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| Status |
Public on Dec 22, 2022 |
| Title |
A DNA tumor virus globally reprograms host 3D genome architecture to achieve immortal growth |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Other
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| Summary |
Epstein-Barr virus (EBV) immortalizes resting human B lymphocytes in vitro through expression of viral transcription factors (TFs). These viral TFs activate the expression of key oncogenes, many through long-range enhancer looping. Here we combined various chromatin conformation capture related methods (HiC, HiChIP, 4C-seq etc) to systematically evaluate the effect of EBV infection on host genome-wide 3D organization.
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| Overall design |
HiC was performed on resting B cells to recapticulate the 3D chromatin feature before EBV infection and transformation. A time-course RNA-seq was performed to track the dynamics of viral infection of resting B cells. Next, HiChIP was performed on conditional cells for the viral TF, EBNA3A, to understand how it rewires the host nucleus, particular enhancer-promoter interactions. In addition, HiChIP for RNA Polymerase II was also performed on primary B cells at Day 0 and Day 28 after EBV infection. Finally, 4C-seq was performed on conditional cells for the viral TF, EBNA3C, to understand how it modulates host chromatin interactions at the CDKN2A and AID loci.
Please note that the peak data (for GSM5456429-GSM5456440) are generated from both replicates and is linked to the corresponding *rep1 sample records.
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| Contributor(s) |
Liang J, Jiang S, Narita Y, Wang C, Teng M, Zhao B |
| Citation(s) |
36949074 |
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| Submission date |
Mar 27, 2019 |
| Last update date |
Jun 22, 2023 |
| Contact name |
Sizun Jiang |
| Organization name |
BIDMC/Harvard
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| Street address |
3 Blackfan Circle
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platforms (2) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (32)
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| GSM3688942 |
EBNA3C-HT 4C-seq CDKN2A 3C On Replicate 1 |
| GSM3688943 |
EBNA3C-HT 4C-seq CDKN2A 3C On Replicate 2 |
| GSM3688944 |
EBNA3C-HT 4C-seq CDKN2A 3C Off Replicate 1 |
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| Relations |
| BioProject |
PRJNA529479 |
| SRA |
SRP189660 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE128952_C2A5_1neg.aligned_rm_self_und.bedGraph.gz |
340.3 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE128952_C2A5_1pos.aligned_rm_self_und.bedGraph.gz |
442.3 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE128952_C2A5_2neg.aligned_rm_self_und.bedGraph.gz |
270.2 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE128952_C2A5_2pos.aligned_rm_self_und.bedGraph.gz |
306.8 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE128952_E3Coff_unique_AllEnhancers.bed.gz |
160.0 Kb |
(ftp)(http) |
BED |
| GSE128952_E3Con_common_AllEnhancers.bed.gz |
245.1 Kb |
(ftp)(http) |
BED |
| GSE128952_E3Con_unique_AllEnhancers.bed.gz |
27.2 Kb |
(ftp)(http) |
BED |
| GSE128952_EBNA3A_Off_Rep0.norm_Rep0.interactions.all.mango.txt.gz |
9.7 Mb |
(ftp)(http) |
TXT |
| GSE128952_EBNA3A_On_Rep0.norm_Rep0.interactions.all.mango.txt.gz |
9.8 Mb |
(ftp)(http) |
TXT |
| GSE128952_RAW.tar |
5.3 Gb |
(http)(custom) |
TAR (of BED, BEDGRAPH, HIC, NARROWPEAK, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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