2022 Fiscal Year Annual Research Report
Sensitive and highly multiplexed assessment of lncRNA interactions with chromatin
| Project/Area Number |
19K16098
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| Research Institution | Institute of Physical and Chemical Research |
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Principal Investigator |
柴山 洋太郎 国立研究開発法人理化学研究所, 生命医科学研究センター, 研究員 (60815819)
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| Project Period (FY) |
2019-04-01 – 2023-03-31
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| Keywords | RNA localization / subcellular localization / long noncoding RNA / H3K27ac |
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| Outline of Annual Research Achievements |
In this study, I conducted a genome-wide investigation of differential subcellular localization of RNA between the chromatin, nucleoplasm and cytoplasm under seven different pathway-defined stress inducers, which target essential mechanisms such as transcription, DNA methylation and translation. This was done by sub-cellular fractionation followed by RNA extraction, which were subjected to CAGE sequencing. A computational pipeline to screen for differentially localized RNA and visualize their shift in localization was established. I showed that RNA localization is dynamic, whereby different stress inducers cause distinct patterns of shift in RNA localization. Remarkably, long non-coding RNA is the principal group of localization-shifting RNA and exhibits unique patterns of displacement compared to other RNA classes. Differential localization was validated in twelve species of RNA by single-molecule fluorescent in-situ hybridization. Some lncRNAs were shown to be differentially expressed under stimulation by multiple stress inducers. In such cases, patterns of shift were either common or unique between treatments. Functional investigation into one localization-shifting lncRNA revealed trans-acting activity through the genome. One of the genes where this lncRNA binds was SMARCA4, a member of the SWI/SNF family of proteins which is known to modulate H3K27ac. Knock down of the lncRNA resulted in reduced levels of H3K27ac.
My results suggest that shift in RNA localization provides a common yet previously under-appreciated layer of regulation in gene expression and function.
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