powerful regulators hidden in the dark.Journal of experimental & clinical cancer research : CR · 2020Review
- Pan-Cancer Analysis of Head-to-Head Gene Pairs in Terms of Transcriptional Activity, Co-expression and Regulation.Frontiers in genetics · 2020Article
- Sustained transgene expression from sleeping beauty DNA transposons containing a core fragment of the HNRPA2B1-CBX3 ubiquitous chromatin opening element (UCOE).BMC biotechnology · 2019Article
- Computational analysis of the evolutionarily conserved Missing In Metastasis/Metastasis Suppressor 1 gene predicts novel interactions, regulatory regions and transcriptional control.Scientific reports · 2019Article
- Gonadal supporting cells acquire sex-specific chromatin landscapes during mammalian sex determination.Developmental biology · 2019Article
- Article
- Integrative analysis of single-cell expression data reveals distinct regulatory states in bidirectional promoters.Epigenetics & chromatin · 2018Article
- Interplay between NRF1, E2F4 and MYC transcription factors regulating common target genes contributes to cancer development and progression.Cellular oncology (Dordrecht, Netherlands) · 2018Review
- Bidirectional promoters exhibit characteristic chromatin modification signature associated with transcription elongation in both sense and antisense directions.BMC genomics · 2018Article
- Kynurenine 3-Monooxygenase Gene Associated With Nicotine Initiation and Addiction: Analysis of Novel Regulatory Features at 5' and 3'-Regions.Frontiers in genetics · 2018Article
22 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
Bidirectional promoters have received considerable attention because of their ability to regulate two downstream genes (divergent genes). They are also highly abundant, directing the transcription of approximately 11% of genes in the human genome. We categorized the presence of DNA sequence motifs, binding of transcription factors, and modified histones as overrepresented, shared, or underrepresented in bidirectional promoters with respect to unidirectional promoters. We found that a small set of motifs, including GABPA, MYC, E2F1, E2F4, NRF-1, CCAAT, YY1, and ACTACAnnTCC are overrepresented in bidirectional promoters, while the majority (73%) of known vertebrate motifs are underrepresented. We performed chromatin-immunoprecipitation (ChIP), followed by quantitative PCR for GABPA, on 118 regions in the human genome and showed that it binds to bidirectional promoters more frequently than unidirectional promoters, and its position-specific scoring matrix is highly predictive of binding. Signatures of active transcription, such as occupancy of RNA polymerase II and the modified histones H3K4me2, H3K4me3, and H3ac, are overrepresented in regions around bidirectional promoters, suggesting that a higher fraction of divergent genes are transcribed in a given cell than the fraction of other genes. Accordingly, analysis of whole-genome microarray data indicates that 68% of divergent genes are transcribed compared with 44% of all human genes. By combining the analysis of publicly available ENCODE data and a detailed study of GABPA, we survey bidirectional promoters with breadth and depth, leading to biological insights concerning their motif composition and bidirectional regulatory mode.
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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.