An integrated approach for mapping RNA protein interactions in the ribosome
| Project/Area Number |
22K19291
|
|---|
| Research Category |
Grant-in-Aid for Challenging Research (Exploratory)
|
| Allocation Type | Multi-year Fund |
|---|
| Review Section |
Medium-sized Section 43:Biology at molecular to cellular levels, and related fields
|
|---|
| Research Institution | Kyoto University |
|---|
Principal Investigator |
|
|---|
| Co-Investigator(Kenkyū-buntansha) |
Packwood Daniel 京都大学, 高等研究院, 准教授 (40640884)
|
|---|
| Project Period (FY) |
2022-06-30 – 2024-03-31
|
| Project Status |
Completed (Fiscal Year 2023)
|
| Budget Amount *help |
¥6,370,000 (Direct Cost: ¥4,900,000、Indirect Cost: ¥1,470,000)
Fiscal Year 2023: ¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000)
Fiscal Year 2022: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000)
|
|---|
| Keywords | ナノポアシークエンシング / リボソーム / RNA-たんぱく質相互作用 / ケミカルプローブ / バイオインフォマティクス / Nanopore / Direct RNA sequencing / RNA-protein interactions / Chemical probe / Machine learning |
|---|
| Outline of Research at the Start |
本研究は、学際的なアプローチを使用して、RNP-BI-NANO-Seqと呼ばれる迅速に適応できるシーケンス技術を開発することを目的としている。これにより、癌のリボソームにおけるRNA-タンパク質相互作用を調べる既存の方法における欠点を克服することが可能である。癌だけでなく他の多くの病気でもリボソームの機能不全は見られる。これら疾患に対する既存の薬剤の多く はリボソームを標的にしており、結果として得られたデータセットは、新しい創薬可能な RNA構造を明らかにし、新しい創薬に役立つ。
|
| Outline of Annual Research Achievements |
During this fiscal year, we accomplished the primary objective of our research: to develop an integrated approach to map RNA modifications and their interaction with proteins. Following the research plan, We have successfully designed, synthesized, and identified the novel bifunctional probe that interacts with an RNA structural modification and their interaction with a peptide sequence of ribosomal proteins. We have advanced an informatic software called Indo-C to distinguish characteristic current signal trace changes due to resulting covalent adducts from the original pattern during nanopore sequencing and achieved a single nucleotide prediction accuracy of 79% using an RNA-targeted CRISPR-CAS13a system. Furthermore, we extended our strategy to map 8-oxo-7,8-dihydroguanine at single-nucleotide resolution in synthesized DNA strands. During our project, we encountered a bottleneck with the compatibility of protein nanopores of smaller sizes with bulkier chemical probes that prompted us to devise a successfully funded proposal for developing a new biomolecular sequencing technology. Our team has already created programmable nanopores using nucleic acids in varied sizes, shapes and constrictions. We plan to demonstrate the sequencing ability of these new nanopores using DNA, RNA, RNA base, structural modifications, and RNA-protein interactions and verify its universal adaptability. Additionally, we summarized the results in a different but closely related theme of nanomaterials, bioinformatic, and selectively reactive chemicals as original articles and reviews.
|
Report
(2 results)
Research Products
(27 results)
