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Series GSE124769 Query DataSets for GSE124769
Status Public on Apr 08, 2021
Title Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Extrachromosomal, circular DNA (ecDNA) is emerging as a prevalent yet less characterized oncogenic alteration in cancer genomes. We leverage ChIA-PET and ChIA-Drop chromatin interaction assays to characterize genome-wide ecDNA-mediated chromatin contacts that impact transcriptional programs in cancers. ecDNAs in glioblastoma patient-derived neurosphere and prostate cancer cell cultures are marked by widespread intra-ecDNA and genome-wide chromosomal interactions. ecDNA-chromatin contact foci are characterized by broad and high-level H3K27ac signals converging predominantly on chromosomal genes of increased expression levels. Prostate cancer cells harboring synthetic ecDNA circles composed of characterized enhancers result in the genome-wide activation of chromosomal gene transcription. Deciphering the chromosomal targets of ecDNAs at single-molecule resolution reveals an association with actively expressed oncogenes spatially clustered within ecDNA-directed interaction networks. Our results suggest that ecDNA can function as mobile transcriptional enhancers to promote tumor progression and manifest a potential synthetic aneuploidy mechanism of transcription control in cancer.
Overall design Perform the chromatin interaction assay ChIA-PET, ChIA-Drop, H3K27ac ChIPseq and RNAseq to define genome-wide ecDNA-mediated chromatin interactomes and to characterize their functional impact on transcription programs in cancers.
Web link
Contributor(s) Zhu Y, Tjong H, Wong CH, Gujar A, Wei CL, Verhaak R
Citation(s) 33836152
Submission date Jan 07, 2019
Last update date Apr 12, 2021
Contact name Chia-Lin Wei
Organization name The Jackson Laboratory
Department Genome Technologies
Lab Chia-Lin Wei
Street address 10 Discovery Dr
City Farmington
State/province CT
ZIP/Postal code 06032
Country USA
Platforms (4)
GPL15520 Illumina MiSeq (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (49)
GSM3553626 HF-2354_chia-pet
GSM3553627 HF-2927_chia-pet
GSM3553628 HF-3016_chia-pet
BioProject PRJNA513379
SRA SRP176485

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE124769_PC3_ecDNA_negative_En-circles_vs_Ctrl-circles.gene_exp.diff.gz 1.2 Mb (ftp)(http) DIFF
GSE124769_RAW.tar 9.5 Gb (http)(custom) TAR (of BW, NARROWPEAK, TXT)
GSE124769_genes.fpkm_tracking.gz 2.1 Mb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Processed data are available on Series record
Processed data provided as supplementary file
Raw data are available in SRA

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