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Chen X, He C, Xu H, Zeng G, Huang Q, Deng Z, Qin X, Shen X, Hu Y. Characterization of the SWI/SNF complex and nucleosome organization in sorghum. FRONTIERS IN PLANT SCIENCE 2024; 15:1430467. [PMID: 38988640 PMCID: PMC11234113 DOI: 10.3389/fpls.2024.1430467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 06/07/2024] [Indexed: 07/12/2024]
Abstract
The switch defective/sucrose non-fermentable (SWI/SNF) multisubunit complex plays an important role in the regulation of gene expression by remodeling chromatin structure. Three SWI/SNF complexes have been identified in Arabidopsis including BAS, SAS, and MAS. Many subunits of these complexes are involved in controlling plant development and stress response. However, the function of these complexes has hardly been studied in other plant species. In this study, we identified the subunits of the SWI/SNF complex in sorghum and analyzed their evolutionary relationships in six grass species. The grass species conserved all the subunits as in Arabidopsis, but gene duplication occurred diversely in different species. Expression pattern analysis in sorghum (Sorghum bicolor) showed that most of the subunit-encoding genes were expressed constitutively, although the expression level was different. Transactivation assays revealed that SbAN3, SbGIF3, and SbSWI3B possessed transactivation activity, which suggests that they may interact with the pre-initiation complex (PIC) to activate transcription. We chose 12 subunits in sorghum to investigate their interaction relationship by yeast two-hybrid assay. We found that these subunits displayed distinct interaction patterns compared to their homologs in Arabidopsis and rice. This suggests that different SWI/SNF complexes may be formed in sorghum to perform chromatin remodeling functions. Through the integrated analysis of MNase-seq and RNA-seq data, we uncovered a positive relationship between gene expression levels and nucleosome phasing. Furthermore, we found differential global nucleosome enrichments between leaves and roots, as well as in response to PEG treatment, suggesting that dynamics of nucleosome occupancy, which is probably mediated by the SWI/SNF complex, may play important roles in sorghum development and stress response.
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Affiliation(s)
- Xiaofei Chen
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Chao He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Huan Xu
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Gongjian Zeng
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Quanjun Huang
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Zhuying Deng
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Xiner Qin
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Xiangling Shen
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Yongfeng Hu
- Hubei Engineering Research Center for Three Gorges Regional Plant Breeding/Biotechnology Research Center, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, China
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Zhang G, Liu Z, Li Z, Zhang B, Yao P, Qiao Y. Therapeutic approach of natural products that treat osteoporosis by targeting epigenetic modulation. Front Genet 2023; 14:1182363. [PMID: 37287533 PMCID: PMC10242146 DOI: 10.3389/fgene.2023.1182363] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/26/2023] [Indexed: 06/09/2023] Open
Abstract
Osteoporosis (OP) is a metabolic disease that affects bone, resulting in a progressive decrease in bone mass, quality, and micro-architectural degeneration. Natural products have become popular for managing OP in recent years due to their minimal adverse side effects and suitability for prolonged use compared to chemically synthesized products. These natural products are known to modulate multiple OP-related gene expressions, making epigenetics an important tool for optimal therapeutic development. In this study, we investigated the role of epigenetics in OP and reviewed existing research on using natural products for OP management. Our analysis identified around twenty natural products involved in epigenetics-based OP modulation, and we discussed potential mechanisms. These findings highlight the clinical significance of natural products and their potential as novel anti-OP therapeutics.
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Affiliation(s)
- Guokai Zhang
- Binzhou Hospital of Traditional Chinese Medicine, Binzhou, China
| | - Zhenying Liu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zihan Li
- The First Affiliated Hospital of Shandong First Medical University Qianfoshan Hospital of Shandong Province, Jinan, China
| | - Bing Zhang
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Pengyu Yao
- Shandong Laboratory of Engineering Technology Suzhou Biomedical Engineering and Technology Chinese Academy of Sciences, Jinan, China
- Jinan Guoke Medical Engineering and Technology Development Company, Jinan, China
| | - Yun Qiao
- Qilu Hospital of Shandong University, Jinan, China
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Maslyonkina KS, Konyukova AK, Alexeeva DY, Sinelnikov MY, Mikhaleva LM. Barrett's esophagus: The pathomorphological and molecular genetic keystones of neoplastic progression. Cancer Med 2021; 11:447-478. [PMID: 34870375 PMCID: PMC8729054 DOI: 10.1002/cam4.4447] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/07/2021] [Accepted: 11/09/2021] [Indexed: 02/06/2023] Open
Abstract
Barrett's esophagus is a widespread chronically progressing disease of heterogeneous nature. A life threatening complication of this condition is neoplastic transformation, which is often overlooked due to lack of standardized approaches in diagnosis, preventative measures and treatment. In this essay, we aim to stratify existing data to show specific associations between neoplastic transformation and the underlying processes which predate cancerous transition. We discuss pathomorphological, genetic, epigenetic, molecular and immunohistochemical methods related to neoplasia detection on the basis of Barrett's esophagus. Our review sheds light on pathways of such neoplastic progression in the distal esophagus, providing valuable insight into progression assessment, preventative targets and treatment modalities. Our results suggest that molecular, genetic and epigenetic alterations in the esophagus arise earlier than cancerous transformation, meaning the discussed targets can help form preventative strategies in at-risk patient groups.
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Affiliation(s)
| | | | - Darya Y Alexeeva
- Research Institute of Human Morphology, Moscow, Russian Federation
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Xiao W, Zhou Q, Wen X, Wang R, Liu R, Wang T, Shi J, Hu Y, Hou J. Small-Molecule Inhibitors Overcome Epigenetic Reprogramming for Cancer Therapy. Front Pharmacol 2021; 12:702360. [PMID: 34603017 PMCID: PMC8484527 DOI: 10.3389/fphar.2021.702360] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/02/2021] [Indexed: 12/12/2022] Open
Abstract
Cancer treatment is a significant challenge for the global health system, although various pharmacological and therapeutic discoveries have been made. It has been widely established that cancer is associated with epigenetic modification, which is reversible and becomes an attractive target for drug development. Adding chemical groups to the DNA backbone and modifying histone proteins impart distinct characteristics on chromatin architecture. This process is mediated by various enzymes modifying chromatin structures to achieve the diversity of epigenetic space and the intricacy in gene expression files. After decades of effort, epigenetic modification has represented the hallmarks of different cancer types, and the enzymes involved in this process have provided novel targets for antitumor therapy development. Epigenetic drugs show significant effects on both preclinical and clinical studies in which the target development and research offer a promising direction for cancer therapy. Here, we summarize the different types of epigenetic enzymes which target corresponding protein domains, emphasize DNA methylation, histone modifications, and microRNA-mediated cooperation with epigenetic modification, and highlight recent achievements in developing targets for epigenetic inhibitor therapy. This article reviews current anticancer small-molecule inhibitors targeting epigenetic modified enzymes and displays their performances in different stages of clinical trials. Future studies are further needed to address their off-target effects and cytotoxicity to improve their clinical translation.
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Affiliation(s)
- Wenjing Xiao
- School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, China.,Department of Pharmacy, The General Hospital of Western Theater Command of PLA, Chengdu, China
| | - Qiaodan Zhou
- Department of Ultrasonic, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xudong Wen
- Department of Gastroenterology and Hepatology, Chengdu First People's Hospital, Chengdu, China
| | - Rui Wang
- Information Department of Medical Security Center, The General Hospital of Western Theater Command of PLA, Chengdu, China
| | - Ruijie Liu
- School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Tingting Wang
- School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Jianyou Shi
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Department of Pharmacy, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yonghe Hu
- School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, China.,Department of Pharmacy, The General Hospital of Western Theater Command of PLA, Chengdu, China
| | - Jun Hou
- School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, China.,Department of Pharmacy, The General Hospital of Western Theater Command of PLA, Chengdu, China
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Gao W, Lai B, Ni B, Zhao K. Genome-wide profiling of nucleosome position and chromatin accessibility in single cells using scMNase-seq. Nat Protoc 2020; 15:68-85. [PMID: 31836865 PMCID: PMC10895462 DOI: 10.1038/s41596-019-0243-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 09/06/2019] [Indexed: 02/07/2023]
Abstract
Nucleosome organization is important for chromatin compaction and accessibility. Profiling nucleosome positioning genome-wide in single cells provides critical information to understand the cell-to-cell heterogeneity of chromatin states within a cell population. This protocol describes single-cell micrococcal nuclease sequencing (scMNase-seq), a method for detecting genome-wide nucleosome positioning and chromatin accessibility simultaneously from a small number of cells or single cells. To generate scMNase-seq libraries, single cells are isolated by FACS sorting, lysed and digested by MNase. DNA is purified, end-repaired and ligated to Y-shaped adaptors. Following PCR amplification with indexing primers, the subnucleosome-sized (fragments with a length of ≤80 bp) and mononucleosome-sized (fragments with a length between 140 and 180 bp) DNA fragments are recovered and sequenced on Illumina HiSeq platforms. On average, 0.5-1 million unique mapped reads are obtained for each single cell. The mononucleosome-sized DNA fragments precisely define genome-wide nucleosome positions in single cells, while the subnucleosome-sized DNA fragments provide information on chromatin accessibility. Library preparation of scMNase-seq takes only 2 d, requires only standard molecular biology techniques and does not require sophisticated laboratory equipment. Processing of high-throughput sequencing data requires basic bioinformatics skills and uses publicly available bioinformatics software.
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Affiliation(s)
- Weiwu Gao
- Department of Pathophysiology, College of High Altitude Military Medicine, Third Military Medical University, Chongqing, People's Republic of China
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA
- Institute of Immunology of PLA, Third Military Medical University, Chongqing, People's Republic of China
- Key Laboratory of Extreme Environmental Medicine, Ministry of Education of China, Chongqing, People's Republic of China
| | - Binbin Lai
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA
| | - Bing Ni
- Department of Pathophysiology, College of High Altitude Military Medicine, Third Military Medical University, Chongqing, People's Republic of China.
- Key Laboratory of Extreme Environmental Medicine, Ministry of Education of China, Chongqing, People's Republic of China.
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA.
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Clarkson CT, Deeks EA, Samarista R, Mamayusupova H, Zhurkin VB, Teif VB. CTCF-dependent chromatin boundaries formed by asymmetric nucleosome arrays with decreased linker length. Nucleic Acids Res 2019; 47:11181-11196. [PMID: 31665434 PMCID: PMC6868436 DOI: 10.1093/nar/gkz908] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/26/2019] [Accepted: 10/02/2019] [Indexed: 11/24/2022] Open
Abstract
The CCCTC-binding factor (CTCF) organises the genome in 3D through DNA loops and in 1D by setting boundaries isolating different chromatin states, but these processes are not well understood. Here we investigate chromatin boundaries in mouse embryonic stem cells, defined by the regions with decreased Nucleosome Repeat Length (NRL) for ∼20 nucleosomes near CTCF sites, affecting up to 10% of the genome. We found that the nucleosome-depleted region (NDR) near CTCF is asymmetrically located >40 nucleotides 5'-upstream from the centre of CTCF motif. The strength of CTCF binding to DNA and the presence of cohesin is correlated with the decrease of NRL near CTCF, and anti-correlated with the level of asymmetry of the nucleosome array. Individual chromatin remodellers have different contributions, with Snf2h having the strongest effect on the NRL decrease near CTCF and Chd4 playing a major role in the symmetry breaking. Upon differentiation, a subset of preserved, common CTCF sites maintains asymmetric nucleosome pattern and small NRL. The sites which lost CTCF upon differentiation are characterized by nucleosome rearrangement 3'-downstream, with unchanged NDR 5'-upstream of CTCF motifs. Boundaries of topologically associated chromatin domains frequently contain several inward-oriented CTCF motifs whose effects, described above, add up synergistically.
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Affiliation(s)
| | - Emma A Deeks
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
- Biological Sciences BSc Program, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Ralph Samarista
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
- Wellcome Trust Vacation Student
| | - Hulkar Mamayusupova
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Victor B Zhurkin
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vladimir B Teif
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
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The many length scales of DNA packaging. Essays Biochem 2019; 63:1-4. [DOI: 10.1042/ebc20190040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 11/17/2022]
Abstract
Abstract
This collection of reviews focuses on the most exciting areas of DNA packaging at the current time. Many of the new discoveries are driven by the development of molecular or imaging techniques, and these are providing insights into the complex world of chromatin. As these new techniques continue to improve, we will be able to answer many of the questions we have now, while likely raising many new ones.
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Gilbert N. Biophysical regulation of local chromatin structure. Curr Opin Genet Dev 2019; 55:66-75. [DOI: 10.1016/j.gde.2019.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/31/2019] [Accepted: 06/02/2019] [Indexed: 10/26/2022]
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