scRNA-Seq brings new miRNA insights

MicroRNAs, the tiny bits of genetic material that regulate gene expression, play a significant – but poorly understood – role in controlling the differences between individual cells. Yale researchers have developed a technology that sheds light on the workings responsible for these differences – a breakthrough that could lead to new insights about cancer development.

Researchers at Yale were able to profile for the first time both microRNA and messenger RNA (mRNA) in the same individual cell. By doing so, they discovered new mechanisms that lead to the heterogeneity – that is, the many variations – of gene expression. The results are published today in Nature Communications.

The research is a collaboration between the laboratories of Rong Fan, associate professor of biomedical engineering, and Jun Lu, an associate professor of genetics at the Yale Stem Cell Center.

“Our work for the first time allowed for the direct measurement of all microRNAs and all mRNAs in single cells, which can provide direct evidence of how microRNAs control their target mRNAs,” Fan said.

To co-sequence microRNA and mRNA from the same cell, the researchers needed to develop a new approach, since conventional methods, such as magnetic capture and gel electrophoresis, don’t work reliably at the single-cell scale. The researchers used a “half-cell genomics” approach. To do so, they physically split a single-cell lysate – that is, the liquid containing all the materials from a single cell – into two equal fractions. This is trickier than it sounds, since ensuring that all the protein-bound nucleic acid materials are fully dissociated is a complicated process.

For the study, the researchers showed that the half-cell approach could lead to robust splitting of microRNA and mRNA from single cell lysates and that they could perform a co-measurement of both from the same cell. In doing so, they found evidence that variability in microRNA expression alone is responsible for non-genetic cell-to-cell heterogeneity.

The innovation could lead to unraveling numerous mysteries of the genome.

Experimental workflow


a Overall strategy for profiling miRNA and mRNA from the same single cells using half-cell genomics. It involves cell lysis, half-cell split, followed by small RNA & large RNA library preparation. b For miRNA library preparation, a pre-adenylated (APP) 3′ adaptor was used to ligate to the 3′ end of miRNA molecules, followed by digestion of unreacted 3′ adaptor, ligation with 5′ adaptor, RT and PCR amplification. c For mRNA library preparation, first-strand cDNA synthesis was primed by the 3′ SMART-Seq CDS Primer IIA. Template switching at the 5′ end of transcript was performed using the SMART-Seq v4 oligonucleotides. After PCR amplification, cDNA was fragmented using Illumina’s Tagmentation process

“This work brings new opportunities to investigate how the changes in small RNA expression in single cells contribute to non-genetic cell-to-cell variability, and how miRNA expression heterogeneity contributes to the control of single-cell level mRNA expression heterogeneity,” said Nayi Wang, a former Ph.D. student in Fan’s laboratory and lead author of the study.

The breakthrough could lead to a better understanding of cancer development, intratumor heterogeneity, and therapeutic resistance. The researchers said the next step may be to seek microRNA targets for cancer treatments.

Source – Yale University

Wang N, Zheng J, Chen Z, Liu Y, Dura B, Kwak M, Xavier-Ferrucio J, Lu YC, Zhang M, Roden C, Cheng J, Krause DS, Ding Y, Fan R. (2019) Single-cell microRNA-mRNA co-sequencing reveals non-genetic heterogeneity and mechanisms of microRNA regulation. Nat Commun 10(1):95. [article]

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