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Related Concept Videos

RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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Related Experiment Video

Updated: Jan 6, 2026

Real-time Imaging of Single Engineered RNA Transcripts in Living Cells Using Ratiometric Bimolecular Beacons
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Click-encoded rolling FISH for visualizing single-cell RNA polyadenylation and structures.

Feng Chen1, Min Bai1, Xiaowen Cao1

  • 1Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xianning West Road, Xi'an, Shaanxi 710049, P. R. China.

Nucleic Acids Research
|October 5, 2019
PubMed
Summary
This summary is machine-generated.

Click-encoded rolling FISH (ClickerFISH) visualizes RNA polyadenylation and structures in single cells. This method reveals cell-specific spatial organization and dynamic changes during the cell cycle.

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Area of Science:

  • Molecular Biology
  • Cell Biology
  • Genomics

Background:

  • Current RNA imaging methods primarily focus on sequence analysis, lacking the ability to visualize RNA processing events and structures.
  • Understanding the spatial organization of RNA processing is crucial for deciphering single-cell RNA function and landscape.

Purpose of the Study:

  • To develop a novel method for visualizing RNA polyadenylation and structures in single cells with spatial resolution.
  • To investigate the cell type-specific and cell cycle-dependent spatial organization of RNA polyadenylation and structures.

Main Methods:

  • Developed click-encoded rolling FISH (ClickerFISH) for chemical labeling of RNA 3' polyadenylation tails, single-stranded, and duplex regions with clickable DNA barcodes.
  • Utilized DNA rolling amplification to generate repetitive templates for Fluorescence In Situ Hybridization (FISH) imaging of subcellular RNA distributions.
  • Integrated ClickerFISH with single-molecule FISH to obtain quantitative RNA information.

Main Results:

  • Demonstrated that RNA poly(A) tailing and higher-order structures exhibit cell type-specific spatial organization with significant cell-to-cell heterogeneity.
  • Revealed dynamic spatiotemporal patterns of RNA polyadenylation and structures during different cell cycle stages, particularly during S phase.
  • Successfully visualized subcellular distributions of labeled RNA components using rolling circle amplification and FISH.

Conclusions:

  • ClickerFISH provides a powerful tool for spatiotemporal visualization of RNA polyadenylation and structures in single cells.
  • The findings highlight the intricate spatial organization of RNA features and their dynamic regulation during the cell cycle.
  • This method advances the study of RNA architecture and its functional implications in cellular processes.