ArticleGenome research2011
Unamplified cap analysis of gene expression on a single-molecule sequencer.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 108 papers.
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Who cites it
108 citing papers in PubMed, 186 citations in OpenAlex.
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- Comprehensive mapping of genetic variation at Epromoters reveals pleiotropic association with multiple disease traits.Nucleic acids research · 2025Article
- Single-cell RNA sequencing of peripheral blood links cell-type-specific regulation of splicing to autoimmune and inflammatory diseases.Nature genetics · 2024Article
- A novel human protein-coding locus identified using a targeted RNA enrichment technique.BMC biology · 2024Article
- Progranulin enhances the engraftment of transplanted human iPS cell-derived cerebral neurons.Stem cells translational medicine · 2024Article
- Widespread 3'UTR capped RNAs derive from G-rich regions in proximity to AGO2 binding sites.BMC biology · 2024Article
- Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq.Nature communications · 2024Article
- Pan-cancer transcriptome analysis reveals widespread regulation through alternative tandem transcription initiation.Science advances · 2024Article
- Physical Peculiarity of Two Sites in Human Promoters: Universality and Diverse Usage in Gene Function.International journal of molecular sciences · 2024Article
- Article
- A systems-level mass spectrometry-based technique for accurate and sensitive quantification of the RNA cap epitranscriptome.Nature protocols · 2023Review
- Cap analysis of gene expression (CAGE) and noncoding regulatory elements.Seminars in immunopathology · 2022Review
- Virtual Gene Concept and a Corresponding Pragmatic Research Program in Genetical Data Science.Entropy (Basel, Switzerland) · 2021Review
- Integrative transcription start site analysis and physiological phenotyping reveal torpor-specific expression program in mouse skeletal muscle.Communications biology · 2021Article
- Global approaches for profiling transcription initiation.Cell reports methods · 2021Review
- Regulation and functional roles of chemokines in liver diseases.Nature reviews. Gastroenterology & hepatology · 2021Review
- Transcription start site-level expression of thyroid transcription factor 1 isoforms in lung adenocarcinoma and its clinicopathological significance.The journal of pathology. Clinical research · 2021Article
- Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.Nature communications · 2021Article
48 more citing papers are in PubMed but not listed here.
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Authors and funding
13 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We report the development of a simplified cap analysis of gene expression (CAGE) protocol adapted for single-molecule sequencers that avoids second strand synthesis, ligation, digestion, and PCR. HeliScopeCAGE directly sequences the 3' end of cap trapped first-strand cDNAs. As with previous versions of CAGE, we better define transcription start sites (TSS) than known models, identify novel regions of transcription and alternative promoters, and find two major classes of TSS signal, sharp peaks and broad regions. However, using this protocol, we observe reproducible evidence of regulation at the much finer level of individual TSS positions. The libraries are quantitative over 5 orders of magnitude and highly reproducible (Pearson's correlation coefficient of 0.987). We have also scaled down the sample requirement to 5 μg of total RNA for a standard HeliScopeCAGE library and 100 ng for a low-quantity version. When the same RNA was run as 5-μg and 100-ng versions, the 100 ng was still able to detect expression for ∼60% of the 13,468 loci detected by a 5-μg library using the same threshold, allowing comparative analysis of even rare cell populations. Testing the protocol for differential gene expression measurements on triplicate HeLa and THP-1 samples, we find that the log fold change compared to Illumina microarray measurements is highly correlated (0.871). In addition, HeliScopeCAGE finds differential expression for thousands more loci including those with probes on the array. Finally, although the majority of tags are 5' associated, we also observe a low level of signal on exons that is useful for defining gene structures.
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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.