Related Experiment Video
Updated: Jan 14, 2026
11:36
Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations
Published on: April 21, 2023
3.0K
Enhancer activation from transposable elements in extrachromosomal DNA
Katerina Kraft1,2, Sedona E Murphy3,4,5,6, Matthew G Jones1,7
1Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
Nature Cell Biology
|October 21, 2025
Summary
Extrachromosomal DNA (ecDNA) in aggressive cancers can incorporate repetitive elements. These elements, like LINE/L1 fragments, become functional on ecDNA, driving MYC oncogene expression and tumor evolution.
Area of Science:
- Oncology
- Genomics
- Molecular Biology
Background:
- Extrachromosomal DNA (ecDNA) is crucial for oncogene amplification and heterogeneity in aggressive cancers.
- Transposable element reactivation is frequent in cancer, but their role on ecDNA is unknown.
Purpose of the Study:
- To investigate the role of transposable elements on ecDNA in colorectal cancer.
- To understand how ecDNA utilizes repetitive elements to influence cancer progression.
Main Methods:
- 3D architecture mapping of MYC-amplified ecDNA.
- CRISPR-CATCH, CRISPR interference, and reporter assays.
- Identification of ecDNA-interacting elements enriched for transposable elements.
Main Results:
- Identified 68 ecDNA-interacting elements, many with transposable elements, frequently integrated onto ecDNA.
- A specific LINE/L1 fragment (L1M4a1#) was co-amplified with MYC on ecDNA and showed enhancer activity.
- This fragment was essential for cancer cell fitness in the ecDNA-amplified context.
Conclusions:
- Repetitive elements can be reactivated and function on ecDNA, driving oncogene expression.
- ecDNA harnesses repetitive elements to shape cancer phenotypes, impacting tumor evolution.
- Findings have implications for cancer diagnosis and therapeutic strategies.
More Related Videos
13:47Lentiviral Vector Platform for the Efficient Delivery of Epigenome-editing Tools into Human Induced Pluripotent Stem Cell-derived Disease Models
Published on: March 29, 2019
10.3K
04:04Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity
Published on: January 20, 2023
2.8K
Related Concept Videos
02:57DNA-only Transposons
17.2K
DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
The donor site from where the transposon is excised is either degraded or...
The donor site from where the transposon is excised is either degraded or...
17.2K
02:13Overview of Transposition and Recombination
18.8K
Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
18.8K
01:24Transposons
1.3K
Transposons, or "jumping genes," are small mobile genetic elements (MGEs) that range from 700 to 40,000 base pairs in length. They are found in all organisms and can move within the same chromosome or transfer to different chromosomes. In some cases, transposons can also jump between different host DNA molecules, such as plasmids or viruses, contributing to genetic variability.Barbara McClintock first discovered these mobile genetic elements in the 1940s while studying maize genetics, and she...
1.3K
03:08LTR Retrotransposons
19.4K
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...
The internal coding region of LTR retrotransposons and their mechanism of transposition closely resembles a...
19.4K
02:42Eukaryotic Transcription Activators
12.5K
Transcription activators are proteins that promote the transcription of genes from DNA to RNA. In most cases, these proteins contain two separate domains ‒ a domain that binds to DNA and a domain for activating transcription; however, in some cases, a single domain is responsible for both binding and activation of transcription, as seen in the glucocorticoid receptor and MyoD.
The binding domains are capable of recognizing and interacting with regulatory sequences on the DNA. These...
The binding domains are capable of recognizing and interacting with regulatory sequences on the DNA. These...
12.5K
03:18Non-LTR Retrotransposons
13.2K
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...
13.2K