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| Status |
Public on Feb 06, 2023 |
| Title |
Single cell quantification of ribosome occupancy in early mouse development |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
Technological limitations precluded transcriptome-wide analyses of translation at single cell resolution. To solve this challenge, we developed a novel microfluidic isotachophoresis approach, named RIBOsome profiling via IsoTachoPhoresis (Ribo-ITP), and characterized translation in single oocytes and embryos during early mouse development. We identified differential translation efficiency as a key regulatory mechanism of genes involved in centrosome organization and N6-methyladenosine modification of RNAs. Our high coverage measurements enabled the first analysis of allele-specific ribosome engagement in early development and led to the discovery of stage-specific differential engagement of zygotic RNAs with ribosomes and reduced translation efficiency of transcripts with allelic-biased expression. Finally, by integrating our measurements with proteomics data, we discovered that ribosome occupancy in germinal vesicle stage oocytes is the predominant determinant of protein abundance in the zygote. The novel Ribo-ITP approach will enable numerous applications by providing high coverage and high resolution ribosome occupancy measurements from ultra-low input samples including single cells.
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| Overall design |
To study translation in mouse development, we performed our novel low-input ribosome profiling method (named Ribo-ITP) and RNA sequencing (Smart-seq3) in mouse oocytes and early stage embryos. To validate our method, we performed Ribo-ITP and conventional ribosome profiling using human K562 cells.
Ribosome profiling by isotachophoresis (Ribo-ITP) of single K562 cells
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| Contributor(s) |
Ozadam H, Tonn T, Han C, Segura A, Hoskins I, Rao S, Ghatpande V, Tran D, Catoe D, Salit M, Cenik C |
| Citation(s) |
37344592 |
| |
| Submission date |
Oct 12, 2021 |
| Last update date |
Sep 11, 2023 |
| Contact name |
Can Cenik |
| E-mail(s) |
ccenik@austin.utexas.edu
|
| Phone |
512-232-2874
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| Organization name |
The University of Texas at Austin
|
| Department |
Molecular Biosciences
|
| Lab |
Cenik
|
| Street address |
Moffett Molecular Biology Building 2.122 2500 Speedway
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712 |
| Country |
USA |
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| Platforms (3) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (58)
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| Relations |
| BioProject |
PRJNA770650 |
| SRA |
SRP341033 |
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