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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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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 Structure01:23

RNA Structure

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Overview
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.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
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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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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 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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High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
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High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

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Host-Pathogen Transcriptomics by Dual RNA-Seq.

Alexander J Westermann1, Jörg Vogel2,3

  • 1Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany. alexander.westermann@uni-wuerzburg.de.

Methods in Molecular Biology (Clifton, N.J.)
|February 28, 2018
PubMed
Summary
This summary is machine-generated.

Dual RNA-sequencing enables simultaneous gene expression analysis in both bacteria and host cells during infection. This protocol optimizes dual transcriptomics for studying bacterial pathogens like Salmonella Typhimurium in human cells.

Keywords:
Cell sortingDual RNA-seqFixationHost-pathogen interactionInfectionNoncoding RNARNA-seqSalmonellaTranscriptomicsrRNA depletion

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Area of Science:

  • Microbiology
  • Genomics
  • Molecular Biology

Background:

  • Transcriptomics offers insights into cellular physiology but traditional methods struggle with cross-kingdom analysis.
  • Studying bacterial infections requires simultaneous gene expression profiling of both pathogen and host.

Purpose of the Study:

  • To present a detailed Dual RNA-sequencing protocol for analyzing gene expression in bacteria and host cells concurrently.
  • To optimize the protocol for human cell culture models infected with Salmonella Typhimurium.

Main Methods:

  • Dual RNA-sequencing protocol development and optimization.
  • Key steps include transcriptome stabilization (RNA fixation), FACS-based enrichment of infected cells, and dual rRNA depletion.
  • Computational analysis methods for dual RNA-seq data are also discussed.

Main Results:

  • Experimental data validates the benefits of optimized steps like RNA fixation and double rRNA depletion.
  • The protocol facilitates simultaneous transcriptome analysis of bacteria and host cells.

Conclusions:

  • The described Dual RNA-seq protocol is a powerful tool for studying host-pathogen interactions at the transcriptomic level.
  • This method enhances the understanding of bacterial infections in eukaryotic systems.