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lncRNA - Long Non-coding RNAs02:39

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In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding RNAs which includes ribosomal RNAs, transfer RNAs, telomerase RNAs, and regulatory RNAs, among other types. A large number of regulatory non-coding RNAs have been classified into two groups depending upon their length – small non-coding RNAs, such as microRNA, which are less than 200 nucleotides in length, and long non-coding RNA...
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Related Experiment Video

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A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells
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Visualization of Enhancer-Derived Noncoding RNA.

Youtaro Shibayama1,2, Stephanie Fanucchi1,2, Musa M Mhlanga3,4,5

  • 1Gene Expression and Biophysics Group, Synthetic Biology ERA, CSIR, Box 395, Pretoria, 0001, South Africa.

Methods in Molecular Biology (Clifton, N.J.)
|September 25, 2016
PubMed
Summary

This study presents a new imaging method to visualize enhancer RNAs (eRNAs) in single cells. This technique allows for simultaneous analysis of eRNA and protein-coding transcripts, offering insights into gene regulation dynamics.

Keywords:
EnhancersFluorescence in situ hybridizationLong ncRNARNA visualizationSingle cell analysisTyramide signal amplificationeRNA

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Area of Science:

  • Molecular Biology
  • Genetics
  • Cell Biology

Background:

  • Enhancers regulate gene expression with spatiotemporal and tissue-specific control.
  • Enhancer-derived long noncoding RNAs (long ncRNAs), such as enhancer RNAs (eRNAs), are implicated in enhancer function.
  • Previous studies lacked single-cell imaging techniques for analyzing eRNA expression and function.

Purpose of the Study:

  • To develop and describe a novel imaging protocol for visualizing eRNAs in single cells.
  • To enable simultaneous analysis of eRNA and protein-coding transcripts at the site of transcriptional elongation.
  • To facilitate the study of dynamic interactions between different transcript species within single cells.

Main Methods:

  • In situ hybridization combined with tyramide signal amplification (TSA) for eRNA imaging.
  • Multiplexing capability to visualize both eRNA and protein-coding transcripts concurrently.
  • Application of the protocol for analyzing transcript dynamics at the single-cell level.

Main Results:

  • Successful imaging of eRNA in single cells using the developed protocol.
  • Demonstration of multiplexed imaging for simultaneous visualization of eRNA and protein-coding transcripts.
  • Establishment of a method to analyze the dynamics between eRNA and protein-coding transcripts.

Conclusions:

  • The described protocol provides a powerful tool for imaging eRNAs in single cells.
  • This method allows for the simultaneous visualization and analysis of eRNA and other transcripts.
  • The approach is versatile and applicable to studying various other RNA species and their functions.