ArticleGenome research2006
Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome.
Article in Genome research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 143 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.
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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
143 citing papers in PubMed, 277 citations in OpenAlex.
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- Stage-resolved gene regulatory network analysis reveals developmental reprogramming and genes with robust stem-preferred expression in sorghum.BMC plant biology · 2025Article
- Transcription Dynamics and DNA Methylation Responses to Growth Modification.Marine biotechnology (New York, N.Y.) · 2025Article
- Charting the regulatory landscape of TP53 on transposable elements in cancer.Genome research · 2025Article
- Dissecting the Kaiso binding profile in clear renal cancer cells.Epigenetics & chromatin · 2024Article
- Augusta: From RNA-Seq to gene regulatory networks and Boolean models.Computational and structural biotechnology journal · 2024Article
- Review
- Latent Dirichlet allocation mixture models for nucleotide sequence analysis.NAR genomics and bioinformatics · 2024Article
- Alternative TSS use is widespread in Cryptococcus fungi in response to environmental cues and regulated genome-wide by the transcription factor Tur1.PLoS biology · 2024Article
- Review
- A Young Boy with 21q21.1 Microdeletion Showing Speech Delay, Spastic Diplegia, and MRI Abnormalities: Original Case Report.Global medical genetics · 2023Article
- DNA Methylation of the Dopamine TransporterInternational journal of molecular sciences · 2023Article
- On the Role of TATA Boxes and TATA-Binding Protein inPlants (Basel, Switzerland) · 2023Review
- A synthetic transcription platform for programmable gene expression in mammalian cells.Nature communications · 2022Article
- Epigenetic responses to heat: From adaptation to maladaptation.Experimental physiology · 2022Review
- Article
- Bioinformatic Design of Dendritic Cell-Specific Synthetic Promoters.ACS synthetic biology · 2022Article
- Muscle-Specific Cellular and Molecular Adaptations to Late-Life Voluntary Concurrent Exercise.Function (Oxford, England) · 2022Article
83 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Transcriptional promoters comprise one of many classes of eukaryotic transcriptional regulatory elements. Identification and characterization of these elements are vital to understanding the complex network of human gene regulation. Using full-length cDNA sequences to identify transcription start sites (TSS), we predicted more than 900 putative human transcriptional promoters in the ENCODE regions, representing a comprehensive sampling of promoters in 1% of the genome. We identified 387 fragments that function as promoters in at least one of 16 cell lines by measuring promoter activity in high-throughput transient transfection reporter assays. These positive functional results demonstrate widespread use of alternative promoters. We show a strong correlation between promoter activity and the corresponding endogenous RNA transcript levels, providing the first experimental quantitative estimate of promoter contribution to gene regulation. Finally, we identified functional regions within a randomly selected subset of 45 promoters using deletion analyses. These experiments showed that, on average, the sequence -300 to -50 bp of the TSS positively contributes to core promoter activity. Interestingly, putative negative elements were identified -1000 to -500 bp upstream of the TSS for 55% of genes tested. These data provide the largest and most comprehensive view of promoter function in the human genome.
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What OpenQuestion holds
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.