Related Experiment Video

Updated: Apr 16, 2026

Retroviral Scanning: Mapping MLV Integration Sites to Define Cell-specific Regulatory Regions
10:10

Retroviral Scanning: Mapping MLV Integration Sites to Define Cell-specific Regulatory Regions

Published on: May 28, 2017

8.9K

3D hotspots of recurrent retroviral insertions reveal long-range interactions with cancer genes

Sepideh Babaei1, Waseem Akhtar2, Johann de Jong3

  • 1Delft Bioinformatics Lab, Faculty of Electrical Engineering Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands.

Nature Communications
|February 28, 2015
PubMed

Insights

Genomic mutations can deregulate cancer genes through 3D chromatin interactions. This study reveals viral insertions cluster in nuclear hotspots, targeting cancer genes and highlighting the genome's 3D structure in mutagenesis screens.

Area of Science:

  • Genomics
  • Cancer Biology
  • Epigenetics

Background:

  • Genomically distal mutations can deregulate cancer genes via chromatin interactions.
  • Insertional mutagenesis screens identify viral insertions that contribute to cancer development.

Purpose of the Study:

  • To investigate how distal mutations affect cancer genes by analyzing chromatin interactions.
  • To understand the spatial organization of viral insertions within the nucleus.

Main Methods:

  • Overlaying data from murine retroviral insertional mutagenesis screens with genome-wide chromatin conformation capture data.
  • Analyzing the 3D clustering patterns of viral insertions.

Main Results:

  • Viral insertions identified in insertional mutagenesis screens tend to cluster in specific 3D hotspots within the nucleus.
  • These hotspots are significantly enriched for known cancer genes and regulatory elements like transcription factor-binding sites.
  • A pattern of mutually exclusive integration was observed, indicating that insertions target the same gene regardless of linear or 3D proximity.

Conclusions:

  • Genomic perturbations, such as viral insertions, can target cancer genes through 3D chromatin interactions.
  • Understanding the genome's three-dimensional structure is crucial for interpreting insertional mutagenesis screening results and their impact on cancer gene regulation.

More Related Videos

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites09:31

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

Published on: March 22, 2016

18.5K
Identification of Functionally-Relevant Lentivirus Integration Sites in an Insertional Mutagenesis Cell Library07:28

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

Published on: January 10, 2025

803

Related Concept Videos

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...
7.3K
Mechanisms of Retrovirus-induced Cancers01:51

Mechanisms of Retrovirus-induced Cancers

3.2K
Non-LTR Retrotransposons03:18

Non-LTR Retrotransposons

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...
14.1K
Rous Sarcoma Virus (RSV) and Cancer01:03

Rous Sarcoma Virus (RSV) and Cancer

Rous Sarcoma virus or RSV was discovered by F. Peyton Rous in the year 1911 as a filterable transmissible agent that could cause tumors in chickens. He won a Nobel Prize for this discovery in 1966. His experiments clearly demonstrated that some cancers could be caused by infectious agents and led to the discovery of many more cancer-causing viruses in animals as well as humans.
RSV is a retrovirus that contains two copies of a plus-strand  RNA genome. Its genome consists of four main open...
6.7K
Rous Sarcoma Virus (RSV) and Cancer01:03

Rous Sarcoma Virus (RSV) and Cancer

6.1K
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’...
16.2K