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Related Concept Videos

Retroviruses02:33

Retroviruses

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Retroviruses and retrotransposons both insert copies of their genetic elements into the genome of the host cell. Thus, the viral genes are passed on when the host genome is replicated or translated. A typical retroviral DNA sequence contains 3-4 genes that encode the different proteins required for its structural assembly and function as a molecular parasite. This DNA is transcribed into a single mRNA, which is very similar in structure to conventional mRNAs, i.e., it is capped at the 5’...
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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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LTR Retrotransposons03:08

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LTR retrotransposons are class I transposable elements with long terminal repeats flanking an internal coding region. These elements are less abundant in mammals compared to other class I transposable elements. About 8 percent of human genomic DNA comprises LTR retrotransposons. Some of the common examples of LTR retrotransposons are Ty elements in yeast and Copia elements in Drosophila.
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Non-LTR Retrotransposons03:18

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As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...
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Retrovirus Life Cycles01:10

Retrovirus Life Cycles

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Retroviruses have a single-stranded RNA genome that undergoes a special form of replication. Once the retrovirus has entered the host cell, an enzyme called reverse transcriptase synthesizes double-stranded DNA from the retroviral RNA genome. This DNA copy of the genome is then integrated into the host’s genome inside the nucleus via an enzyme called integrase. Consequently, the retroviral genome is transcribed into RNA whenever the host’s genome is transcribed, allowing the...
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Viruses with RNA Genomes01:29

Viruses with RNA Genomes

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RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...
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Updated: Mar 30, 2026

Microarray-based Identification of Individual HERV Loci Expression: Application to Biomarker Discovery in Prostate Cancer
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Differential expression analysis of human endogenous retroviruses based on ENCODE RNA-seq data.

Kerstin Haase1, Anja Mösch2, Dmitrij Frishman3,4,5

  • 1Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, TU München, Maximus-von-Imhof-Forum 3, Freising, 85354, Germany. haase@wzw.tum.de.

BMC Medical Genomics
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Summary

Human endogenous retroviruses (HERVs) show altered expression patterns in cancer. Analysis of ENCODE data reveals HERV expression can indicate cell differentiation and disease states, offering insights beyond protein-coding genes.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Cancer Research

Background:

  • Human endogenous retroviruses (HERVs) possess promoter activity via long terminal repeats (LTRs), influencing neighboring gene expression.
  • HERV involvement in cancer is known, but systematic expression pattern studies across diverse cell types in health and disease are lacking.
  • The ENCODE dataset offers a resource for gene expression studies, yet HERV-specific analyses remain underexplored.

Purpose of the Study:

  • To conduct a comprehensive differential analysis of HERV expression patterns.
  • To investigate HERV expression in normal versus cancer cell types using ENCODE data.
  • To assess the utility of HERV expression analysis for understanding cell differentiation and disease states.

Main Methods:

  • Differential expression analysis of individual HERV loci and families.
  • Utilized ENCODE Tier 1 and Tier 2 RNA-seq data from twelve cell lines (six normal, six cancer).
  • Principal component analysis to compare expression patterns between cell groups and contributing labs.

Main Results:

  • Distinguishable HERV expression patterns were observed between normal and cancer cell groups.
  • Specific HERV families could not be definitively linked to the observed expression differences.
  • Two samples showed anomalous expression patterns, including pluripotency marker HERVH, suggesting potential misclassification or early cancer development.

Conclusions:

  • ENCODE data are comparable across contributing labs, supporting robust HERV expression analysis.
  • HERV element analysis provides novel insights into cell differentiation and disease states, often missed by focusing solely on protein-coding genes.
  • Findings suggest a significant role for altered HERV expression during cancerogenesis.