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Related Concept Videos

Eukaryotic RNA Polymerases00:58

Eukaryotic RNA Polymerases

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RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
All three eukaryotic RNAPs require specific transcription factors, of which the...
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RNA Interference01:23

RNA Interference

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RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
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RNA Splicing01:32

RNA Splicing

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Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
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RNA Stability01:53

RNA Stability

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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...
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Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

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Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
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RNA Editing02:23

RNA Editing

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RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
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Related Experiment Video

Updated: Feb 11, 2026

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
07:30

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

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RNA sequencing.

Karl Waern1, Ugrappa Nagalakshmi, Michael Snyder

  • 1Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA.

Methods in Molecular Biology (Clifton, N.J.)
|August 25, 2011
PubMed
Summary
This summary is machine-generated.

This chapter details the RNA sequencing (RNA-Seq) protocol for preparing yeast RNA for Illumina sequencing. The protocol covers RNA extraction, cDNA synthesis, fragmentation, library generation, and bioinformatic analysis, adaptable for other organisms.

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Identification of Circular RNAs using RNA Sequencing
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Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq

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Related Experiment Videos

Last Updated: Feb 11, 2026

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
07:30

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

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Identification of Circular RNAs using RNA Sequencing
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Identification of Circular RNAs using RNA Sequencing

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Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq
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Identification of Footprints of RNA:Protein Complexes via RNA Immunoprecipitation in Tandem Followed by Sequencing RIPiT-Seq

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • RNA sequencing (RNA-Seq) is a powerful technique for analyzing the transcriptome.
  • Standardized protocols are essential for reproducible RNA-Seq experiments.

Purpose of the Study:

  • To describe a comprehensive RNA sequencing protocol.
  • To enable RNA-Seq library preparation for yeast and other organisms using Illumina technology.

Main Methods:

  • Detailed steps for RNA extraction from yeast cells.
  • cDNA synthesis and fragmentation procedures.
  • Illumina cDNA library generation and preparation for sequencing.

Main Results:

  • A complete protocol for RNA-Seq library preparation is presented.
  • The protocol is adaptable for RNA from various organisms.
  • Includes considerations for downstream bioinformatic analysis.

Conclusions:

  • This protocol provides a robust method for RNA-Seq library preparation.
  • Facilitates transcriptomic analysis across different species.
  • A valuable resource for researchers utilizing Illumina sequencing platforms.