期刊
GENOME RESEARCH
卷 32, 期 3, 页码 545-557出版社
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1101/gr.276139.121
关键词
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资金
- National Institutes of Health [R35GM138192, R01HL161389, R00CA207865]
- Lynn Sage Breast Cancer Research Foundation
- Lynn Sage Scholar fund
- Searle Leadership Fund in the Life Sciences from Northwestern University
We developed a low-input RNase footprinting technique for rapid quantification of ribosome-protected fragments, applicable to small samples and translation studies under different physiological conditions.
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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