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| Status |
Public on Oct 17, 2012 |
| Title |
Decoding human cytomegalovirus using ribosome profiling |
| Organism |
Human betaherpesvirus 5 |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The human cytomegalovirus (HCMV) genome was sequenced 20 years ago. However, like other complex viruses, our understanding of its protein coding potential is far from complete. Here, we use ribosome profiling and transcript analysis to experimentally define the HCMV translation products and follow their temporal expression. We identified several hundred previously unidentified open reading frames and confirmed a fraction by mass spectrometry. We found that regulated use of alternative transcript start sites plays a broad role in enabling tight temporal control of HCMV protein expression and allowing multiple distinct polypeptides to be generated from a single genomic locus. Our results reveal an unanticipated complexity to the HCMV coding capacity and illustrate the role of regulated changes in transcript start sites in generating this complexity.
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| Overall design |
Ribosome profiling and mRNA-seq from 3 time points (5hr, 24hr, 72hr) along HCMV infection.
The supplementary file 'GSE41605_merlin_final_orfs.bed.gz' includes the 751 ORFs of HCMV that were identified in this study.
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| Contributor(s) |
Stern-Ginossar N, Weisburd B, Michalski A, Le VT, Hein MY, Huang SX, Ma M, Shen B, Qian SB, Hengel H, Mann M, Ingolia NT, Weissman JS |
| Citation(s) |
23180859 |
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| Submission date |
Oct 15, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Noam Ginossar |
| Organization name |
UCSF
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| Street address |
1700 4th street
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| City |
San Francisco |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platforms (2) |
| GPL16185 |
Illumina Genome Analyzer II (Human herpesvirus 5) |
| GPL16186 |
Illumina HiSeq 2000 (Human herpesvirus 5) |
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| Samples (16)
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| GSM1020234 |
Footprints from cells infected with HCMV for 5hr, pretreated with cycloheximide |
| GSM1020235 |
Footprints from cells infected with HCMV for 24hr, pretreated with cycloheximide |
| GSM1020236 |
Footprints from cells infected with HCMV for 72hr, pretreated with cycloheximide |
| GSM1020237 |
Footprints from cells infected with HCMV for 72hr, pretreated with cycloheximide, replicate |
| GSM1020238 |
Footprints from cells infected with HCMV for 5hr, pretreated with Harringtonine |
| GSM1020239 |
Footprints from cells infected with HCMV for 72hr, pretreated with Harringtonine |
| GSM1020240 |
Footprints from cells infected with HCMV for 5hr, pretreated with LTM |
| GSM1020241 |
Footprints from cells infected with HCMV for 72hr, pretreated with LTM |
| GSM1020242 |
Footprints from cells infected with HCMV for 5hr, no drug pretreatment |
| GSM1020243 |
Footprints from cells infected with HCMV for 72hr, no drug pretreatment |
| GSM1020244 |
mRNA-seq from cells infected with HCMV for 5hr |
| GSM1020245 |
mRNA-seq from cells infected with HCMV for 24hr |
| GSM1020246 |
mRNA-seq from cells infected with HCMV for 72hr |
| GSM1020247 |
mRNA-seq from cells infected with HCMV for 5hr, replicate |
| GSM1020248 |
mRNA-seq from cells infected with HCMV for 24hr, replicate |
| GSM1020249 |
mRNA-seq from cells infected with HCMV for 72hr, replicate |
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| Relations |
| BioProject |
PRJNA177721 |
| SRA |
SRP016143 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE41605_RAW.tar |
7.9 Mb |
(http)(custom) |
TAR (of WIG) |
| GSE41605_merlin_final_orfs.bed.gz |
12.4 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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