1. C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution
- Author
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Yi Huang, Takahiro Arakawa, Michael Böttcher, Harukazu Suzuki, Imad Abugessaisa, Jessica Severin, Youtaro Shibayama, Mickaël Mendez, Charles Plessy, Jonathan Moody, Piero Carninci, Timo Lassmann, Jay A. A. West, Andrew T. Kwon, Satoshi Takizawa, Takeya Kasukawa, Sachi Kato, Erik Arner, Chung-Chau Hon, Tsukasa Kouno, Naveen Ramalingam, Masaaki Furuno, Jay W. Shin, Joachim Luginbühl, Efthymios Motakis, and Akira Hasegawa
- Subjects
0301 basic medicine ,Polyadenylation ,Sequence analysis ,Science ,Cell ,General Physics and Astronomy ,Genomics ,Enhancer RNAs ,02 engineering and technology ,Computational biology ,In situ hybridization ,Article ,General Biochemistry, Genetics and Molecular Biology ,Cell Line ,Transcriptome ,Mice ,03 medical and health sciences ,Transforming Growth Factor beta ,medicine ,Animals ,Humans ,RNA, Messenger ,lcsh:Science ,Promoter Regions, Genetic ,Enhancer ,In Situ Hybridization, Fluorescence ,Transcription start ,Multidisciplinary ,Sequence Analysis, RNA ,Chemistry ,Gene Expression Profiling ,RNA ,General Chemistry ,Fibroblasts ,Microfluidic Analytical Techniques ,Single-molecule experiment ,021001 nanoscience & nanotechnology ,Cell biology ,Gene expression profiling ,medicine.anatomical_structure ,Enhancer Elements, Genetic ,030104 developmental biology ,A549 Cells ,lcsh:Q ,Single-Cell Analysis ,Transcription Initiation Site ,0210 nano-technology - Abstract
Single-cell transcriptomic profiling is a powerful tool to explore cellular heterogeneity. However, most of these methods focus on the 3′-end of polyadenylated transcripts and provide only a partial view of the transcriptome. We introduce C1 CAGE, a method for the detection of transcript 5′-ends with an original sample multiplexing strategy in the C1TM microfluidic system. We first quantifiy the performance of C1 CAGE and find it as accurate and sensitive as other methods in the C1 system. We then use it to profile promoter and enhancer activities in the cellular response to TGF-β of lung cancer cells and discover subpopulations of cells differing in their response. We also describe enhancer RNA dynamics revealing transcriptional bursts in subsets of cells with transcripts arising from either strand in a mutually exclusive manner, validated using single molecule fluorescence in situ hybridization., Single-cell transcriptomic profiling allows the exploration of cellular heterogeneity but commonly focuses on the 3′-end of the transcript. Here the authors introduce C1 CAGE, which detects the 5′ transcript end in a multiplexed microfluidic system.
- Published
- 2018
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