Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Enhancer activation from transposable elements in extrachromosomal DNA

ABSTRACT: Enhancer activation from transposable elements in extrachromosomal DNA

PROVIDER: PRJNA1162517 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Enhancer activation from transposable elements in extrachromosomal DNA

Project description:Extrachromosomal DNA (ecDNA) is a hallmark of aggressive cancer, contributing to both oncogene amplification and tumor heterogeneity. Here, we used Hi-C, super-resolution imaging, and long-read sequencing to explore the nuclear architecture of MYC-amplified ecDNA in colorectal cancer cells. Intriguingly, we observed frequent spatial proximity between ecDNA and 68 repetitive elements which we called ecDNA-interacting elements or EIEs. To characterize a potential regulatory role of EIEs, we focused on a fragment of the L1M4a1#LINE/L1 which we found to be co-amplified with MYC on ecDNA, gaining enhancer-associated chromatin marks in contrast to its normally silenced state. This EIE, in particular, existed as a naturally occurring structural variant upstream of MYC, gaining oncogenic potential in the transcriptionally permissive ecDNA environment. This EIE sequence is sufficient to enhance MYC expression and is required for cancer cell fitness. These findings suggest that silent repetitive genomic elements can be reactivated on ecDNA, leading to functional cooption and amplification. Repeat element activation on ecDNA represents a mechanism of accelerated evolution and tumor heterogeneity and may have diagnostic and therapeutic potential.

2024-09-25 | GSE277492 | GEO

Project description:Enhancer activation from transposable elements in extrachromosomal DNA

| PRJNA1162466 | ENA

C. difficile extrachromosomal elements

Project description:An in silico survey of Clostridioides difficile extrachromosomal elements

| PRJEB32360 | ENA

Integrated analysis of extrachromosomal DNA elements in SCLC [scCNV]

Project description:Integrated analysis of whole-genome sequencing, long-range optical mapping, single-cell DNA sequencing, and fluorescence in situ hybridization to find extrachromosomal DNA (ecDNA) as the primary source of MYC amplifications and driver fusions in SCLC. ecDNAs bring to proximity enhancer elements and oncogenes through circularization, creating transcription-amplifying units, driving heterogeneity of MYC gene dosage and expression of SCLC lineage-defining transcription factors.

2023-01-24 | GSE206352 | GEO

Integrated analysis of extrachromosomal DNA elements in SCLC [HiChIP]

2023-01-24 | GSE206351 | GEO

Integrated analysis of extrachromosomal DNA elements in SCLC [DNA-seq]

2023-01-24 | GSE206353 | GEO

Transposable Elements in Frontotemporal Lobar Degeneration

Project description:Transposable Elements in Frontotemporal Lobar Degeneration

| PRJNA561866 | ENA

Transposable Elements in Frontotemporal Lobar Degeneration

Project description:Transposable Elements in Frontotemporal Lobar Degeneration

| PRJNA561865 | ENA

Integrated analysis of extrachromosomal DNA elements in SCLC