ArticleGenome research2010
Sequence features that drive human promoter function and tissue specificity.
Article in Genome research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed, 108 citations in OpenAlex.
- Article
- Design and initial characterization of a novel mini-promoter for gene therapies targeting the central nervous system.Molecular therapy. Advances · 2026Article
- Sequence-based modeling of low-affinity transcription factor-DNA binding through deep learning.NAR genomics and bioinformatics · 2026Article
- Tissue-specific and tissue-agnostic effects of genome sequence variation modulating blood pressure.Cell reports · 2023Article
- Review
- Article
- Massively parallel reporter perturbation assays uncover temporal regulatory architecture during neural differentiation.Nature communications · 2022Article
- Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq.Nucleic acids research · 2021Article
- Nuclear FGFR1 Regulates Gene Transcription and Promotes Antiestrogen Resistance in ERClinical cancer research : an official journal of the American Association for Cancer Research · 2021Article
- Genetic and epigenetic features of promoters with ubiquitous chromatin accessibility support ubiquitous transcription of cell-essential genes.Nucleic acids research · 2021Article
- Transcription initiation of distant core promoters in a large-sized genome of an insect.BMC biology · 2021Article
- CD28 Gene Polymorphisms in the Promoter Region Are Associated with Transfusion Reactions: A Functional Study.Journal of clinical medicine · 2021Article
- Long first exons and epigenetic marks distinguish conserved pachytene piRNA clusters from other mammalian genes.Nature communications · 2021Article
- Review
- Pervasive and CpG-dependent promoter-like characteristics of transcribed enhancers.Nucleic acids research · 2020Article
- TheG3 (Bethesda, Md.) · 2020Article
- Determinants of enhancer and promoter activities of regulatory elements.Nature reviews. Genetics · 2020Review
- A comparison of curated gene sets versus transcriptomics-derived gene signatures for detecting pathway activation in immune cells.BMC bioinformatics · 2020Article
- Analysis of endogenous and exogenous tumor upregulated promoter expression in canine tumors.PloS one · 2020Article
- A report on DNA sequence determinants in gene expression.Bioinformation · 2020Article
2 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
8 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Promoters are important regulatory elements that contain the necessary sequence features for cells to initiate transcription. To functionally characterize a large set of human promoters, we measured the transcriptional activities of 4575 putative promoters across eight cell lines using transient transfection reporter assays. In parallel, we measured gene expression in the same cell lines and observed a significant correlation between promoter activity and endogenous gene expression (r = 0.43). As transient transfection assays directly measure the promoting effect of a defined fragment of DNA sequence, decoupled from epigenetic, chromatin, or long-range regulatory effects, we sought to predict whether a promoter was active using sequence features alone. CG dinucleotide content was highly predictive of ubiquitous promoter activity, necessitating the separation of promoters into two groups: high CG promoters, mostly ubiquitously active, and low CG promoters, mostly cell line-specific. Computational models trained on the binding potential of transcriptional factor (TF) binding motifs could predict promoter activities in both high and low CG groups: average area under the receiver operating characteristic curve (AUC) of the models was 91% and exceeded the AUC of CG content by an average of 23%. Known relationships, for example, between HNF4A and hepatocytes, were recapitulated in the corresponding cell lines, in this case the liver-derived cell line HepG2. Half of the associations between tissue-specific TFs and cell line-specific promoters were new. Our study underscores the importance of collecting functional information from complementary assays and conditions to understand biology in a systematic framework.
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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.