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Shi Z, Wu H. CTPredictor: A comprehensive and robust framework for predicting cell types by integrating multi-scale features from single-cell Hi-C data. Comput Biol Med 2024; 173:108336. [PMID: 38513390 DOI: 10.1016/j.compbiomed.2024.108336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/01/2024] [Accepted: 03/17/2024] [Indexed: 03/23/2024]
Abstract
Single-cell Hi-C (scHi-C) has emerged as a powerful technology for deciphering cell-to-cell variability in three-dimensional (3D) chromatin organization, providing insights into genome-wide chromatin interactions and their correlation with cellular functions. Nevertheless, the accurate identification of cell types across different datasets remains a formidable challenge, hindering comprehensive investigations into genome structure. In response, we introduce CTPredictor, an innovative computational method that integrates multi-scale features to accurately predict cell types in various datasets. CTPredictor strategically incorporates three distinct feature sets, namely, small intra-domain contact probability (SICP), smoothed small intra-domain contact probability (SSICP), and smoothed bin contact probability (SBCP). The resulting fusion classification model significantly enhances the accuracy of cell type prediction based on single-cell Hi-C data (scHi-C). Rigorous benchmarking against established methods and three conventional machine learning approaches demonstrates the robust performance of CTPredictor, positioning it as an advanced tool for cell type prediction within scHi-C data. Beyond its prediction capabilities, CTPredictor holds promise in illuminating 3D genome structures and their functional significance across a wide array of biological processes.
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Affiliation(s)
- Zhenqi Shi
- School of Software, Shandong University, 250100, Jinan, China
| | - Hao Wu
- School of Software, Shandong University, 250100, Jinan, China.
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Wang P, Wu B, You S, Lu S, Xiong S, Zou Y, Jia P, Guo X, Zhang Y, Cao L, Sun Y, Zhang N. DNA Polymerase Gamma Recovers Mitochondrial Function and Inhibits Vascular Calcification by Interacted with p53. Int J Biol Sci 2022; 18:409-425. [PMID: 34975341 PMCID: PMC8692132 DOI: 10.7150/ijbs.65030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
DNA polymerase gamma (PolG) is the major polymerase of mitochondrial DNA (mtDNA) and essential for stabilizing mitochondrial function. Vascular calcification (VC) is common senescence related degenerative pathology phenomenon in the end-stage of multiple chronic diseases. Mitochondrial dysfunction was often observed in calcified vessels, but the function and mechanism of PolG in the calcification process was still unknown. The present study found PolGD257A/D257A mice presented more severe calcification of aortas than wild type (WT) mice with vitamin D3 (Vit D3) treatment, and this phenomenon was also confirmed in vitro. Mechanistically, PolG could enhance the recruitment and interaction of p53 in calcification condition to recover mitochondrial function and eventually to resist calcification. Meanwhile, we found the mutant PolG (D257A) failed to achieve the same rescue effects, suggesting the 3'-5' exonuclease activity guarantee the enhanced interaction of p53 and PolG in response to calcification stimulation. Thus, we believed that it was PolG, not mutant PolG, could maintain mitochondrial function and attenuate calcification in vitro and in vivo. And PolG could be a novel potential therapeutic target against calcification, providing a novel insight to clinical treatment.
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Affiliation(s)
- Pengbo Wang
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People Republic of China
| | - Boquan Wu
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People Republic of China
| | - Shilong You
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People Republic of China
| | - Saien Lu
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People Republic of China
| | - Shengjun Xiong
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People Republic of China
| | - Yuanming Zou
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People Republic of China
| | - Pengyu Jia
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People Republic of China
| | - Xiaofan Guo
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People Republic of China
| | - Ying Zhang
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People Republic of China
| | - Liu Cao
- College of Basic Medical Science, Institute of Translational Medicine, Key Laboratory of Medical Cell Biology, Ministry of Education, Key Laboratory of Liaoning Province, China Medical University, Shenyang, 110122, Liaoning Province, People Republic of China
| | - Yingxian Sun
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People Republic of China
| | - Naijin Zhang
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People Republic of China
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