Investigating phase separation properties of chromatin-associated proteins using gradient elution of 1,6-hexanediol
Abstract Background Chromatin-associated phase separation proteins establish various biomolecular condensates via liquid–liquid phase separation (LLPS), which regulates vital biological processes spatially and temporally. However, the widely used methods to characterize phase separation proteins are...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-08-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-023-09600-1 |
| _version_ | 1797453766985777152 |
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| author | Peiyu Zhu Chao Hou Manlin Liu Taoyu Chen Tingting Li Likun Wang |
| author_facet | Peiyu Zhu Chao Hou Manlin Liu Taoyu Chen Tingting Li Likun Wang |
| author_sort | Peiyu Zhu |
| collection | DOAJ |
| description | Abstract Background Chromatin-associated phase separation proteins establish various biomolecular condensates via liquid–liquid phase separation (LLPS), which regulates vital biological processes spatially and temporally. However, the widely used methods to characterize phase separation proteins are still based on low-throughput experiments, which consume time and could not be used to explore protein LLPS properties in bulk. Results By combining gradient 1,6-hexanediol (1,6-HD) elution and quantitative proteomics, we developed chromatin enriching hexanediol separation coupled with liquid chromatography-mass spectrometry (CHS-MS) to explore the LLPS properties of different chromatin-associated proteins (CAPs). First, we found that CAPs were enriched more effectively in the 1,6-HD treatment group than in the isotonic solution treatment group. Further analysis showed that the 1,6-HD treatment group could effectively enrich CAPs prone to LLPS. Finally, we compared the representative proteins eluted by different gradients of 1,6-HD and found that the representative proteins of the 2% 1,6-HD treatment group had the highest percentage of IDRs and LCDs, whereas the 10% 1,6-HD treatment group had the opposite trend. Conclusion This study provides a convenient high-throughput experimental method called CHS-MS. This method can efficiently enrich proteins prone to LLPS and can be extended to explore LLPS properties of CAPs in different biological systems. |
| first_indexed | 2024-03-09T15:27:37Z |
| format | Article |
| id | doaj.art-c42f7621e092430cafefc7b91da21282 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-09T15:27:37Z |
| publishDate | 2023-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-c42f7621e092430cafefc7b91da212822023-11-26T12:26:26ZengBMCBMC Genomics1471-21642023-08-0124111110.1186/s12864-023-09600-1Investigating phase separation properties of chromatin-associated proteins using gradient elution of 1,6-hexanediolPeiyu Zhu0Chao Hou1Manlin Liu2Taoyu Chen3Tingting Li4Likun Wang5Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science CenterDepartment of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science CenterThe MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking UniversityDepartment of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science CenterDepartment of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science CenterDepartment of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science CenterAbstract Background Chromatin-associated phase separation proteins establish various biomolecular condensates via liquid–liquid phase separation (LLPS), which regulates vital biological processes spatially and temporally. However, the widely used methods to characterize phase separation proteins are still based on low-throughput experiments, which consume time and could not be used to explore protein LLPS properties in bulk. Results By combining gradient 1,6-hexanediol (1,6-HD) elution and quantitative proteomics, we developed chromatin enriching hexanediol separation coupled with liquid chromatography-mass spectrometry (CHS-MS) to explore the LLPS properties of different chromatin-associated proteins (CAPs). First, we found that CAPs were enriched more effectively in the 1,6-HD treatment group than in the isotonic solution treatment group. Further analysis showed that the 1,6-HD treatment group could effectively enrich CAPs prone to LLPS. Finally, we compared the representative proteins eluted by different gradients of 1,6-HD and found that the representative proteins of the 2% 1,6-HD treatment group had the highest percentage of IDRs and LCDs, whereas the 10% 1,6-HD treatment group had the opposite trend. Conclusion This study provides a convenient high-throughput experimental method called CHS-MS. This method can efficiently enrich proteins prone to LLPS and can be extended to explore LLPS properties of CAPs in different biological systems.https://doi.org/10.1186/s12864-023-09600-1Liquid–liquid phase separationChromatin-associated proteins1,6-hexanediolHigh-throughput experimental methods |
| spellingShingle | Peiyu Zhu Chao Hou Manlin Liu Taoyu Chen Tingting Li Likun Wang Investigating phase separation properties of chromatin-associated proteins using gradient elution of 1,6-hexanediol BMC Genomics Liquid–liquid phase separation Chromatin-associated proteins 1,6-hexanediol High-throughput experimental methods |
| title | Investigating phase separation properties of chromatin-associated proteins using gradient elution of 1,6-hexanediol |
| title_full | Investigating phase separation properties of chromatin-associated proteins using gradient elution of 1,6-hexanediol |
| title_fullStr | Investigating phase separation properties of chromatin-associated proteins using gradient elution of 1,6-hexanediol |
| title_full_unstemmed | Investigating phase separation properties of chromatin-associated proteins using gradient elution of 1,6-hexanediol |
| title_short | Investigating phase separation properties of chromatin-associated proteins using gradient elution of 1,6-hexanediol |
| title_sort | investigating phase separation properties of chromatin associated proteins using gradient elution of 1 6 hexanediol |
| topic | Liquid–liquid phase separation Chromatin-associated proteins 1,6-hexanediol High-throughput experimental methods |
| url | https://doi.org/10.1186/s12864-023-09600-1 |
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