C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution

• DOI: 10.1038/s41467-018-08126-5
• Publication Date: 2019-01-21T11:02:40Z
• Authors: Tsukasa Kouno; Jonathan Moody; Andrew Tae-Jun Kwon; Youtaro Shibayama; Sachi Kato; Yi Huang; Michael Böttcher; Efthymios Motakis; Mickaël Mendez; Jessica Severin; Joachim Luginbühl; Imad Abugessaisa; Akira Hasegawa; Satoshi Takizawa; Takahiro Arakawa; Masaaki Furuno; Naveen Ramalingam; Jay West; Harukazu Suzuki; Takeya Kasukawa; Timo Lassmann; Chung-Chau Hon; Erik Arner; Piero Carninci; Charles Plessy; Jay W. Shin
• Keywords: Cage; Transcription; Enhancer RNAs

Abstract Single-cell transcriptomic profiling is a powerful tool to explore cellular heterogeneity. However, most of these methods focus on the 3′-end polyadenylated transcripts and provide only partial view transcriptome. We introduce C1 CAGE, method for detection transcript 5′-ends with an original sample multiplexing strategy in TM microfluidic system. first quantifiy performance CAGE find it as accurate sensitive other then use profile promoter enhancer activities response TGF-β lung cancer cells discover subpopulations differing their response. also describe RNA dynamics revealing transcriptional bursts subsets arising from either strand mutually exclusive manner, validated using single molecule fluorescence situ hybridization.