ArticleGenome research2018
SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA.
Article in Genome research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 44 citations in OpenAlex.
- Review
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Evaluating the reliability of tools for mRNA annotation and IRES studies.bioRxiv : the preprint server for biology · 2026Article
- RNA multi-omics in single cells reveal rhythmical RNA reshaping during human and mouse oocyte maturation.BMC biology · 2025Article
- True length of diverse capped RNA sequencing (TLDR-seq): 5'-3'-end sequencing of capped RNAs regardless of 3'-end status.Nucleic acids research · 2025Article
- Liver kinase B1 (LKB1) regulates the epigenetic landscape of mouse pancreatic beta cells.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2024Article
- MYC activity at enhancers drives prognostic transcriptional programs through an epigenetic switch.Nature genetics · 2024Article
- An improved method for the highly specific detection of transcription start sites.Nucleic acids research · 2024Article
- CamoTSS: analysis of alternative transcription start sites for cellular phenotypes and regulatory patterns from 5' scRNA-seq data.Nature communications · 2023Article
- SCAFE: a software suite for analysis of transcribed cis-regulatory elements in single cells.Bioinformatics (Oxford, England) · 2022Article
- Bookend: precise transcript reconstruction with end-guided assembly.Genome biology · 2022Article
- Transcriptional enhancers and their communication with gene promoters.Cellular and molecular life sciences : CMLS · 2021Review
- Global approaches for profiling transcription initiation.Cell reports methods · 2021Review
- Flexible analysis of TSS mapping data and detection of TSS shifts with TSRexploreR.NAR genomics and bioinformatics · 2021Article
- Neuronal genes deregulated in Cornelia de Lange Syndrome respond to removal and re-expression of cohesin.Nature communications · 2021Article
- Integrator is recruited to promoter-proximally paused RNA Pol II to generate Caenorhabditis elegans piRNA precursors.The EMBO journal · 2021Article
- A Comprehensive Toolbox to Analyze Enhancer-Promoter Functions.Methods in molecular biology (Clifton, N.J.) · 2021Review
- TBPL2/TFIIA complex establishes the maternal transcriptome through oocyte-specific promoter usage.Nature communications · 2020Article
- The RNA exosome shapes the expression of key protein-coding genes.Nucleic acids research · 2020Article
- Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq.Genome research · 2020Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 4 countries.
Funding
Abstract
Cap analysis of gene expression (CAGE) is a methodology for genome-wide quantitative mapping of mRNA 5' ends to precisely capture transcription start sites at a single nucleotide resolution. In combination with high-throughput sequencing, CAGE has revolutionized our understanding of the rules of transcription initiation, led to discovery of new core promoter sequence features, and discovered transcription initiation at enhancers genome-wide. The biggest limitation of CAGE is that even the most recently improved version (nAnT-iCAGE) still requires large amounts of total cellular RNA (5 µg), preventing its application to scarce biological samples such as those from early embryonic development or rare cell types. Here, we present SLIC-CAGE, a Super-Low Input Carrier-CAGE approach to capture 5' ends of RNA polymerase II transcripts from as little as 5-10 ng of total RNA. This dramatic increase in sensitivity is achieved by specially designed, selectively degradable carrier RNA. We demonstrate the ability of SLIC-CAGE to generate data for genome-wide promoterome with 1000-fold less material than required by existing CAGE methods, by generating a complex, high-quality library from mouse embryonic day 11.5 primordial germ cells.
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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.