ArticleProceedings of the National Academy of Sciences of the United States of America2003
Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 388 papers.
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Who cites it
388 citing papers in PubMed.
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- Annotating genomes at increased scale and resolution.Nature reviews. Genetics · 2026Review
- Profiling active RNA polymerase II transcription start sites from total RNA by capped small RNA sequencing (csRNA-seq).Nature protocols · 2026Review
- Long Noncoding RNA Isoform Specificity and Chemical Modification on tRNA-Derived Fragments Leading to Divergent Functions.The American journal of pathology · 2026Review
- 5' UTR length shapes alternative N-terminal protein isoforms across cancers and in rare disease.EMBO reports · 2026Article
- Designing DNA With Tunable Regulatory Activity Using Discrete Diffusion.bioRxiv : the preprint server for biology · 2026Article
- Targeting dysregulated epigenetic and transcription factor networks inBlood neoplasia · 2026Article
- Deciphering the regulatory landscape of enhancer RNAs in health and disease.Signal transduction and targeted therapy · 2026Review
- 5' UTR length regulates alternative N-terminal protein isoform production in health and disease.bioRxiv : the preprint server for biology · 2026Article
- SnakeAltPromoter Facilitates Differential Alternative Promoter Analysis.Computational and structural biotechnology journal · 2026Article
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- Cross-Species Insights Into Gamma Herpesvirus Transcriptomes: Long-Read and Multi-Omics Perspectives.Journal of medical virology · 2026Review
328 more citing papers are in PubMed but not listed here.
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Authors and funding
17 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We introduce cap analysis gene expression (CAGE), which is based on preparation and sequencing of concatamers of DNA tags deriving from the initial 20 nucleotides from 5' end mRNAs. CAGE allows high-throughout gene expression analysis and the profiling of transcriptional start points (TSP), including promoter usage analysis. By analyzing four libraries (brain, cortex, hippocampus, and cerebellum), we redefined more accurately the TSPs of 11-27% of the analyzed transcriptional units that were hit. The frequency of CAGE tags correlates well with results from other analyses, such as serial analysis of gene expression, and furthermore maps the TSPs more accurately, including in tissue-specific cases. The high-throughput nature of this technology paves the way for understanding gene networks via correlation of promoter usage and gene transcriptional factor expression.
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