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Zhao Y, Dong Y, Hong W, Jiang C, Yao K, Cheng C. Computational modeling of chromatin accessibility identified important epigenomic regulators. BMC Genomics 2022; 23:19. [PMID: 34996354 PMCID: PMC8742372 DOI: 10.1186/s12864-021-08234-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/03/2021] [Indexed: 11/28/2022] Open
Abstract
Chromatin accessibility is essential for transcriptional activation of genomic regions. It is well established that transcription factors (TFs) and histone modifications (HMs) play critical roles in chromatin accessibility regulation. However, there is a lack of studies that quantify these relationships. Here we constructed a two-layer model to predict chromatin accessibility by integrating DNA sequence, TF binding, and HM signals. By applying the model to two human cell lines (GM12878 and HepG2), we found that DNA sequences had limited power for accessibility prediction, while both TF binding and HM signals predicted chromatin accessibility with high accuracy. According to the HM model, HM features determined chromatin accessibility in a cell line shared manner, with the prediction power attributing to five core HM types. Results from the TF model indicated that chromatin accessibility was determined by a subset of informative TFs including both cell line-specific and generic TFs. The combined model of both TF and HM signals did not further improve the prediction accuracy, indicating that they provide redundant information in terms of chromatin accessibility prediction. The TFs and HM models can also distinguish the chromatin accessibility of proximal versus distal transcription start sites with high accuracy.
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Affiliation(s)
- Yanding Zhao
- Department of Medicine, Baylor College of Medicine, Room ICTR 100D, One Baylor Plaza, Baylor College of Medicine, Houston, TX, 77030, USA
- The Institute for Clinical and Translational Research, Baylor College of Medicine, Room ICTR 100D, One Baylor Plaza, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yadong Dong
- Department of Medicine, Baylor College of Medicine, Room ICTR 100D, One Baylor Plaza, Baylor College of Medicine, Houston, TX, 77030, USA
- The Institute for Clinical and Translational Research, Baylor College of Medicine, Room ICTR 100D, One Baylor Plaza, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Wei Hong
- Department of Medicine, Baylor College of Medicine, Room ICTR 100D, One Baylor Plaza, Baylor College of Medicine, Houston, TX, 77030, USA
- The Institute for Clinical and Translational Research, Baylor College of Medicine, Room ICTR 100D, One Baylor Plaza, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chongming Jiang
- Department of Medicine, Baylor College of Medicine, Room ICTR 100D, One Baylor Plaza, Baylor College of Medicine, Houston, TX, 77030, USA
- The Institute for Clinical and Translational Research, Baylor College of Medicine, Room ICTR 100D, One Baylor Plaza, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kevin Yao
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Chao Cheng
- Department of Medicine, Baylor College of Medicine, Room ICTR 100D, One Baylor Plaza, Baylor College of Medicine, Houston, TX, 77030, USA.
- The Institute for Clinical and Translational Research, Baylor College of Medicine, Room ICTR 100D, One Baylor Plaza, Baylor College of Medicine, Houston, TX, 77030, USA.
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Garcia-Manteiga JM, D’Alessandro R, Meldolesi J. News about the Role of the Transcription Factor REST in Neurons: From Physiology to Pathology. Int J Mol Sci 2019; 21:E235. [PMID: 31905747 PMCID: PMC6982158 DOI: 10.3390/ijms21010235] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 12/13/2022] Open
Abstract
RE-1 silencing transcription factor (REST) (known also as NRSF) is a well-known transcription repressor whose strong decrease induces the distinction of neurons with respect to the other cells. Such distinction depends on the marked increased/decreased expression of specific genes, accompanied by parallel changes of the corresponding proteins. Many properties of REST had been identified in the past. Here we report those identified during the last 5 years. Among physiological discoveries are hundreds of genes governed directly/indirectly by REST, the mechanisms of its neuron/fibroblast conversions, and the cooperations with numerous distinct factors induced at the epigenetic level and essential for REST specific functions. New effects induced in neurons during brain diseases depend on the localization of REST, in the nucleus, where functions and toxicity occur, and in the cytoplasm. The effects of REST, including cell aggression or protection, are variable in neurodegenerative diseases in view of the distinct mechanisms of their pathology. Moreover, cooperations are among the mechanisms that govern the severity of brain cancers, glioblastomas, and medulloblastomas. Interestingly, the role in cancers is relevant also for therapeutic perspectives affecting the REST cooperations. In conclusion, part of the new REST knowledge in physiology and pathology appears promising for future developments in research and brain diseases.
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Affiliation(s)
| | | | - Jacopo Meldolesi
- IRCCS San Raffaele Scientific Institute, via Olgettina 58, 20132 Milan, Italy;
- Department of Neuroscience, San Raffaele University, via Olgettina 58, 20132 Milan, Italy
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Deng Z, Li W, Alahdal M, Zhang N, Xie J, Hu X, Chen Y, Fang H, Duan L, Gu L, Wang D. Overexpression of ClC-3 Chloride Channel in Chondrosarcoma: An In Vivo Immunohistochemical Study with Tissue Microarray. Med Sci Monit 2019; 25:5044-5053. [PMID: 31281178 PMCID: PMC6637820 DOI: 10.12659/msm.917382] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background Recently, ClC-3 chloride channel expression has been noted to be high in some tumors. In chondrosarcoma, which is a malignant tumor with a high incidence in the bone, there has been no previous literature regarding ClC-3 chloride channel expression. Here we evaluated the expression of ClC-3 chloride channel in chondrosarcoma and explored its clinical significance. Material/Methods In this study, 75 chondrosarcoma and 5 normal cartilage tissues were collected. Thereafter, tissue microarray was performed. Immunohistochemistry was also used to observe the level of ClC-3 chloride channel expression between normal and chondrosarcoma tissues. Results Results showed that the expression of ClC-3 chloride channel in the normal chondrocyte was thinner, since it showed distinct differentiation among chondrosarcoma specimens. Interestingly, we noticed that the moderately-differentiated chondrosarcoma (MDC) and the poorly-differentiated chondrosarcoma (PDC) exhibited 94.44% of ClC-3 chloride channel. Besides, the subcellular localization of ClC-3 chloride channel was changed in association with malignant degree changes. The subcellular localization of ClC-3 chloride channel in the MDC and PDC tissue was localized in the cytoplasm and both nucleus and cytoplasm: 83.33% (5 out of 6 cases) and 91.66% (11 out of 12 cases) respectively. On the other hand, we noticed that patient age and gender could have a relation with ClC-3 chloride channel expression; 30- to 60-year-old males showed more expression. Conclusions These results demonstrated a high frequency of ClC-3 chloride channel overexpression and subcellular localization differences in MDC and PDC tissue, suggesting a specific role of ClC-3 chloride channel in the pathogenesis of chondrosarcoma.
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Affiliation(s)
- Zhiqin Deng
- Department of Microsurgery and Orthopedic Trauma, The First Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China (mainland).,Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Hand and Foot Surgery Department, Shenzhen Second People's Hospital (The First Hospital Affiliated to Shenzhen University), Shenzhen, Guangdong, China (mainland)
| | - Wencui Li
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Hand and Foot Surgery Department, Shenzhen Second People's Hospital (The First Hospital Affiliated to Shenzhen University), Shenzhen, Guangdong, China (mainland)
| | - Murad Alahdal
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Hand and Foot Surgery Department, Shenzhen Second People's Hospital (The First Hospital Affiliated to Shenzhen University), Shenzhen, Guangdong, China (mainland)
| | - Ningfeng Zhang
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Hand and Foot Surgery Department, Shenzhen Second People's Hospital (The First Hospital Affiliated to Shenzhen University), Shenzhen, Guangdong, China (mainland)
| | - Junxiong Xie
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Hand and Foot Surgery Department, Shenzhen Second People's Hospital (The First Hospital Affiliated to Shenzhen University), Shenzhen, Guangdong, China (mainland)
| | - Xiaotian Hu
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Hand and Foot Surgery Department, Shenzhen Second People's Hospital (The First Hospital Affiliated to Shenzhen University), Shenzhen, Guangdong, China (mainland)
| | - Yang Chen
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Hand and Foot Surgery Department, Shenzhen Second People's Hospital (The First Hospital Affiliated to Shenzhen University), Shenzhen, Guangdong, China (mainland)
| | - Huankun Fang
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Hand and Foot Surgery Department, Shenzhen Second People's Hospital (The First Hospital Affiliated to Shenzhen University), Shenzhen, Guangdong, China (mainland)
| | - Li Duan
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Hand and Foot Surgery Department, Shenzhen Second People's Hospital (The First Hospital Affiliated to Shenzhen University), Shenzhen, Guangdong, China (mainland)
| | - Liqiang Gu
- Department of Microsurgery and Orthopedic Trauma, The First Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou, Guangdong, China (mainland)
| | - Daping Wang
- Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Hand and Foot Surgery Department, Shenzhen Second People's Hospital (The First Hospital Affiliated to Shenzhen University), Shenzhen, Guangdong, China (mainland)
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Vo HT, Phillips ML, Herskowitz JH, King GD. Klotho deficiency affects the spine morphology and network synchronization of neurons. Mol Cell Neurosci 2019; 98:1-11. [PMID: 30991103 PMCID: PMC6613977 DOI: 10.1016/j.mcn.2019.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/25/2019] [Accepted: 04/09/2019] [Indexed: 01/01/2023] Open
Abstract
Klotho-deficient mice rapidly develop cognitive impairment and show some evidence of the onset of neurodegeneration. However, it is impossible to investigate the long-term consequences on the brain because of the dramatic shortening of lifespan caused by systemic klotho deficiency. As klotho expression is downregulated with advancing organismal age, understanding the mechanisms of klotho action is important for developing novel strategies to support healthy brain aging. Previously, we reported that klotho-deficient mice show enhanced long-term potentiation prior to the onset of cognitive impairment. To inform this unusual phenotype, herein, we examined neuronal structure and in vitro synaptic function. Our results indicate that klotho deficiency causes the population of dendritic spines to shift towards increased head diameter and decreased length consistent with mature, mushroom type spines. Multi-electrode array recordings from klotho-deficient neurons show increased synchronous firing and activity changes reflective of increased neuronal network activity. Supplementation of the neuronal growth media with recombinant shed klotho corrected some but not all of the activity changes caused by klotho deficiency. Last, in vivo we found that klotho-deficient mice have a decreased latency to induced seizure activity. Together these data show that klotho-deficient memory impairments are underpinned by structural and functional changes that may preclude ongoing normal cognition.
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Affiliation(s)
- Hai T Vo
- Department of Neurobiology, University of Alabama at Birmingham, 1825 University Blvd. Shelby 913, Birmingham 35294, AL, USA
| | - Mary L Phillips
- Department of Neurobiology, University of Alabama at Birmingham, 1825 University Blvd. Shelby 913, Birmingham 35294, AL, USA
| | - Jeremy H Herskowitz
- Department of Neurology, University of Alabama at Birmingham, 1825 University Blvd. Shelby 1114, Birmingham 35294, AL, USA
| | - Gwendalyn D King
- Department of Neurobiology, University of Alabama at Birmingham, 1825 University Blvd. Shelby 913, Birmingham 35294, AL, USA.
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