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NASC-seq monitors RNA synthesis in single cells

ABSTRACT: NASC-seq monitors RNA synthesis in single cells

PROVIDER: PRJNA526921 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8723850_1.fastq.gz	Fastqsanger.gz
	SRR8723850_2.fastq.gz	Fastqsanger.gz
	SRR8723860_1.fastq.gz	Fastqsanger.gz
	SRR8723860_2.fastq.gz	Fastqsanger.gz
	SRR8723870_1.fastq.gz	Fastqsanger.gz

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NASC-seq monitors RNA synthesis in single cells.

Project description:Sequencing of newly synthesised RNA can monitor transcriptional dynamics with great sensitivity and high temporal resolution, but is currently restricted to populations of cells. Here, we develop new transcriptome alkylation-dependent single-cell RNA sequencing (NASC-seq), to monitor newly synthesised and pre-existing RNA simultaneously in single cells. We validate the method on pre-labelled RNA, and by demonstrating that more newly synthesised RNA was detected for genes with known high mRNA turnover. Monitoring RNA synthesis during Jurkat T-cell activation with NASC-seq reveals both rapidly up- and down-regulated genes, and that induced genes are almost exclusively detected as newly transcribed. Moreover, the newly synthesised and pre-existing transcriptomes after T-cell activation are distinct, confirming that NASC-seq simultaneously measures gene expression corresponding to two time points in single cells. Altogether, NASC-seq enables precise temporal monitoring of RNA synthesis at single-cell resolution during homoeostasis, perturbation responses and cellular differentiation.

| S-EPMC6637240 | biostudies-literature

NASC-seq monitors RNA synthesis in single cells

Project description:Sequencing of newly synthesized RNA can monitor transcriptional dynamics with great sensitivity and high temporal resolution, but is currently restricted to populations of cells. Here, we develop new transcriptome alkylation-dependent single-cell RNA sequencing (NASC-seq), to monitor newly synthesized and pre-existing RNA in single cells. We validate the method on pre-alkylated RNA, and by demonstrating that more newly synthesized RNA was detected for genes with known high mRNA turnover. NASC-seq reveals rapidly up- and down-regulated genes during T-cell activation, and RNA arising from induced genes is essentially only newly synthesized. The newly synthesized and pre-existing transcriptomes after T-cell activation are distinct, confirming that we simultaneously measure gene expression at two time points in single cells. Altogether, NASC-seq is an accessible and powerful tool to investigate transcriptional dynamics that enables the precise monitoring of RNA synthesis at flexible time periods during homeostasis, perturbation responses and cellular differentiation.

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Single cell RNA-seq by mostly-natural sequencing by synthesis

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scDUAL-seq Simultaneously Measures RNA Synthesis and Degradation Rates in Single Cells

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Project description:The interplay between RNA transcription and degradation tightly regulates the dynamic changes of RNA abundance. To unveil the underlying regulatory mechanism of RNA in shaping gene expression patterns, it is essential yet challenging to profile the coordinated regulation of RNA synthesis and degradation rates at the single-cell level during dynamic programs such as cell differentiation and cell state transition. Herein, we propose scDUAL-seq, a double metabolic RNA labeling-based single-cell RNA sequencing method to simultaneously measure RNA synthesis and degradation rates in thousands of single cells during dynamic processes. In a cortisol response model of colorectal cancer cells, scDUAL-seq identifies the RNA regulatory strategies for 5,930 genes, discovers key regulons driving the strategy transitions, and disentangles the interplay between RNA synthesis and degradation that control distinct strategy transitions during cortisol response. We anticipate that scDUAL-seq will be broadly applied to record RNA kinetic rates and the underlying regulatory mechanism in diverse dynamic processes.

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