Journal
NATURE COMMUNICATIONS
Volume 9, Issue -, Pages -Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/s41467-018-02866-0
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Funding
- Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan
- Japan Agency for Medical Research and development (AMED)
- Projects for Technological Development, Research Center Network for Realization of Regenerative Medicine by AMED
- Japan Science and Technology Agency (JST)
- JSPS KAKENHI [JP24651218, JP26640120]
- MEXT KAKENHI [221S0002]
- Special Postdoctoral Researchers Program from RIKEN
- JST CREST, Japan [JPMJCR16G3]
- Grants-in-Aid for Scientific Research [26640120] Funding Source: KAKEN
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Total RNA sequencing has been used to reveal poly(A) and non-poly(A) RNA expression, RNA processing and enhancer activity. To date, no method for full-length total RNA sequencing of single cells has been developed despite the potential of this technology for single-cell biology. Here we describe random displacement amplification sequencing (RamDA-seq), the first full-length total RNA-sequencing method for single cells. Compared with other methods, RamDA-seq shows high sensitivity to non-poly(A) RNA and near-complete full-length transcript coverage. Using RamDA-seq with differentiation time course samples of mouse embryonic stem cells, we reveal hundreds of dynamically regulated non-poly(A) transcripts, including histone transcripts and long noncoding RNA Neat1. Moreover, RamDA-seq profiles recursive splicing in >300-kb introns. RamDA-seq also detects enhancer RNAs and their cell type-specific activity in single cells. Taken together, we demonstrate that RamDA-seq could help investigate the dynamics of gene expression, RNA-processing events and transcriptional regulation in single cells.
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