Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation
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ABSTRACT:
PROVIDER: PRJNA638017 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11950038_1.fastq.gz | Fastqsanger.gz | |||
| SRR11950038_2.fastq.gz | Fastqsanger.gz | |||
| SRR11950039_1.fastq.gz | Fastqsanger.gz | |||
| SRR11950039_2.fastq.gz | Fastqsanger.gz | |||
| SRR11950040_1.fastq.gz | Fastqsanger.gz |
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Project description:We treated HEK293T cells with different doses of RNase and sequence RNA fragements after the treatments. Furthermore, we developed a low-input RNase footprinting approach to quantify genome-wide RNA translation using 50,000 and 1,000 HEK293T and K562 cells. The ribosome profiling and RNA-seq data were used as the control.
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Project description:We describe a low-input RNase footprinting approach for the rapid quantification of ribosome-protected fragments with as few as 1000 cultured cells. The assay uses a simplified procedure to selectively capture ribosome footprints based on optimized RNase digestion. It simultaneously maps cytosolic and mitochondrial translation with single-nucleotide resolution. We applied it to reveal selective functions of the elongation factor TUFM in mitochondrial translation, as well as synchronized repression of cytosolic translation after TUFM perturbation. We show the assay is applicable to small amounts of primary tissue samples with low protein synthesis rates, including snap-frozen tissues and immune cells from an individual's blood draw. We showed its feasibility to characterize the personalized immuno-translatome. Our analyses revealed that thousands of genes show lower translation efficiency in monocytes compared with lymphocytes, and identified thousands of translated noncanonical open reading frames (ORFs). Altogether, our RNase footprinting approach opens an avenue to assay transcriptome-wide translation using low-input samples from a wide range of physiological conditions.
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Project description:This SuperSeries is composed of the SubSeries listed below.
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