|
| Status |
Public on May 11, 2016 |
| Title |
Synchronized translation programs across cellular compartments |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
Oxidative phosphorylation (OXPHOS) is fundamental for life. OXPHOS complexes pose a unique challenge for the cell, because their subunits are encoded on two different genomes, the nuclear genome and the mitochondrial genome. Genomic approaches designed to study nuclear/cytosolic and bacterial gene expression have not been broadly applied to the mitochondrial system, thus the co-regulation of OXPHOS genes remains largely unexplored. Here we globally monitored mitochondrial and nuclear gene expression processes during mitochondrial biogenesis when OXPHOS complexes are synthesized. Nuclear- and mitochondrial- encoded OXPHOS transcript levels do not increase concordantly. Instead, we observe that mitochondrial and cytosolic translation are rapidly and dynamically regulated in a strikingly synchronous fashion. Furthermore, the coordinated translation programs are controlled unidirectionally through the intricate and dynamic control of cytosolic translation. Thus the nuclear genome carefully directs the coordination of mitochondrial and cytosolic translation to orchestrate the timely synthesis of each OXPHOS complex, representing an unappreciated regulatory layer shaping the mitochondrial proteome. Our whole-cell genomic profiling approach establishes a foundation for global gene regulatory studies of mitochondrial biology.
|
| |
|
| Overall design |
Examination of whole-cell RNA levels (rRNA-depleted RNA-seq) and both cytosolic and mitochondrial translation regulation (cytoribosome profiling and mitoribosome profiling) through mitochondrial biogenesis in S. cerevisiae
|
| |
|
| Contributor(s) |
Couvillion MT, Soto IC, Shipkovenska G, Churchman SL |
| Citation(s) |
27225121 |
| |
| Submission date |
Oct 28, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Mary T Couvillion |
| E-mail(s) |
mtcouvi@gmail.com
|
| Organization name |
Harvard Medical School
|
| Department |
Genetics
|
| Lab |
Stirling Churchman
|
| Street address |
77 Avenue Louis Pasteur
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL17143 |
Illumina MiSeq (Saccharomyces cerevisiae) |
| GPL19756 |
Illumina NextSeq 500 (Saccharomyces cerevisiae) |
|
| Samples (36)
|
|
| Relations |
| BioProject |
PRJNA300880 |
| SRA |
SRP065628 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE74454_CytoriboProfiling_RPKM.txt.gz |
563.7 Kb |
(ftp)(http) |
TXT |
| GSE74454_MitoriboProfiling_RPKmitoM_TlnEfficiency.xlsx |
63.0 Kb |
(ftp)(http) |
XLSX |
| GSE74454_RAW.tar |
1.7 Mb |
(http)(custom) |
TAR (of BEDGRAPH, TXT, WIG) |
| GSE74454_README.txt |
1.7 Kb |
(ftp)(http) |
TXT |
| GSE74454_RNAseq_RPKM.txt.gz |
595.9 Kb |
(ftp)(http) |
TXT |
| GSE74454_RNAseq_RPKS.txt.gz |
337.8 Kb |
(ftp)(http) |
TXT |
| GSE74454_RNAseq_RPKS_Log2.txt.gz |
195.7 Kb |
(ftp)(http) |
TXT |
| GSE74454_TranslationEfficiency.txt.gz |
558.0 Kb |
(ftp)(http) |
TXT |
| GSE74454_TranslationEfficiency_Log2.txt.gz |
358.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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