Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs

Tetsutaro Hayashi, Haruka Ozaki, Yohei Sasagawa, Mana Umeda, Hiroki Danno and Itoshi Nikaido ()
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Tetsutaro Hayashi: RIKEN
Haruka Ozaki: RIKEN
Yohei Sasagawa: RIKEN
Mana Umeda: RIKEN
Hiroki Danno: RIKEN
Itoshi Nikaido: RIKEN

Nature Communications, 2018, vol. 9, issue 1, 1-16

Abstract: Abstract 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.

Date: 2018
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DOI: 10.1038/s41467-018-02866-0

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