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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.
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RNA Splicing01:32

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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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Types of RNA01:23

Types of RNA

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Overview
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
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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.
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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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Flow-sorting and Exome Sequencing of the Reed-Sternberg Cells of Classical Hodgkin Lymphoma
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RNA Sequencing in B-Cell Lymphomas.

Da Wei Huang1, Moez Dawood1,2, Calvin A Johnson3

  • 1Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.

Methods in Molecular Biology (Clifton, N.J.)
|February 20, 2019
PubMed
Summary
This summary is machine-generated.

High-throughput mRNA sequencing (RNA-Seq) offers detailed transcriptome analysis. This protocol details RNA-Seq using Illumina platforms and bioinformatic analysis for comprehensive gene expression and variant detection.

Keywords:
B cellB-cell lymphomaGene expressionHigh-throughput sequencingImmunoglobulin genesMutationRNA-SeqTranscriptomeVDJ

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • High-throughput mRNA sequencing (RNA-Seq) is a powerful technique for transcriptome analysis.
  • It enables both qualitative and quantitative evaluation of gene expression.
  • RNA-Seq has become a standard tool in life sciences research.

Purpose of the Study:

  • To describe a protocol for performing mRNA sequencing using Illumina platforms.
  • To present essential sequencing data quality metrics.
  • To outline a comprehensive bioinformatic pipeline for RNA-Seq data analysis.

Main Methods:

  • Utilizes complementary DNA (cDNA) to generate millions of short sequence reads.
  • Employs Illumina NextSeq or MiSeq platforms for sequencing.
  • Bioinformatic pipeline includes sequence alignment, digital gene expression analysis, and variant annotation.

Main Results:

  • Provides a detailed protocol for RNA-Seq implementation.
  • Defines key quality metrics for sequencing data.
  • Outlines a pipeline for diverse transcriptomic analyses including gene fusions and variant detection.

Conclusions:

  • RNA-Seq is a versatile method for comprehensive transcriptome characterization.
  • The described protocol and pipeline facilitate advanced molecular biology research.
  • This approach supports applications ranging from gene expression to variant discovery.