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Cap analysis of gene expression (CAGE) and noncoding regulatory elements

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Abstract

Cap analysis of gene expression (CAGE) was developed to detect the 5′ end of RNA. Trapping of the RNA 5′-cap structure enables the enrichment and selective sequencing of complete transcripts. Upscaled high-throughput versions of CAGE have enabled the genome-wide identification of transcription start sites, including transcriptionally active promoters and enhancers. CAGE sequencing can be exploited to draw comprehensive maps of active genomic regulatory elements in a cell type- and activation-specific manner. The cells of the immune system are among the best candidates to be analyzed in humans, since they are easily accessible. In this review, we discuss how CAGE data are instrumental for integrative analyses with quantitative trait loci and omics data, and their usefulness in the mechanistic interpretation of the effects of genetic variations over the entire human genome. Integrating CAGE data with the currently available omics information will contribute to better understanding of the genome-wide association study variants that lie outside of annotated genes, deepening our knowledge on human diseases, and enabling the targeted design of more specific therapeutic interventions.

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Authors and Affiliations

  1. Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan

    Matteo Maurizio Guerrini & Akari Suzuki

  2. RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan

    Akiko Oguchi & Yasuhiro Murakawa

  3. IFOM―the FIRC Institute of Molecular Oncology, Milan, Italy

    Yasuhiro Murakawa

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  1. Matteo Maurizio Guerrini
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  2. Akiko Oguchi
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  3. Akari Suzuki
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  4. Yasuhiro Murakawa
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Correspondence to Matteo Maurizio Guerrini.

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This article is a contribution to the special issue on: Genetics and functional genetics of Autoimmune diseases - Guest Editors: Yukinori Okada & Kazuhiko Yamamoto

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Guerrini, M.M., Oguchi, A., Suzuki, A. et al. Cap analysis of gene expression (CAGE) and noncoding regulatory elements. Semin Immunopathol 44, 127–136 (2022). https://doi.org/10.1007/s00281-021-00886-5

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