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Peng X, Li Y, Zou M, Kong X, Sheng Y. CATAD: exploring topologically associating domains from an insight of core-attachment structure. Brief Bioinform 2023:7188844. [PMID: 37279476 DOI: 10.1093/bib/bbad204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/23/2023] [Accepted: 05/10/2023] [Indexed: 06/08/2023] Open
Abstract
Identifying topologically associating domains (TADs), which are considered as the basic units of chromosome structure and function, can facilitate the exploration of the 3D-structure of chromosomes. Methods have been proposed to identify TADs by detecting the boundaries of TADs or identifying the closely interacted regions as TADs, while the possible inner structure of TADs is seldom investigated. In this study, we assume that a TAD is composed of a core and its surrounding attachments, and propose a method, named CATAD, to identify TADs based on the core-attachment structure model. In CATAD, the cores of TADs are identified based on the local density and cosine similarity, and the surrounding attachments are determined based on boundary insulation. CATAD was applied to the Hi-C data of two human cell lines and two mouse cell lines, and the results show that the boundaries of TADs identified by CATAD are significantly enriched by structural proteins, histone modifications, transcription start sites and enzymes. Furthermore, CATAD outperforms other methods in many cases, in terms of the average peak, boundary tagged ratio and fold change. In addition, CATAD is robust and rarely affected by the different resolutions of Hi-C matrices. Conclusively, identifying TADs based on the core-attachment structure is useful, which may inspire researchers to explore TADs from the angles of possible spatial structures and formation process.
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Affiliation(s)
- Xiaoqing Peng
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, 410083, Hunan, China
| | - Yiming Li
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, 410083, Hunan, China
| | - Mengxi Zou
- Division of Biosciences, University College London, 410083, Hunan, China
| | - Xiangyan Kong
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, 410083, Hunan, China
| | - Yu Sheng
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, 410083, Hunan, China
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Han H, Tan J, Wang R, Wan H, He Y, Yan X, Guo J, Gao Q, Li J, Shang S, Chen F, Tian R, Liu W, Liao L, Tang B, Zhang Z. PINK1 phosphorylates Drp1 S616 to regulate mitophagy-independent mitochondrial dynamics. EMBO Rep 2020; 21:e48686. [PMID: 32484300 PMCID: PMC7403662 DOI: 10.15252/embr.201948686] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 04/20/2020] [Accepted: 05/05/2020] [Indexed: 11/09/2022] Open
Abstract
Impairment of PINK1/parkin-mediated mitophagy is currently proposed to be the molecular basis of mitochondrial abnormality in Parkinson's disease (PD). We here demonstrate that PINK1 directly phosphorylates Drp1 on S616. Drp1S616 phosphorylation is significantly reduced in cells and mouse tissues deficient for PINK1, but unaffected by parkin inactivation. PINK1-mediated mitochondrial fission is Drp1S616 phosphorylation dependent. Overexpression of either wild-type Drp1 or of the phosphomimetic mutant Drp1S616D , but not a dephosphorylation-mimic mutant Drp1S616A , rescues PINK1 deficiency-associated phenotypes in Drosophila. Moreover, Drp1 restores PINK1-dependent mitochondrial fission in ATG5-null cells and ATG7-null Drosophila. Reduced Drp1S616 phosphorylation is detected in fibroblasts derived from 4 PD patients harboring PINK1 mutations and in 4 out of 7 sporadic PD cases. Taken together, we have identified Drp1 as a substrate of PINK1 and a novel mechanism how PINK1 regulates mitochondrial fission independent of parkin and autophagy. Our results further link impaired PINK1-mediated Drp1S616 phosphorylation with the pathogenesis of both familial and sporadic PD.
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Affiliation(s)
- Hailong Han
- Key Laboratory of Molecular Precision Medicine of Hunan Province and Center for Medical GeneticsInstitute of Molecular Precision MedicineXiangya HospitalCentral South UniversityChangshaChina
- Department of NeurologyXiangya HospitalCentral South UniversityChangshaChina
| | - Jieqiong Tan
- Key Laboratory of Molecular Precision Medicine of Hunan Province and Center for Medical GeneticsInstitute of Molecular Precision MedicineXiangya HospitalCentral South UniversityChangshaChina
- Department of NeurologyXiangya HospitalCentral South UniversityChangshaChina
| | - Ruoxi Wang
- Key Laboratory of Molecular Precision Medicine of Hunan Province and Center for Medical GeneticsInstitute of Molecular Precision MedicineXiangya HospitalCentral South UniversityChangshaChina
- Department of NeurologyXiangya HospitalCentral South UniversityChangshaChina
| | - Huida Wan
- Shanghai Key Laboratory of Regulatory BiologySchool of Life SciencesEast China Normal UniversityShanghaiChina
| | - Yaohui He
- Fujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiamenChina
| | - Xinxiang Yan
- Department of NeurologyXiangya HospitalCentral South UniversityChangshaChina
| | - Jifeng Guo
- Department of NeurologyXiangya HospitalCentral South UniversityChangshaChina
| | - Qingtao Gao
- Key Laboratory of Molecular Precision Medicine of Hunan Province and Center for Medical GeneticsInstitute of Molecular Precision MedicineXiangya HospitalCentral South UniversityChangshaChina
- Department of NeurologyXiangya HospitalCentral South UniversityChangshaChina
| | - Jie Li
- Key Laboratory of Molecular Precision Medicine of Hunan Province and Center for Medical GeneticsInstitute of Molecular Precision MedicineXiangya HospitalCentral South UniversityChangshaChina
- Department of NeurologyXiangya HospitalCentral South UniversityChangshaChina
| | - Shuai Shang
- Key Laboratory of Molecular Precision Medicine of Hunan Province and Center for Medical GeneticsInstitute of Molecular Precision MedicineXiangya HospitalCentral South UniversityChangshaChina
- Department of NeurologyXiangya HospitalCentral South UniversityChangshaChina
| | - Fang Chen
- Key Laboratory of Molecular Precision Medicine of Hunan Province and Center for Medical GeneticsInstitute of Molecular Precision MedicineXiangya HospitalCentral South UniversityChangshaChina
- Department of NeurologyXiangya HospitalCentral South UniversityChangshaChina
| | - Runyi Tian
- Key Laboratory of Molecular Precision Medicine of Hunan Province and Center for Medical GeneticsInstitute of Molecular Precision MedicineXiangya HospitalCentral South UniversityChangshaChina
- Department of NeurologyXiangya HospitalCentral South UniversityChangshaChina
| | - Wen Liu
- Fujian Provincial Key Laboratory of Innovative Drug Target ResearchSchool of Pharmaceutical SciencesXiamen UniversityXiamenChina
| | - Lujian Liao
- Shanghai Key Laboratory of Regulatory BiologySchool of Life SciencesEast China Normal UniversityShanghaiChina
| | - Beisha Tang
- Department of NeurologyXiangya HospitalCentral South UniversityChangshaChina
| | - Zhuohua Zhang
- Key Laboratory of Molecular Precision Medicine of Hunan Province and Center for Medical GeneticsInstitute of Molecular Precision MedicineXiangya HospitalCentral South UniversityChangshaChina
- Department of NeurologyXiangya HospitalCentral South UniversityChangshaChina
- Department of NeurosciencesUniversity of South China Medical SchoolHengyangChina
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Wan Z, Peng X, Ma L, Tian Q, Wu S, Li J, Ling J, Lv W, Ding B, Tan J, Zhang Z. Targeted Sequencing of Genomic Repeat Regions Detects Circulating Cell-free Echinococcus DNA. PLoS Negl Trop Dis 2020; 14:e0008147. [PMID: 32155159 PMCID: PMC7083330 DOI: 10.1371/journal.pntd.0008147] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 03/20/2020] [Accepted: 02/18/2020] [Indexed: 11/20/2022] Open
Abstract
Background Echinococcosis is a chronic zoonosis caused by tapeworms of the genus Echinococcus. Treatment of the disease is often expensive and complicated, sometimes requiring extensive surgery. Ultrasonographic imaging is currently the main technique for diagnosis, while immunological analysis provides additional information. Confirmation still needs pathological analysis. However, these diagnostic techniques generally detect infection in late stages of the disease. An accurate, early and non-invasive molecular diagnostic method is still unavailable. Methodology/Principal findings We sequenced the cell-free DNA (cfDNA) from plasma of echinococcosis patients and confirmed the presence of Echinococcus DNA. To improve detection sensitivity, we developed a method based on targeted next-generation sequencing of repeat regions. Simulation experiments demonstrate that the targeted sequencing is sensitive enough to detect as little as 0.1% of an Echinococcus genome in 1 mL of plasma. Results obtained using patient plasma shows that the Area Under the Curve (AUC) of the method is 0.862, with a detection sensitivity of 62.50% and specificity of 100%, corresponding to a Youden-index of 0.625. Conclusions/Significance This study provides evidence that hydatid cysts release cfDNA fragments into patient plasma. Using the repeat region targeted sequencing method, highly specific detection of Echinococcus infection was achieved. This study paves a new avenue for potential non-invasive screening and diagnosis of echinococcosis. Echinococcosis is a severe chronic parasitic disease caused by tapeworms of the genus Echinococcus. According to the World Health Organization, there are more than 1 million people living with echinococcosis worldwide. For decades, little progress has been made to develop a molecular diagnosis and specific treatment for the disease. Although imaging and immunological detection are used for diagnosis, these technologies are either only effective for late stages of the disease or hardly conclusive. The detection of cell-free DNA has been a powerful tool for precise diagnosis. In this study, we showed the presence of Echinococcus-derived cell-free DNA in plasma of echinococcosis patients. We further established an assay to detect parasite DNA in blood samples based on amplification of Echinococcus specific repeat regions followed by targeted next-generation sequencing. This technique provides a new method for potential extensive screening and precision diagnosis of echinococcosis with high specificity.
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Affiliation(s)
- Zhengqing Wan
- Institute of Molecular Precision Medicine, Xiangya Hospital, Key Laboratory of Molecular Precision Medicine of Hunan Province, Central South University, Changsha, Hunan, China
- Center for Medical Genetics, Central South University, Changsha, Hunan, China
| | - Xiaoqing Peng
- Institute of Molecular Precision Medicine, Xiangya Hospital, Key Laboratory of Molecular Precision Medicine of Hunan Province, Central South University, Changsha, Hunan, China
- Center for Medical Genetics, Central South University, Changsha, Hunan, China
| | - Lu Ma
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Qingshan Tian
- Center for Prevention and Treatment of Echinococcosis, Qinghai Provincial People's Hospital, Xining, Qinghai, China
| | - Shizheng Wu
- Department of Neurology, Qinghai Provincial People's Hospital, Xining, Qinghai, China
| | - Junqi Li
- Sunrain Biotechnology Corporation, Changsha, Hunan, China
| | - Jie Ling
- Institute of Molecular Precision Medicine, Xiangya Hospital, Key Laboratory of Molecular Precision Medicine of Hunan Province, Central South University, Changsha, Hunan, China
| | - Weigang Lv
- Center for Medical Genetics, Central South University, Changsha, Hunan, China
| | - Binrong Ding
- Institute of Molecular Precision Medicine, Xiangya Hospital, Key Laboratory of Molecular Precision Medicine of Hunan Province, Central South University, Changsha, Hunan, China
- Center for Medical Genetics, Central South University, Changsha, Hunan, China
| | - Jieqiong Tan
- Institute of Molecular Precision Medicine, Xiangya Hospital, Key Laboratory of Molecular Precision Medicine of Hunan Province, Central South University, Changsha, Hunan, China
- Center for Medical Genetics, Central South University, Changsha, Hunan, China
| | - Zhuohua Zhang
- Institute of Molecular Precision Medicine, Xiangya Hospital, Key Laboratory of Molecular Precision Medicine of Hunan Province, Central South University, Changsha, Hunan, China
- Center for Medical Genetics, Central South University, Changsha, Hunan, China
- Department of Neurosciences, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- * E-mail:
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