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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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Transcription01:10

Transcription

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Overview
Transcription is the process of synthesizing RNA from a DNA sequence by RNA polymerase. It is the first step in producing a protein from a gene sequence. Additionally, many other proteins and regulatory sequences are involved in the proper synthesis of messenger RNA (mRNA). Regulation of transcription is responsible for the differentiation of all the different types of cells and often for the proper cellular response to environmental signals.
Transcription Can Produce Different Kinds...
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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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Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

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Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein....
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Nuclear Fusion02:45

Nuclear Fusion

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The process of converting very light nuclei into heavier nuclei is also accompanied by the conversion of mass into large amounts of energy, a process called fusion. The principal source of energy in the sun is a net fusion reaction in which four hydrogen nuclei fuse and ultimately produce one helium nucleus and two positrons.
A helium nucleus has a mass that is 0.7% less than that of four hydrogen nuclei; this lost mass is converted into energy during the fusion. This reaction produces about...
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Transcription Factors02:16

Transcription Factors

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Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
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Related Experiment Video

Updated: Feb 12, 2026

RNA-seq Analysis of Transcriptomes in Thrombin-treated and Control Human Pulmonary Microvascular Endothelial Cells
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RNA-seq Analysis of Transcriptomes in Thrombin-treated and Control Human Pulmonary Microvascular Endothelial Cells

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RNA-Seq Analysis to Detect Abnormal Fusion Transcripts Linked to Chromothripsis.

Anne-Laure Bougé1,2, Florence Rufflé1,2, Sébastien Riquier1,2

  • 1Institut de Médecine Régénératrice et de Biothérapie, INSERM U1183, CHU Montpellier, Montpellier, France.

Methods in Molecular Biology (Clifton, N.J.)
|March 23, 2018
PubMed
Summary

This study introduces an RNA-Seq method to detect chimeric transcripts from complex genomic rearrangements, offering a sensitive and specific alternative to DNA-level analysis for identifying these RNA events.

Keywords:
ChimerasChimeric RNAsChromothripsisFusion genesGenomic rearrangementNGSRNA-SeqTranscription

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Area of Science:

  • Genomics
  • Transcriptomics
  • Bioinformatics

Background:

  • Fusion and chimeric transcripts are linked to complex genomic rearrangements.
  • Traditional methods for identifying these events focus on the DNA level.

Purpose of the Study:

  • To present a comprehensive RNA-Seq procedure for detecting and characterizing chimeric transcripts.
  • To introduce a novel bioinformatics approach for inferring chimeric junctions with high sensitivity and specificity.
  • To provide best practices for bioinformatics analysis and experimental validation of RNA events.

Main Methods:

  • Utilizing RNA-Sequencing (RNA-Seq) for transcript detection.
  • Implementing a novel read analysis method combining genomic locations and local coverage.
  • Directly inferring chimeric junctions from RNA-Seq data.
  • Recommending bioinformatics analysis workflows.
  • Describing experimental validation using real-time PCR and sequencing.

Main Results:

  • The developed method allows for direct inference of chimeric junctions from RNA-Seq data.
  • High sensitivity and specificity in detecting different classes of chimeric RNA events.
  • Successful identification of chimeric transcripts associated with genomic rearrangements.
  • Established best practices for bioinformatics analysis and RNA validation.

Conclusions:

  • The RNA-Seq approach provides a powerful tool for characterizing chimeric transcripts.
  • The novel bioinformatics method enhances the sensitivity and specificity of chimeric junction detection.
  • This procedure facilitates a more comprehensive understanding of genomic rearrangements through transcriptomic analysis.