Identification and partial characterization of new cell density-dependent nucleocytoplasmic shuttling proteins and open chromatin
Abstract The contact inhibition of proliferation (CIP) denotes the cell density-dependent inhibition of growth, and the loss of CIP represents a hallmark of cancer. However, the mechanism by which CIP regulates gene expression remains poorly understood. Chromatin is a highly complex structure consis...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2023-12-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-49100-6 |
| _version_ | 1827590667912609792 |
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| author | Kangjing Li Yaxin Li Fumihiko Nakamura |
| author_facet | Kangjing Li Yaxin Li Fumihiko Nakamura |
| author_sort | Kangjing Li |
| collection | DOAJ |
| description | Abstract The contact inhibition of proliferation (CIP) denotes the cell density-dependent inhibition of growth, and the loss of CIP represents a hallmark of cancer. However, the mechanism by which CIP regulates gene expression remains poorly understood. Chromatin is a highly complex structure consisting of DNA, histones, and trans-acting factors (TAFs). The binding of TAF proteins to specific chromosomal loci regulates gene expression. Therefore, profiling chromatin is crucial for gaining insight into the gene expression mechanism of CIP. In this study, using modified proteomics of TAFs bound to DNA, we identified a protein that shuttles between the nucleus and cytosol in a cell density-dependent manner. We identified TIPARP, PTGES3, CBFB, and SMAD4 as cell density-dependent nucleocytoplasmic shuttling proteins. In low-density cells, these proteins predominantly reside in the nucleus; however, upon reaching high density, they relocate to the cytosol. Given their established roles in gene regulation, our findings propose their involvement as CIP-dependent TAFs. We also identified and characterized potential open chromatin regions sensitive to changes in cell density. These findings provide insights into the modulation of chromatin structure by CIP. |
| first_indexed | 2024-03-09T01:20:03Z |
| format | Article |
| id | doaj.art-eee46e92976746c5853be2d5eaf14e3d |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-09T01:20:03Z |
| publishDate | 2023-12-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-eee46e92976746c5853be2d5eaf14e3d2023-12-10T12:14:16ZengNature PortfolioScientific Reports2045-23222023-12-0113111510.1038/s41598-023-49100-6Identification and partial characterization of new cell density-dependent nucleocytoplasmic shuttling proteins and open chromatinKangjing Li0Yaxin Li1Fumihiko Nakamura2School of Pharmaceutical Science and Technology, Tianjin University, Nankai DistrictSchool of Pharmaceutical Science and Technology, Tianjin University, Nankai DistrictSchool of Pharmaceutical Science and Technology, Tianjin University, Nankai DistrictAbstract The contact inhibition of proliferation (CIP) denotes the cell density-dependent inhibition of growth, and the loss of CIP represents a hallmark of cancer. However, the mechanism by which CIP regulates gene expression remains poorly understood. Chromatin is a highly complex structure consisting of DNA, histones, and trans-acting factors (TAFs). The binding of TAF proteins to specific chromosomal loci regulates gene expression. Therefore, profiling chromatin is crucial for gaining insight into the gene expression mechanism of CIP. In this study, using modified proteomics of TAFs bound to DNA, we identified a protein that shuttles between the nucleus and cytosol in a cell density-dependent manner. We identified TIPARP, PTGES3, CBFB, and SMAD4 as cell density-dependent nucleocytoplasmic shuttling proteins. In low-density cells, these proteins predominantly reside in the nucleus; however, upon reaching high density, they relocate to the cytosol. Given their established roles in gene regulation, our findings propose their involvement as CIP-dependent TAFs. We also identified and characterized potential open chromatin regions sensitive to changes in cell density. These findings provide insights into the modulation of chromatin structure by CIP.https://doi.org/10.1038/s41598-023-49100-6 |
| spellingShingle | Kangjing Li Yaxin Li Fumihiko Nakamura Identification and partial characterization of new cell density-dependent nucleocytoplasmic shuttling proteins and open chromatin Scientific Reports |
| title | Identification and partial characterization of new cell density-dependent nucleocytoplasmic shuttling proteins and open chromatin |
| title_full | Identification and partial characterization of new cell density-dependent nucleocytoplasmic shuttling proteins and open chromatin |
| title_fullStr | Identification and partial characterization of new cell density-dependent nucleocytoplasmic shuttling proteins and open chromatin |
| title_full_unstemmed | Identification and partial characterization of new cell density-dependent nucleocytoplasmic shuttling proteins and open chromatin |
| title_short | Identification and partial characterization of new cell density-dependent nucleocytoplasmic shuttling proteins and open chromatin |
| title_sort | identification and partial characterization of new cell density dependent nucleocytoplasmic shuttling proteins and open chromatin |
| url | https://doi.org/10.1038/s41598-023-49100-6 |
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