Minimal twister sister-like self-cleaving ribozymes in the human genome revealed by deep mutational scanning
Despite their importance in a wide range of living organisms, self-cleaving ribozymes in the human genome are few and poorly studied. Here, we performed deep mutational scanning and covariance analysis of two previously proposed self-cleaving ribozymes (LINE-1 and OR4K15). We found that the regions...
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eLife Sciences Publications Ltd
2024-12-01
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| Online Access: | https://elifesciences.org/articles/90254 |
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| author | Zhe Zhang Xu Hong Peng Xiong Junfeng Wang Yaoqi Zhou Jian Zhan |
| author_facet | Zhe Zhang Xu Hong Peng Xiong Junfeng Wang Yaoqi Zhou Jian Zhan |
| author_sort | Zhe Zhang |
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| description | Despite their importance in a wide range of living organisms, self-cleaving ribozymes in the human genome are few and poorly studied. Here, we performed deep mutational scanning and covariance analysis of two previously proposed self-cleaving ribozymes (LINE-1 and OR4K15). We found that the regions essential for ribozyme activities are made of two short segments, with a total of 35 and 31 nucleotides only. The discovery makes them the simplest known self-cleaving ribozymes. Moreover, the essential regions are circular permutated with two nearly identical catalytic internal loops, supported by two stems of different lengths. These two self-cleaving ribozymes, which are shaped like lanterns, are similar to the catalytic regions of the twister sister ribozymes in terms of sequence and secondary structure. However, the nucleotides at the cleavage site have shown that mutational effects on two twister sister-like (TS-like) ribozymes are different from the twister sister ribozyme. The discovery of TS-like ribozymes reveals a ribozyme class with the simplest and, perhaps, the most primitive structure needed for self-cleavage. |
| format | Article |
| id | doaj-art-8f97ad4700a048e0931da6ab62e04caf |
| institution | OA Journals |
| issn | 2050-084X |
| language | English |
| publishDate | 2024-12-01 |
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| spelling | doaj-art-8f97ad4700a048e0931da6ab62e04caf2025-08-20T02:31:24ZengeLife Sciences Publications LtdeLife2050-084X2024-12-011210.7554/eLife.90254Minimal twister sister-like self-cleaving ribozymes in the human genome revealed by deep mutational scanningZhe Zhang0https://orcid.org/0000-0001-7783-7683Xu Hong1Peng Xiong2Junfeng Wang3Yaoqi Zhou4https://orcid.org/0000-0002-9958-5699Jian Zhan5Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China; University of Science and Technology of China, Hefei, China; Institute for Biomedicine and Glycomics, Griffith University, Southport, AustraliaInstitute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China; University of Science and Technology of China, Hefei, ChinaUniversity of Science and Technology of China, Hefei, China; Institute for Biomedicine and Glycomics, Griffith University, Southport, Australia; Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, ChinaHigh Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China; Institute of Physical Science and Information Technology, Anhui University, Hefei, ChinaInstitute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China; Institute for Biomedicine and Glycomics, Griffith University, Southport, Australia; School of Information and Communication Technology, Griffith University, Southport, AustraliaInstitute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China; Institute for Biomedicine and Glycomics, Griffith University, Southport, Australia; Ribopeutic Inc, Guangzhou International Bio Island, Guangzhou, ChinaDespite their importance in a wide range of living organisms, self-cleaving ribozymes in the human genome are few and poorly studied. Here, we performed deep mutational scanning and covariance analysis of two previously proposed self-cleaving ribozymes (LINE-1 and OR4K15). We found that the regions essential for ribozyme activities are made of two short segments, with a total of 35 and 31 nucleotides only. The discovery makes them the simplest known self-cleaving ribozymes. Moreover, the essential regions are circular permutated with two nearly identical catalytic internal loops, supported by two stems of different lengths. These two self-cleaving ribozymes, which are shaped like lanterns, are similar to the catalytic regions of the twister sister ribozymes in terms of sequence and secondary structure. However, the nucleotides at the cleavage site have shown that mutational effects on two twister sister-like (TS-like) ribozymes are different from the twister sister ribozyme. The discovery of TS-like ribozymes reveals a ribozyme class with the simplest and, perhaps, the most primitive structure needed for self-cleavage.https://elifesciences.org/articles/90254self-cleaving ribozymedeep mutational scanningRNA structurecovariationcatalytic RNA |
| spellingShingle | Zhe Zhang Xu Hong Peng Xiong Junfeng Wang Yaoqi Zhou Jian Zhan Minimal twister sister-like self-cleaving ribozymes in the human genome revealed by deep mutational scanning eLife self-cleaving ribozyme deep mutational scanning RNA structure covariation catalytic RNA |
| title | Minimal twister sister-like self-cleaving ribozymes in the human genome revealed by deep mutational scanning |
| title_full | Minimal twister sister-like self-cleaving ribozymes in the human genome revealed by deep mutational scanning |
| title_fullStr | Minimal twister sister-like self-cleaving ribozymes in the human genome revealed by deep mutational scanning |
| title_full_unstemmed | Minimal twister sister-like self-cleaving ribozymes in the human genome revealed by deep mutational scanning |
| title_short | Minimal twister sister-like self-cleaving ribozymes in the human genome revealed by deep mutational scanning |
| title_sort | minimal twister sister like self cleaving ribozymes in the human genome revealed by deep mutational scanning |
| topic | self-cleaving ribozyme deep mutational scanning RNA structure covariation catalytic RNA |
| url | https://elifesciences.org/articles/90254 |
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