TY - JOUR T1 - C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution JF - bioRxiv DO - 10.1101/330845 SP - 330845 AU - Tsukasa Kouno AU - Jonathan Moody AU - Andrew Kwon AU - Youtaro Shibayama AU - Sachi Kato AU - Yi Huang AU - Michael Böttcher AU - Efthymios Motakis AU - Mickaёl Mendez AU - Jessica Severin AU - Joachim Luginbühl AU - Imad Abugessaisa AU - Akira Hasegawa AU - Satoshi Takizawa AU - Takahiro Arakawa AU - Masaaki Furuno AU - Naveen Ramalingam AU - Jay West AU - Harukazu Suzuki AU - Takeya Kasukawa AU - Timo Lassmann AU - Chung-Chau Hon AU - Erik Arner AU - Piero Carninci AU - Charles Plessy AU - Jay W Shin Y1 - 2018/01/01 UR - http://biorxiv.org/content/early/2018/06/14/330845.abstract N2 - 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 C1™ microfluidic system. We first quantified the performance of C1 CAGE and found it as accurate and sensitive as other methods in C1 system. We then used it to profile promoter and enhancer activities in the cellular response to TGF-β of lung cancer cells and discovered 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 within a single-cell in a mutually exclusive manner, which was validated using single molecule fluorescence in-situ hybridization. ER -