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Highly specific imaging of mRNA in single cells by target RNA-initiated rolling circle amplification.

ABSTRACT: Detection of single-cell gene expression with high spatial and sequence resolution is a key challenge in single cell biology. Herein, we propose a robust method for the direct detection of mRNA, termed target RNA-initiated rolling circle amplification, which enables imaging of mRNA with single-nucleotide and near-single-molecule resolution in single cells. By utilizing a Splint R ligase capable of efficiently catalyzing the ligation of a padlock probe by the target RNA, the method can enable the efficient detection of mRNA without reverse transcription (detection efficiency over 20%). Meanwhile, attributed to the ligation-based recognition process, the method confers specificity sufficient to genotype mRNAs with one-nucleotide variations. The method has enabled the spatial mapping and correlation analysis of gene expression in single cells which could help us to elucidate the gene functions and regulatory mechanisms. This method offers an mRNA profiling ability with high spatial resolution and sequence specificity, thus is expected to be a single-cell analysis platform for not only investigating gene expression, but also potentially for analyzing single-nucleotide variants or mRNA alternative splicing at single-cell level.

SUBMITTER: Deng R

PROVIDER: S-EPMC5437493 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature

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Highly specific imaging of mRNA in single cells by target RNA-initiated rolling circle amplification.

Deng Ruijie R Zhang Kaixiang K Sun Yupeng Y Ren Xiaojun X Li Jinghong J

Chemical science 20170307 5

Detection of single-cell gene expression with high spatial and sequence resolution is a key challenge in single cell biology. Herein, we propose a robust method for the direct detection of mRNA, termed target RNA-initiated rolling circle amplification, which enables imaging of mRNA with single-nucleotide and near-single-molecule resolution in single cells. By utilizing a Splint R ligase capable of efficiently catalyzing the ligation of a padlock probe by the target RNA, the method can enable the ...[more]

PMID: 28580104

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Project description:Nucleic acid amplification is a hugely important technology for biology and medicine. While the polymerase chain reaction (PCR) has been highly useful and effective, its reliance on heating and cooling cycles places some constraints on its utility. For example, the heating step of PCR can destroy biological molecules under investigation and heat/cool cycles are not applicable in living systems. Thus, isothermal approaches to DNA and RNA amplification are under widespread study. Perhaps the simplest of these are the rolling circle approaches, including rolling circle amplification (RCA) and rolling circle transcription (RCT). In this strategy, a very small circular oligonucleotide (e.g., 25-100 nucleotides in length) acts as a template for a DNA or an RNA polymerase, producing long repeating product strands that serve as amplified copies of the circle sequence. Here we describe the early developments and studies involving circular oligonucleotides that ultimately led to the burgeoning rolling circle technologies currently under development. This Account starts with our studies on the design of circular oligonucleotides as novel DNA- and RNA-binding motifs. We describe how we developed chemical and biochemical strategies for synthesis of well-defined circular oligonucleotides having defined sequence and open (unpaired) structure, and we outline the unusual ways in which circular DNAs can interact with other nucleic acids. We proceed next to the discovery of DNA and RNA polymerase activity on these very small cyclic DNAs. DNA polymerase "rolling circle" activities were discovered concurrently in our laboratory and that of Andrew Fire. We describe the surprising efficiency of this process even on shockingly small circular DNAs, producing repeating DNAs thousands of nucleotides in length. RNA polymerase activity on circular oligonucleotides was first documented in our group in 1995; especially surprising in this case was the finding that the process occurs efficiently even without promoter sequences in the circle. We describe how one can encode cleavable sites into the product DNAs and RNAs from RCA/RCT, which can then be resolved into large quantities of almost pure oligonucleotides. Our Account then proceeds with a summary describing a broad variety of tools and methods built in many laboratories around the rolling circle concept. Among the important developments are the discovery of highly efficient DNA polymerases for RCA; the invention of exponential ("hyperbranched") RCA amplification made possible by use of a second primer; the development of the "padlock" process for detection of nucleic acids and proteins coupled with RCA; the use of circular oligonucleotides as vectors in cells to encode biologically active RNAs via RCT; and the use of small DNA circles to encode and extend human telomeres. Finally, we finish with some ideas about where the field may go in the future.

Dataset Information

Highly specific imaging of mRNA in single cells by target RNA-initiated rolling circle amplification.

Publications

Highly specific imaging of mRNA in single cells by target RNA-initiated rolling circle amplification.

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