Large-scale ORF screening based on LC-MS to discover novel lncRNA-encoded peptides responding to ionizing radiation and microgravity
In the human genome, 98% of genes can be transcribed into non-coding RNAs (ncRNAs), among which lncRNAs and their encoded peptides play important roles in regulating various aspects of cellular processes and may serve as crucial factors in modulating the biological effects induced by ionizing radiat...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-01-01
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| Series: | Computational and Structural Biotechnology Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037023003963 |
| _version_ | 1797384080477650944 |
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| author | Wanshi Li Yongduo Yu Guangming Zhou Guang Hu Bingyan Li Hong Ma Wenying Yan Hailong Pei |
| author_facet | Wanshi Li Yongduo Yu Guangming Zhou Guang Hu Bingyan Li Hong Ma Wenying Yan Hailong Pei |
| author_sort | Wanshi Li |
| collection | DOAJ |
| description | In the human genome, 98% of genes can be transcribed into non-coding RNAs (ncRNAs), among which lncRNAs and their encoded peptides play important roles in regulating various aspects of cellular processes and may serve as crucial factors in modulating the biological effects induced by ionizing radiation and microgravity. Unfortunately, there are few reports in space radiation biology on lncRNA-encoded peptides below 10kD due to limitations in detection techniques. To fill this gap, we integrated a variety of methods based on genomics and peptidomics, and discovered 22 lncRNA-encoded small peptides that are sensitive to space radiation and microgravity, which have never been reported before. We concurrently validated the transmembrane helix, subcellular localization, and biological function of these small peptides using bioinformatics and molecular biology techniques. More importantly, we found that these small peptides function independently of the lncRNAs that encode them. Our findings have uncovered a previously unknown human proteome encoded by 'non-coding' genes in response to space conditions and elucidated their involvement in biological processes, providing valuable strategies for individual protection mechanisms for astronauts who carry out deep space exploration missions in space radiation environments. |
| first_indexed | 2024-03-08T21:30:21Z |
| format | Article |
| id | doaj.art-a3d30beca7ba429eaf6d872a9c26fab9 |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-03-08T21:30:21Z |
| publishDate | 2023-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-a3d30beca7ba429eaf6d872a9c26fab92023-12-21T07:32:24ZengElsevierComputational and Structural Biotechnology Journal2001-03702023-01-012152015211Large-scale ORF screening based on LC-MS to discover novel lncRNA-encoded peptides responding to ionizing radiation and microgravityWanshi Li0Yongduo Yu1Guangming Zhou2Guang Hu3Bingyan Li4Hong Ma5Wenying Yan6Hailong Pei7State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, ChinaState Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, ChinaState Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, ChinaDepartment of Bioinformatics, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215123, China; Center for Systems Biology, Soochow University, Suzhou 215123, China; Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Suzhou 215123, ChinaState Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, ChinaBeijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing 100081, ChinaDepartment of Bioinformatics, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215123, China; Center for Systems Biology, Soochow University, Suzhou 215123, China; Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Suzhou 215123, China; Corresponding author at: Department of Bioinformatics, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215123, China.State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China; Corresponding author.In the human genome, 98% of genes can be transcribed into non-coding RNAs (ncRNAs), among which lncRNAs and their encoded peptides play important roles in regulating various aspects of cellular processes and may serve as crucial factors in modulating the biological effects induced by ionizing radiation and microgravity. Unfortunately, there are few reports in space radiation biology on lncRNA-encoded peptides below 10kD due to limitations in detection techniques. To fill this gap, we integrated a variety of methods based on genomics and peptidomics, and discovered 22 lncRNA-encoded small peptides that are sensitive to space radiation and microgravity, which have never been reported before. We concurrently validated the transmembrane helix, subcellular localization, and biological function of these small peptides using bioinformatics and molecular biology techniques. More importantly, we found that these small peptides function independently of the lncRNAs that encode them. Our findings have uncovered a previously unknown human proteome encoded by 'non-coding' genes in response to space conditions and elucidated their involvement in biological processes, providing valuable strategies for individual protection mechanisms for astronauts who carry out deep space exploration missions in space radiation environments.http://www.sciencedirect.com/science/article/pii/S2001037023003963Space radiationMicrogravityLong non-coding RNAPeptideMulti-omics integration |
| spellingShingle | Wanshi Li Yongduo Yu Guangming Zhou Guang Hu Bingyan Li Hong Ma Wenying Yan Hailong Pei Large-scale ORF screening based on LC-MS to discover novel lncRNA-encoded peptides responding to ionizing radiation and microgravity Computational and Structural Biotechnology Journal Space radiation Microgravity Long non-coding RNA Peptide Multi-omics integration |
| title | Large-scale ORF screening based on LC-MS to discover novel lncRNA-encoded peptides responding to ionizing radiation and microgravity |
| title_full | Large-scale ORF screening based on LC-MS to discover novel lncRNA-encoded peptides responding to ionizing radiation and microgravity |
| title_fullStr | Large-scale ORF screening based on LC-MS to discover novel lncRNA-encoded peptides responding to ionizing radiation and microgravity |
| title_full_unstemmed | Large-scale ORF screening based on LC-MS to discover novel lncRNA-encoded peptides responding to ionizing radiation and microgravity |
| title_short | Large-scale ORF screening based on LC-MS to discover novel lncRNA-encoded peptides responding to ionizing radiation and microgravity |
| title_sort | large scale orf screening based on lc ms to discover novel lncrna encoded peptides responding to ionizing radiation and microgravity |
| topic | Space radiation Microgravity Long non-coding RNA Peptide Multi-omics integration |
| url | http://www.sciencedirect.com/science/article/pii/S2001037023003963 |
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