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| Status |
Public on Jul 08, 2024 |
| Title |
Epstein-Barr virus induces host shutoff extensively via BGLF5-independent mechanisms [RNA-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
This study characterizes the effects of Epstein-Barr virus (EBV) reactivation on the host and virus transcriptomes. For this work, a dual-fluorescent lytic reporter (DFLR) EBV was constructed based on the M81 EBV strain and used to transform primary B cells into lymphoblastoid cell lines (LCL). Deposited here is RNA-seq data from these DFLR LCLs that were induced by BCR crosslinking and sorted into latent, early lytic, and late lytic fractions. All samples consist of 40,000 sorted cells and include equal quantities of ERCC spike-in RNAs for normalization. We also performed the same experimental approach on a second DFLR LCL in which the EBV BGLF5 host shutoff nuclease was deleted. This allowed us to define which changes in the transcriptome during EBV replication were due to BGLF5. This approach demonstrated extensive shutoff of host genes during EBV replication and, unexpectedly, revealed that most of those changes were independent of BGLF5.
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| Overall design |
DFLR and DFLR BGLF5-knockout (dBGLF5) LCLs induced into lytic EBV replication were FAC-sorted and RNA-sequenced (5 and 3 biological replicates, respectively) to characterize transcriptomic changes during early and late lytic phases and investigate BGLF5's role in host shutoff. Differential gene expression and alternative splicing/readthrough transcription were analyzed between latent and lytic fractions in WT and BGLF5-deficient LCLs.
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| Contributor(s) |
Casco A, Makoto O, Johannsen E |
| Citation(s) |
39298313 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| P01 CA022443 |
Molecular Biology and Genetics of Human Tumor Viruses |
UNIVERSITY OF WISCONSIN MADISON |
Paul F. Lambert |
| U01 CA275247 |
Role of Epstein-Barr virus LMP2A protein in maintaining oncogenic IgM signaling in EBV+ B cell lymphomas |
UNIVERSITY OF WISCONSIN MADISON |
Eric C Johannsen |
| T32 CA009135 |
Training in Cancer Biology Training Grant |
UNIVERSITY OF WISCONSIN MADISON |
William M. Sugden |
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| Submission date |
Jul 08, 2024 |
| Last update date |
Sep 23, 2024 |
| Contact name |
Alejandro Casco |
| E-mail(s) |
casco@wisc.edu
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| Phone |
2812530570
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| Organization name |
University of Wisconsin-Madison
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| Street address |
1111 Highland Ave
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| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53705 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (29)
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| GSM8383377 |
DFLR LCL, late lytic fraction, c3-1 |
| GSM8383378 |
DFLR LCL, bulk fraction, c3-2 |
| GSM8383379 |
DFLR LCL, latent fraction, c3-2 |
| GSM8383380 |
DFLR LCL, early lytic fraction, c3-2 |
| GSM8383381 |
DFLR LCL, late lytic fraction, c3-2 |
| GSM8383382 |
DFLR LCL, bulk fraction, c3-3 |
| GSM8383383 |
DFLR LCL, latent fraction, c3-3 |
| GSM8383384 |
DFLR LCL, early lytic fraction, c3-3 |
| GSM8383385 |
DFLR LCL, late lytic fraction, c3-3 |
| GSM8383386 |
DFLR LCL, bulk fraction, c4-1 |
| GSM8383387 |
DFLR LCL, latent fraction, c4-1 |
| GSM8383388 |
DFLR LCL, early lytic fraction, c4-1 |
| GSM8383389 |
DFLR LCL, late lytic fraction, c4-1 |
| GSM8383390 |
DFLR LCL, bulk fraction, c4-2 |
| GSM8383391 |
DFLR LCL, latent fraction, c4-2 |
| GSM8383392 |
DFLR LCL, early lytic fraction, c4-2 |
| GSM8383393 |
DFLR LCL, late lytic fraction, c4-2 |
| GSM8383394 |
DFLR dBGLF5 LCL, latent fraction, c2-1 |
| GSM8383395 |
DFLR dBGLF5 LCL, early lytic fraction, c2-1 |
| GSM8383396 |
DFLR dBGLF5 LCL, late lytic fraction, c2-1 |
| GSM8383397 |
DFLR dBGLF5 LCL, latent fraction, c2-2 |
| GSM8383398 |
DFLR dBGLF5 LCL, early lytic fraction, c2-2 |
| GSM8383399 |
DFLR dBGLF5 LCL, late lytic fraction, c2-2 |
| GSM8383400 |
DFLR dBGLF5 LCL, latent fraction, c2-3 |
| GSM8383401 |
DFLR dBGLF5 LCL, early lytic fraction, c2-3 |
| GSM8383402 |
DFLR dBGLF5 LCL, late lytic fraction, c2-3 |
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| Relations |
| BioProject |
PRJNA1132980 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE271717_RAW.tar |
160.0 Mb |
(http)(custom) |
TAR (of RESULTS) |
SRA Run Selector |
| Raw data are available in SRA |
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