Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Size and Structure of Viral Genomes01:26

Size and Structure of Viral Genomes

Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...
Retrovirus Life Cycles01:10

Retrovirus Life Cycles

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 retrovirus to...
Retroviruses02:33

Retroviruses

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’...
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
LTR Retrotransposons03:08

LTR Retrotransposons

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.
The internal coding region of LTR retrotransposons and their mechanism of transposition closely resembles a...
Mechanisms of Retrovirus-induced Cancers01:51

Mechanisms of Retrovirus-induced Cancers

Retroviruses are RNA viruses that have been shown to cause cancers in diverse species, including chickens, mice, cats, and monkeys. The RNA genomes of these viruses are first reverse-transcribed into single and then double-stranded DNA (dsDNA) copies. This dsDNA called proviral DNA then integrates into the host genome. Subsequently, the host cell transcribes the proviral DNA in concert with the chromosomal DNA. This leads to the production of viral RNA and proteins that assemble at the host...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Subtype-specific differences in susceptibility to monoclonal antibodies and vaccines among contemporary RSV-A and RSV-B isolates.

bioRxiv : the preprint server for biology·2026
Same author

Transition from infectivity and immune escape to pure escape as an evolutionary strategy during the COVID-19 pandemic.

bioRxiv : the preprint server for biology·2026
Same author

CCL3 is produced by aged neutrophils across cancers and promotes tumor growth.

Cancer cell·2026
Same author

Noncanonical roles of chemokine regions in CCR9 activation revealed by structural modeling and mutational mapping.

Nature communications·2025
Same author

Computationally designed proteins mimic antibody immune evasion in viral evolution.

Immunity·2025
Same author

Molecular basis for the increased fusion activity of the Ebola virus glycoprotein epidemic variant A82V: Insights from simulations and experiments.

Cell reports·2025
Same journal

Combinatorial multiomic analysis from a pedigree of Sox10Dom Hirschsprung mice identifies multiple high confidence candidate modifiers of Enteric Nervous System development.

PLoS computational biology·2026
Same journal

Extracting host-specific developmental signatures from longitudinal microbiome data.

PLoS computational biology·2026
Same journal

Population sparseness determines strength of Hebbian plasticity for maximal memory lifetime in associative networks.

PLoS computational biology·2026
Same journal

Predictive coding explains asymmetric connectivity in the brain: A neural network study.

PLoS computational biology·2026
Same journal

Zooplankton feeding behavioral signatures in the morphology of macroscale prey spatial distribution.

PLoS computational biology·2026
Same journal

A brief overview of 20 years of neuroscience in PLoS Computational Biology.

PLoS computational biology·2026
See all related articles

Related Experiment Video

Updated: Jun 6, 2026

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites
09:31

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

Published on: March 22, 2016

Deciphering the code for retroviral integration target site selection.

Federico Andrea Santoni1, Oliver Hartley, Jeremy Luban

  • 1Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland.

Plos Computational Biology
|December 3, 2010
PubMed
Summary
This summary is machine-generated.

Retroviral integration site selection is not random. Researchers identified a "supermarker" using ChIP-Seq data that predicts favored integration sites, aiding in understanding retroviral mechanisms and proto-oncogene activation.

More Related Videos

Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library
07:28

Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library

Published on: January 10, 2025

Bidirectional Retroviral Integration Site PCR Methodology and Quantitative Data Analysis Workflow
12:53

Bidirectional Retroviral Integration Site PCR Methodology and Quantitative Data Analysis Workflow

Published on: June 14, 2017

Related Experiment Videos

Last Updated: Jun 6, 2026

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites
09:31

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

Published on: March 22, 2016

Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library
07:28

Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library

Published on: January 10, 2025

Bidirectional Retroviral Integration Site PCR Methodology and Quantitative Data Analysis Workflow
12:53

Bidirectional Retroviral Integration Site PCR Methodology and Quantitative Data Analysis Workflow

Published on: June 14, 2017

Area of Science:

  • Molecular Biology
  • Genetics
  • Virology

Background:

  • Retroviruses integrate DNA copies of their RNA genome into host chromosomes.
  • Integration site selection is non-random, with retroviral subgroups showing preferences for specific chromosomal features.
  • Understanding these preferences is crucial for identifying host factors and mechanisms involved in retroviral integration.

Purpose of the Study:

  • To identify predictive markers for retroviral integration sites.
  • To elucidate the mechanisms underlying retroviral target site selection.
  • To develop a tool for predicting cell-type specific proto-oncogene activation by retroviruses.

Main Methods:

  • Utilized Precision-Recall methods for analyzing highly skewed datasets.
  • Compared ChIP-Seq data for over 60 factors with 14 retroviral integration datasets (MLV, PERV, XMRV).
  • Developed a combined 'supermarker' from ChIP-Seq peaks to predict integration sites.

Main Results:

  • Identified strong associations between integration sites and STAT1, H3/H4 acetylation, and H2AZ/H3K4/K9 methylation.
  • The developed supermarker localized within 2kB of 75% of MLV proviruses.
  • The supermarker accurately predicted cell-type specific integration preferences, including for the LMO2 proto-oncogene.

Conclusions:

  • The supermarker effectively identifies chromosomal features favored by retroviral integration.
  • Provides insights into the mechanisms of retroviral integration site selection.
  • Offers a predictive tool for assessing retroviral-induced proto-oncogene activation in specific cell types.