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Low-input RNase footprinting to profile RNA translation

ABSTRACT: Low-input RNase footprinting to profile RNA translation

PROVIDER: PRJNA638018 | ENA |

REPOSITORIES: ENA

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Low-input RNase footprinting to profile RNA translation

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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Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation

Project description:Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation

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Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation

Project description:This SuperSeries is composed of the SubSeries listed below.

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LRPPRC-mediated folding of the mitochondrial transcriptome [RNase footprinting]

Project description:The roles of RNA-binding proteins as chaperones in the lifecycles of mRNAs are not well understood. The mammalian mitochondrial genome has been compressed over evolution to a size of just 16 kb, nevertheless the expression of its genes requires transcription, RNA processing, translation and RNA decay, much like the more complex chromosomal systems, providing an opportunity to use it as a model system to understand the fundamental aspects of gene expression. Here we combine RNase footprinting with PAR-CLIP at unprecedented depth to reveal the importance of RNA-protein interactions guided by the LRPPRC/SLIRP complex in dictating RNA folding within the mitochondrial transcriptome. We show that LRPPRC, in complex with its protein partner SLIRP, binds throughout the mitochondrial transcriptome, with a preference for mRNAs, and its loss affects the entire secondary structure and stability of the transcriptome. We demonstrate that the LRPPRC/SLIRP complex is a global RNA chaperone that stabilizes RNA structures to expose the required sites for translation, stabilization and polyadenylation. Our findings reveal a general mechanism where extensive RNA-protein interactions ensure that RNA is accessible for its biological functions.

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Project description:We performed RNase footprinting and RNA-seq to examine the regulation of RNA translation after TUFM knockout in HeLa cells

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Regulation of RNA translation among human primary immune cells

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