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Related Concept Videos

RNA-seq03:21

RNA-seq

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 microarray-based...
RNA Stability01:53

RNA Stability

Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
RNA Stability01:53

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Nonsense-mediated mRNA Decay02:27

Nonsense-mediated mRNA Decay

The Upf proteins that carry out nonsense-mediated decay (NMD) are found in all eukaryotic organisms, including humans. Each protein has an individual role, but they need to work in collaboration. Upf1 is an ATP-dependent RNA helicase that unwinds the RNA helix. Because Upf1 can unwind any RNA, Upf2 and Upf3 are required to help Upf1 discriminate between nonsense and normal mRNAs.
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Nonsense-mediated mRNA Decay02:27

Nonsense-mediated mRNA Decay

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Experimental RNAi

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Related Experiment Video

Updated: May 22, 2026

A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells
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A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells

Published on: October 28, 2025

Stable stem enabled Shannon entropies distinguish non-coding RNAs from random backgrounds.

Yingfeng Wang1, Amir Manzour, Pooya Shareghi

  • 1Department of Computer Science, University of Georgia, Athens, Georgia 30602, USA. ywang802@uga.edu

BMC Bioinformatics
|April 28, 2012
PubMed
Summary

Improving RNA secondary structure analysis with a constrained ensemble method enhances the detection of non-coding RNAs (ncRNAs). This approach refines base pairing entropy calculations for more accurate ncRNA gene finding.

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A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells
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Optimized Quantitative Assessment of Enhancer RNA Stability in Mouse Embryonic Stem Cells

Published on: November 21, 2025

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Accurate identification of non-coding RNAs (ncRNAs) in genomic sequences is crucial.
  • Shannon base pairing entropy is used to assess RNA secondary structure fold certainty.
  • Current entropy measures struggle to effectively distinguish ncRNAs from random sequences.

Purpose of the Study:

  • To enhance the performance of base pairing entropy for detecting structural ncRNAs.
  • To develop improved methods for ncRNA gene finding based on RNA structure detection.

Main Methods:

  • Utilizing a constrained secondary structure ensemble.
  • Assuming only canonical base pairs in energetically stable stems.
  • Computing base pairing entropies with the constrained model.

Main Results:

  • Significantly improved performance of base pairing entropy measurement.
  • Reduced the space of secondary structures considered.
  • Demonstrated substantially narrowed Z-score gaps between ncRNAs and increased Z-scores for tested ncRNA sets compared to shuffled sequences.

Conclusions:

  • The constrained secondary structure ensemble approach is viable for improving RNA structure-based gene finding.
  • Investigating secondary structure ensembles offers a promising avenue for effective ncRNA gene finding methods.