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Geng T, Sun Q, He J, Chen Y, Cheng W, Shen J, Liu B, Zhang M, Wang S, Asan K, Song M, Gao Q, Song Y, Liu R, Liu X, Ding Y, Jing A, Ye X, Ren H, Zeng K, Zhou Y, Zhang B, Ma S, Liu W, Liu S, Ji J. CXXC5 drove inflammation and ovarian cancer proliferation via transcriptional activation of ZNF143 and EGR1. Cell Signal 2024; 119:111180. [PMID: 38642782 DOI: 10.1016/j.cellsig.2024.111180] [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: 01/01/2024] [Revised: 03/28/2024] [Accepted: 04/14/2024] [Indexed: 04/22/2024]
Abstract
CXXC5, a zinc-finger protein, is known for its role in epigenetic regulation via binding to unmethylated CpG islands in gene promoters. As a transcription factor and epigenetic regulator, CXXC5 modulates various signaling processes and acts as a key coordinator. Altered expression or activity of CXXC5 has been linked to various pathological conditions, including tumorigenesis. Despite its known role in cancer, CXXC5's function and mechanism in ovarian cancer are unclear. We analyzed multiple public databases and found that CXXC5 is highly expressed in ovarian cancer, with high expression correlating with poor patient prognosis. We show that CXXC5 expression is regulated by oxygen concentration and is a direct target of HIF1A. CXXC5 is critical for maintaining the proliferative potential of ovarian cancer cells, with knockdown decreasing and overexpression increasing cell proliferation. Loss of CXXC5 led to inactivation of multiple inflammatory signaling pathways, while overexpression activated these pathways. Through in vitro and in vivo experiments, we confirmed ZNF143 and EGR1 as downstream transcription factors of CXXC5, mediating its proliferative potential in ovarian cancer. Our findings suggest that the CXXC5-ZNF143/EGR1 axis forms a network driving ovarian cell proliferation and tumorigenesis, and highlight CXXC5 as a potential therapeutic target for ovarian cancer treatment.
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Affiliation(s)
- Ting Geng
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Qigang Sun
- Department of Hepatobiliary and Pancreatic Surgery, Hainan General Hospital, Affiliated Hainan Hospital of Hainan Medical College, Haikou 570311, China
| | - Jingliang He
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Yulu Chen
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Wenhao Cheng
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Jing Shen
- Department of Obstetrics and Gynecology, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, Hubei, China
| | - Bin Liu
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Meiqi Zhang
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Sen Wang
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Kadirya Asan
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Mengwei Song
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Qi Gao
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Yizhuo Song
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Ruotong Liu
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Xing Liu
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Yuanyuan Ding
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Aixin Jing
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Xiaoqing Ye
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Hongyu Ren
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Kaile Zeng
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Ying Zhou
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Boyu Zhang
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Shaojie Ma
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China.
| | - Wei Liu
- Cancer Center and Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| | - Shunfang Liu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Jing Ji
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China.
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Hu S, Liu Y, Zhang Q, Bai J, Xu C. A continuum of zinc finger transcription factor retention on native chromatin underlies dynamic genome organization. Mol Syst Biol 2024; 20:799-824. [PMID: 38745107 PMCID: PMC11220090 DOI: 10.1038/s44320-024-00038-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
Transcription factor (TF) residence on chromatin translates into quantitative transcriptional or structural outcomes on genome. Commonly used formaldehyde crosslinking fixes TF-DNA interactions cumulatively and compromises the measured occupancy level. Here we mapped the occupancy level of global or individual zinc finger TFs like CTCF and MAZ, in the form of highly resolved footprints, on native chromatin. By incorporating reinforcing perturbation conditions, we established S-score, a quantitative metric to proxy the continuum of CTCF or MAZ retention across different motifs on native chromatin. The native chromatin-retained CTCF sites harbor sequence features within CTCF motifs better explained by S-score than the metrics obtained from other crosslinking or native assays. CTCF retention on native chromatin correlates with local SUMOylation level, and anti-correlates with transcriptional activity. The S-score successfully delineates the otherwise-masked differential stability of chromatin structures mediated by CTCF, or by MAZ independent of CTCF. Overall, our study established a paradigm continuum of TF retention across binding sites on native chromatin, explaining the dynamic genome organization.
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Affiliation(s)
- Siling Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yangying Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qifan Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Juan Bai
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chenhuan Xu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
- China National Center for Bioinformation, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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Kamalyan S, Kyrchanova O, Klimenko N, Babosha V, Vasileva Y, Belova E, Fursenko D, Maksimenko O, Georgiev P. The N-terminal dimerization domains of human and Drosophila CTCF have similar functionality. Epigenetics Chromatin 2024; 17:9. [PMID: 38561749 PMCID: PMC10983669 DOI: 10.1186/s13072-024-00534-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND CTCF is highly likely to be the ancestor of proteins that contain large clusters of C2H2 zinc finger domains, and its conservation is observed across most bilaterian organisms. In mammals, CTCF is the primary architectural protein involved in organizing chromosome topology and mediating enhancer-promoter interactions over long distances. In Drosophila, CTCF (dCTCF) cooperates with other architectural proteins to establish long-range interactions and chromatin boundaries. CTCFs of various organisms contain an unstructured N-terminal dimerization domain (DD) and clusters comprising eleven zinc-finger domains of the C2H2 type. The Drosophila (dCTCF) and human (hCTCF) CTCFs share sequence homology in only five C2H2 domains that specifically bind to a conserved 15 bp motif. RESULTS Previously, we demonstrated that CTCFs from different organisms carry unstructured N-terminal dimerization domains (DDs) that lack sequence homology. Here we used the CTCFattP(mCh) platform to introduce desired changes in the Drosophila CTCF gene and generated a series of transgenic lines expressing dCTCF with different variants of the N-terminal domain. Our findings revealed that the functionality of dCTCF is significantly affected by the deletion of the N-terminal DD. Additionally, we observed a strong impact on the binding of the dCTCF mutant to chromatin upon deletion of the DD. However, chromatin binding was restored in transgenic flies expressing a chimeric CTCF protein with the DD of hCTCF. Although the chimeric protein exhibited lower expression levels than those of the dCTCF variants, it efficiently bound to chromatin similarly to the wild type (wt) protein. CONCLUSIONS Our findings suggest that one of the evolutionarily conserved functions of the unstructured N-terminal dimerization domain is to recruit dCTCF to its genomic sites in vivo.
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Affiliation(s)
- Sofia Kamalyan
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
| | - Olga Kyrchanova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
| | - Natalia Klimenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
| | - Valentin Babosha
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
| | - Yulia Vasileva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
| | - Elena Belova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
| | - Dariya Fursenko
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia
| | - Oksana Maksimenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia.
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St, Moscow, 119334, Russia.
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Li X, Zeng S, Chen L, Zhang Y, Li X, Zhang B, Su D, Du Q, Zhang J, Wang H, Zhong Z, Zhang J, Li P, Jiang A, Long K, Li M, Ge L. An intronic enhancer of Cebpa regulates adipocyte differentiation and adipose tissue development via long-range loop formation. Cell Prolif 2024; 57:e13552. [PMID: 37905345 PMCID: PMC10905358 DOI: 10.1111/cpr.13552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/29/2023] [Accepted: 09/11/2023] [Indexed: 11/02/2023] Open
Abstract
Cebpa is a master transcription factor gene for adipogenesis. However, the mechanisms of enhancer-promoter chromatin interactions controlling Cebpa transcriptional regulation during adipogenic differentiation remain largely unknown. To reveal how the three-dimensional structure of Cebpa changes during adipogenesis, we generated high-resolution chromatin interactions of Cebpa in 3T3-L1 preadipocytes and 3T3-L1 adipocytes using circularized chromosome conformation capture sequencing (4C-seq). We revealed dramatic changes in chromatin interactions and chromatin status at interaction sites during adipogenic differentiation. Based on this, we identified five active enhancers of Cebpa in 3T3-L1 adipocytes through epigenomic data and luciferase reporter assays. Next, epigenetic repression of Cebpa-L1-AD-En2 or -En3 by the dCas9-KRAB system significantly down-regulated Cebpa expression and inhibited adipocyte differentiation. Furthermore, experimental depletion of cohesin decreased the interaction intensity between Cebpa-L1-AD-En2 and the Cebpa promoter and down-regulated Cebpa expression, indicating that long-range chromatin loop formation was mediated by cohesin. Two transcription factors, RXRA and PPARG, synergistically regulate the activity of Cebpa-L1-AD-En2. To test whether Cebpa-L1-AD-En2 plays a role in adipose tissue development, we injected dCas9-KRAB-En2 lentivirus into the inguinal white adipose tissue (iWAT) of mice to suppress the activity of Cebpa-L1-AD-En2. Repression of Cebpa-L1-AD-En2 significantly decreased Cebpa expression and adipocyte size, altered iWAT transcriptome, and affected iWAT development. We identified functional enhancers regulating Cebpa expression and clarified the crucial roles of Cebpa-L1-AD-En2 and Cebpa promoter interaction in adipocyte differentiation and adipose tissue development.
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Affiliation(s)
- Xiaokai Li
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Sha Zeng
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Li Chen
- Chongqing Academy of Animal SciencesChongqingChina
- National Center of Technology Innovation for PigsChongqingChina
- Key Laboratory of Pig Industry ScienceMinistry of AgricultureChongqingChina
| | - Yu Zhang
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Xuemin Li
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Biwei Zhang
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Duo Su
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Qinjiao Du
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Jiaman Zhang
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Haoming Wang
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Zhining Zhong
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Jinwei Zhang
- Chongqing Academy of Animal SciencesChongqingChina
- National Center of Technology Innovation for PigsChongqingChina
- Key Laboratory of Pig Industry ScienceMinistry of AgricultureChongqingChina
| | - Penghao Li
- Jinxin Research Institute for Reproductive Medicine and GeneticsSichuan Jinxin Xi'nan Women's and Children's HospitalChengduChina
| | - Anan Jiang
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Keren Long
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
- Chongqing Academy of Animal SciencesChongqingChina
| | - Mingzhou Li
- State Key Laboratory of Swine and Poultry Breeding IndustrySichuan Agricultural UniversityChengduChina
- Livestock and Poultry Multi‐omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Liangpeng Ge
- Chongqing Academy of Animal SciencesChongqingChina
- National Center of Technology Innovation for PigsChongqingChina
- Key Laboratory of Pig Industry ScienceMinistry of AgricultureChongqingChina
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5
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Ren L, Ma W, Wang Y. SpecLoop predicts cell type-specific chromatin loop via transcription factor cooperation. Comput Biol Med 2024; 171:108182. [PMID: 38422958 DOI: 10.1016/j.compbiomed.2024.108182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/18/2024] [Accepted: 02/18/2024] [Indexed: 03/02/2024]
Abstract
Cell-type-Specific Chromatin Loops (CSCLs) are crucial for gene regulation and cell fate determination. However, the mechanisms governing their establishment remain elusive. Here, we present SpecLoop, a network regularization-based machine learning framework, to investigate the role of transcription factors (TFs) cooperation in CSCL formation. SpecLoop integrates multi-omics data, including gene expression, chromatin accessibility, sequence, protein-protein interaction, and TF binding motif data, to predict CSCLs and identify TF cooperations. Using high resolution Hi-C data as the gold standard, SpecLoop accurately predicts CSCL in GM12878, IMR90, HeLa-S3, K562, HUVEC, HMEC, and NHEK seven cell types, with the AUROC values ranging from 0.8645 to 0.9852 and AUPR values ranging from 0.8654 to 0.9734. Notably SpecLoop demonstrates improved accuracy in predicting long-distance CSCLs and identifies TF complexes with strong predictive ability. Our study systematically explores the TFs and TF pairs associated with CSCL through effective integration of diverse omics data. SpecLoop is freely available at https://github.com/AMSSwanglab/SpecLoop.
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Affiliation(s)
- Lixin Ren
- Department of Applied Mathematics, School of Mathematics and Physics, University of Science and Technology Beijing, 100083, Beijing, China.
| | - Wanbiao Ma
- Department of Applied Mathematics, School of Mathematics and Physics, University of Science and Technology Beijing, 100083, Beijing, China.
| | - Yong Wang
- CEMS, NCMIS, HCMS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China; School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China; Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, 330106, China.
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6
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Zhang M, Huang H, Li J, Wu Q. ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry. Cell Rep 2024; 43:113663. [PMID: 38206813 DOI: 10.1016/j.celrep.2023.113663] [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: 09/20/2023] [Revised: 11/28/2023] [Accepted: 12/22/2023] [Indexed: 01/13/2024] Open
Abstract
The transcription factor ZNF143 contains a central domain of seven zinc fingers in a tandem array and is involved in 3D genome construction. However, the mechanism by which ZNF143 functions in chromatin looping remains unclear. Here, we show that ZNF143 directionally recognizes a diverse range of genomic sites directly within enhancers and promoters and is required for chromatin looping between these sites. In addition, ZNF143 is located between CTCF and cohesin at numerous CTCF sites, and ZNF143 removal narrows the space between CTCF and cohesin. Moreover, genetic deletion of ZNF143, in conjunction with acute CTCF degradation, reveals that ZNF143 and CTCF collaborate to regulate higher-order topological chromatin organization. Finally, CTCF depletion enlarges direct ZNF143 chromatin looping. Thus, ZNF143 is recruited by CTCF to the CTCF sites to regulate CTCF/cohesin configuration and TAD (topologically associating domain) formation, whereas directional recognition of genomic DNA motifs directly by ZNF143 itself regulates promoter activity via chromatin looping.
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Affiliation(s)
- Mo Zhang
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Medical Genomics, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China; WLA Laboratories, Shanghai 201203, China
| | - Haiyan Huang
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Medical Genomics, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China; WLA Laboratories, Shanghai 201203, China
| | - Jingwei Li
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Medical Genomics, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China; WLA Laboratories, Shanghai 201203, China
| | - Qiang Wu
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Medical Genomics, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China; WLA Laboratories, Shanghai 201203, China.
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7
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Chakkarappan SR, Umadharshini KV, Dhamodharan S, Rose MM, Gopu G, Murugan AK, Inoue I, Munirajan AK. Super enhancer loci of EGFR regulate EGFR variant 8 through enhancer RNA and strongly associate with survival in HNSCCs. Mol Genet Genomics 2024; 299:3. [PMID: 38236481 DOI: 10.1007/s00438-023-02089-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 10/21/2023] [Indexed: 01/19/2024]
Abstract
Epidermal growth factor receptor (EGFR) has been shown to be overexpressed in human cancers due to mutation, amplification, and epigenetic hyperactivity, which leads to deregulated transcriptional mechanism. Among the eight different EGFR isoforms, the mechanism of regulation of full-length variant 1 is well-known, no studies have examined the function & factors regulating the expression of variant 8. This study aimed to understand the function of EGFR super-enhancer loci and its associated transcription factors regulating the expression of EGFR variant 8. Our study shows that overexpression of variant 8 and its transcription was more prevalent than variant 1 in many cancers and positively correlated with the EGFR-AS1 expression in oral cancer and HNSCC. Notably, individuals overexpressing variant 8 showed shorter overall survival and had a greater connection with other clinical traits than patients with overexpression of variant 1. In this study, TCGA enhancer RNA profiling on the constituent enhancer (CE1 and CE2) region revealed that the multiple enhancer RNAs formed from CE2 by employing CE1 as a promoter. Our bioinformatic analysis further supports the enrichment of enhancer RNA specific chromatin marks H3K27ac, H3K4me1, POL2 and H2AZ on CE2. GeneHancer and 3D chromatin capture analysis showed clustered interactions between CE1, CE2 loci and this interaction may regulates expression of both EGFR-eRNA and variant 8. Moreover, increased expression of SNAI2 and its close relationship to EGFR-AS1 and variant 8 suggest that SNAI2 could regulates variant 8 overexpression by building a MegaTrans complex with both EGFR-eRNA and EGFR-AS1. Our findings show that EGFR variant 8 and its transcriptional regulation & chromatin modification by eRNAs may provide a rationale for targeting RNA splicing in combination with targeted EGFR therapies in cancer.
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Affiliation(s)
- Sundaram Reddy Chakkarappan
- Department of Health Research, Multi Disciplinary Research Unit (DHR-MRU), Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, 600 113, India
| | | | - Shankar Dhamodharan
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, 600 113, India
| | - Mathew Maria Rose
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, 600 113, India
| | - Govindasamy Gopu
- Department of Surgical Oncology, Rajiv Gandhi Government General Hospital, Madras Medical College, Chennai, 600003, India
| | - Avaniyapuram Kannan Murugan
- Department of Molecular Oncology, King Faisal Specialist Hospital and Research Centre, 11211, Riyadh, Saudi Arabia
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Arasambattu Kannan Munirajan
- Department of Health Research, Multi Disciplinary Research Unit (DHR-MRU), Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, 600 113, India.
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani Campus, Chennai, 600 113, India.
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8
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Xiao M, Kondo S, Nomura M, Kato S, Nishimura K, Zang W, Zhang Y, Akashi T, Viny A, Shigehiro T, Ikawa T, Yamazaki H, Fukumoto M, Tanaka A, Hayashi Y, Koike Y, Aoyama Y, Ito H, Nishikawa H, Kitamura T, Kanai A, Yokoyama A, Fujiwara T, Goyama S, Noguchi H, Lee SC, Toyoda A, Hinohara K, Abdel-Wahab O, Inoue D. BRD9 determines the cell fate of hematopoietic stem cells by regulating chromatin state. Nat Commun 2023; 14:8372. [PMID: 38102116 PMCID: PMC10724271 DOI: 10.1038/s41467-023-44081-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
ATP-dependent chromatin remodeling SWI/SNF complexes exist in three subcomplexes: canonical BAF (cBAF), polybromo BAF (PBAF), and a newly described non-canonical BAF (ncBAF). While cBAF and PBAF regulate fates of multiple cell types, roles for ncBAF in hematopoietic stem cells (HSCs) have not been investigated. Motivated by recent discovery of disrupted expression of BRD9, an essential component of ncBAF, in multiple cancers, including clonal hematopoietic disorders, we evaluate here the role of BRD9 in normal and malignant HSCs. BRD9 loss enhances chromatin accessibility, promoting myeloid lineage skewing while impairing B cell development. BRD9 significantly colocalizes with CTCF, whose chromatin recruitment is augmented by BRD9 loss, leading to altered chromatin state and expression of myeloid-related genes within intact topologically associating domains. These data uncover ncBAF as critical for cell fate specification in HSCs via three-dimensional regulation of gene expression and illuminate roles for ncBAF in normal and malignant hematopoiesis.
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Affiliation(s)
- Muran Xiao
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Shinji Kondo
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, National Institute of Genetics, Mishima, Japan
- Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
| | - Masaki Nomura
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Facility for iPS Cell Therapy, CiRA Foundation, Kyoto, Japan
| | - Shinichiro Kato
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Institute for Advanced Study, Nagoya University, Nagoya, Japan
- Center for 5D Cell Dynamics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Koutarou Nishimura
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Weijia Zang
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yifan Zhang
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomohiro Akashi
- Center for 5D Cell Dynamics, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Division of Systems Biology, Center for Neurological Diseases and Cancer, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Aaron Viny
- Department of Medicine, Division of Hematology and Oncology, and Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Tsukasa Shigehiro
- Division of Immunobiology, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, Japan
| | - Tomokatsu Ikawa
- Division of Immunobiology, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, Japan
| | - Hiromi Yamazaki
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Miki Fukumoto
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Atsushi Tanaka
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Laboratory of Immunology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yasutaka Hayashi
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Yui Koike
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Yumi Aoyama
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiromi Ito
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Hiroyoshi Nishikawa
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Institute for Advanced Study, Nagoya University, Nagoya, Japan
- Center for 5D Cell Dynamics, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo/Chiba, Japan
| | - Toshio Kitamura
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Akinori Kanai
- Department of Molecular Oncology and Leukemia Program Project, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Akihiko Yokoyama
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Yamagata, Japan
| | - Tohru Fujiwara
- Department of Hematology and Rheumatology, Tohoku University Graduate School of Medicine, Sendai, Japan
- Laboratory Diagnostics, Tohoku University Hospital, Sendai, Japan
| | - Susumu Goyama
- Division of Molecular Oncology, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Hideki Noguchi
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, National Institute of Genetics, Mishima, Japan
- Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
| | - Stanley C Lee
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Kunihiko Hinohara
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Institute for Advanced Study, Nagoya University, Nagoya, Japan
- Center for 5D Cell Dynamics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daichi Inoue
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan.
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
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9
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Wei D, Wang J, Jiupan Z, Khan R, Abbas Raza SH, Yaping S, Chao J, Ayari-Akkari A, Ahmed DAEM. Roles of MEF2A and HOXA5 in the transcriptional regulation of the bovine FoxO1 gene. Anim Biotechnol 2023; 34:4367-4379. [PMID: 36449378 DOI: 10.1080/10495398.2022.2150632] [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] [Indexed: 12/03/2022]
Abstract
The Forkhead box factor 1 (FoxO1) gene plays a vital role in the growth and development of skeletal muscle. In the present study, expression analysis of the bovine FoxO1 gene exhibited the highest expression in longissimus dorsi muscle followed by its expression in adipose tissue. Moreover, high mRNA expression of FoxO1 gene was found in differentiated bovine myoblasts and adipocytes at day 6 of induced differentiation (p < 0.05). The regulatory pattern of the bovine FoxO1 gene was investigated through screening and dual-luciferase activity of the 1.7 kb 5'UTR (untranslated region) within pGL3-basic vector and a core promoter region was explored at (-285/-27) upstream of the transcription start site. The transcription factors (TFs) MEF2A and HOXA5 within the core promoter region (-285/-27) were found as the regulatory cis-acting element. The siRNA interference of the TFs, chromatin immunoprecipitation (ChIP) assay, and site-directed mutation validated that MEF2A and HOXA5 binding occurs in the region -285/-27 bp and performs an essential role in the transcriptional regulation of bovine FoxO1 gene. These findings explored the regulatory network mechanism of the FoxO1 gene in skeletal muscle development and adipogenesis for the bovine breed improvement program.
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Affiliation(s)
- Dawei Wei
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Jin Wang
- Institute of Animal Sciences, Ningxia Academy of Agricultural and Forestry Sciences, Yinchuan, China
| | - Zhang Jiupan
- Institute of Animal Sciences, Ningxia Academy of Agricultural and Forestry Sciences, Yinchuan, China
| | - Rajwali Khan
- Livestock Management, Breeding and Genetics, The University of Agriculture, Peshawar, Pakistan
| | | | - Song Yaping
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Jiang Chao
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Amel Ayari-Akkari
- Biology Department, College of Science, King Khalid University, Abha, Saudi Arabia
- Laboratory of Diversity, Management and Conservation of Biological Systems, Faculty of Science of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Dalia Abd El Moneim Ahmed
- Laboratory of Diversity, Management and Conservation of Biological Systems, Faculty of Science of Tunis, University of Tunis El Manar, Tunis, Tunisia
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10
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Winans T, Oaks Z, Choudhary G, Patel A, Huang N, Faludi T, Krakko D, Nolan J, Lewis J, Blair S, Lai Z, Landas SK, Middleton F, Asara JM, Chung SK, Wyman B, Azadi P, Banki K, Perl A. mTOR-dependent loss of PON1 secretion and antiphospholipid autoantibody production underlie autoimmunity-mediated cirrhosis in transaldolase deficiency. J Autoimmun 2023; 140:103112. [PMID: 37742509 PMCID: PMC10957505 DOI: 10.1016/j.jaut.2023.103112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/26/2023]
Abstract
Transaldolase deficiency predisposes to chronic liver disease progressing from cirrhosis to hepatocellular carcinoma (HCC). Transition from cirrhosis to hepatocarcinogenesis depends on mitochondrial oxidative stress, as controlled by cytosolic aldose metabolism through the pentose phosphate pathway (PPP). Progression to HCC is critically dependent on NADPH depletion and polyol buildup by aldose reductase (AR), while this enzyme protects from carbon trapping in the PPP and growth restriction in TAL deficiency. Although AR inactivation blocked susceptibility to hepatocarcinogenesis, it enhanced growth restriction, carbon trapping in the non-oxidative branch of the PPP and failed to reverse the depletion of glucose 6-phosphate (G6P) and liver cirrhosis. Here, we show that inactivation of the TAL-AR axis results in metabolic stress characterized by reduced mitophagy, enhanced overall autophagy, activation of the mechanistic target of rapamycin (mTOR), diminished glycosylation and secretion of paraoxonase 1 (PON1), production of antiphospholipid autoantibodies (aPL), loss of CD161+ NK cells, and expansion of CD38+ Ito cells, which are responsive to treatment with rapamycin in vivo. The present study thus identifies glycosylation and secretion of PON1 and aPL production as mTOR-dependent regulatory checkpoints of autoimmunity underlying liver cirrhosis in TAL deficiency.
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Affiliation(s)
- T Winans
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA; Departments of Biochemistry and Molecular Biology, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - Z Oaks
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA; Departments of Biochemistry and Molecular Biology, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - G Choudhary
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA; Departments of Biochemistry and Molecular Biology, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - A Patel
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA; Departments of Biochemistry and Molecular Biology, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - N Huang
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA; Departments of Biochemistry and Molecular Biology, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - T Faludi
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - D Krakko
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - J Nolan
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - J Lewis
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - Sarah Blair
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - Z Lai
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - S K Landas
- Departments of Pathology, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - F Middleton
- Departments of Neuroscience, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - J M Asara
- Division of Signal Transduction, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - S K Chung
- Faculty of Medicine, Macau University of Science and Technology, Taipa, Macau
| | - B Wyman
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA; Departments of Biochemistry and Molecular Biology, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - P Azadi
- University of Georgia, Athens, GA 30602, USA
| | - K Banki
- Departments of Pathology, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA
| | - A Perl
- Departments of Medicine, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA; Departments of Microbiology and Immunology, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA; Departments of Biochemistry and Molecular Biology, State University of New York, Norton College of Medicine, Syracuse, NY, 13210, USA.
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11
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Liu Y, Wan X, Li H, Chen Y, Hu X, Chen H, Zhu D, Li C, Zhang Y. CTCF coordinates cell fate specification via orchestrating regulatory hubs with pioneer transcription factors. Cell Rep 2023; 42:113259. [PMID: 37851578 DOI: 10.1016/j.celrep.2023.113259] [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: 07/18/2022] [Revised: 06/17/2023] [Accepted: 09/28/2023] [Indexed: 10/20/2023] Open
Abstract
CCCTC-binding factor (CTCF), a ubiquitously expressed architectural protein, has emerged as a key regulator of cell identity gene transcription. However, the precise molecular mechanism underlying specialized functions of CTCF remains elusive. Here, we investigate the mechanism through integrative analyses of primary hepatocytes, myocytes, and B cells from mouse and human. We demonstrate that CTCF cooperates with lineage-specific pioneer transcription factors (TFs), including MyoD, FOXA, and PU.1, to control cell identity at 1D and 3D levels. At the 1D level, pioneer TFs facilitate lineage-specific CTCF occupancy via opening chromatin. At the 3D level, CTCF and pioneer TFs form regulatory hubs to govern the expression of cell identity genes. This mechanism is validated using MyoD-null mice, CTCF knockout mice, and CRISPR editing during myogenic differentiation. Collectively, these findings uncover a general mechanism whereby CTCF acts as a cell identity cofactor to control cell identity genes via orchestrating regulatory hubs with pioneer TFs.
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Affiliation(s)
- Yuting Liu
- School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing 100871, China
| | - Xin Wan
- State Key Laboratory of Complex Severe and Rare Disease, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China
| | - Hu Li
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510320, China
| | - Yingxi Chen
- State Key Laboratory of Complex Severe and Rare Disease, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China
| | - Xiaodi Hu
- State Key Laboratory of Complex Severe and Rare Disease, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China
| | - Hebing Chen
- Institute of Health Service and Transfusion Medicine, Taiping Road 27TH, Haidian District, Beijing 100850, China
| | - Dahai Zhu
- State Key Laboratory of Complex Severe and Rare Disease, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510320, China.
| | - Cheng Li
- School of Life Sciences, Center for Bioinformatics, Center for Statistical Science, Peking University, Beijing 100871, China.
| | - Yong Zhang
- State Key Laboratory of Complex Severe and Rare Disease, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510320, China.
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12
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An autoimmune pleiotropic SNP modulates IRF5 alternative promoter usage through ZBTB3-mediated chromatin looping. Nat Commun 2023; 14:1208. [PMID: 36869052 PMCID: PMC9984425 DOI: 10.1038/s41467-023-36897-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 02/22/2023] [Indexed: 03/05/2023] Open
Abstract
Genetic sharing is extensively observed for autoimmune diseases, but the causal variants and their underlying molecular mechanisms remain largely unknown. Through systematic investigation of autoimmune disease pleiotropic loci, we found most of these shared genetic effects are transmitted from regulatory code. We used an evidence-based strategy to functionally prioritize causal pleiotropic variants and identify their target genes. A top-ranked pleiotropic variant, rs4728142, yielded many lines of evidence as being causal. Mechanistically, the rs4728142-containing region interacts with the IRF5 alternative promoter in an allele-specific manner and orchestrates its upstream enhancer to regulate IRF5 alternative promoter usage through chromatin looping. A putative structural regulator, ZBTB3, mediates the allele-specific loop to promote IRF5-short transcript expression at the rs4728142 risk allele, resulting in IRF5 overactivation and M1 macrophage polarization. Together, our findings establish a causal mechanism between the regulatory variant and fine-scale molecular phenotype underlying the dysfunction of pleiotropic genes in human autoimmunity.
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13
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Mechanisms of Interaction between Enhancers and Promoters in Three Drosophila Model Systems. Int J Mol Sci 2023; 24:ijms24032855. [PMID: 36769179 PMCID: PMC9917889 DOI: 10.3390/ijms24032855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/26/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
In higher eukaryotes, the regulation of developmental gene expression is determined by enhancers, which are often located at a large distance from the promoters they regulate. Therefore, the architecture of chromosomes and the mechanisms that determine the functional interaction between enhancers and promoters are of decisive importance in the development of organisms. Mammals and the model animal Drosophila have homologous key architectural proteins and similar mechanisms in the organization of chromosome architecture. This review describes the current progress in understanding the mechanisms of the formation and regulation of long-range interactions between enhancers and promoters at three well-studied key regulatory loci in Drosophila.
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14
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Kyrchanova OV, Bylino OV, Georgiev PG. Mechanisms of enhancer-promoter communication and chromosomal architecture in mammals and Drosophila. Front Genet 2022; 13:1081088. [PMID: 36531247 PMCID: PMC9751008 DOI: 10.3389/fgene.2022.1081088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/18/2022] [Indexed: 12/03/2022] Open
Abstract
The spatial organization of chromosomes is involved in regulating the majority of intranuclear processes in higher eukaryotes, including gene expression. Drosophila was used as a model to discover many transcription factors whose homologs play a key role in regulation of gene expression in mammals. According to modern views, a cohesin complex mostly determines the architecture of mammalian chromosomes by forming chromatin loops on anchors created by the CTCF DNA-binding architectural protein. The role of the cohesin complex in chromosome architecture is poorly understood in Drosophila, and CTCF is merely one of many Drosophila architectural proteins with a proven potential to organize specific long-range interactions between regulatory elements in the genome. The review compares the mechanisms responsible for long-range interactions and chromosome architecture between mammals and Drosophila.
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15
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Hao RH, Guo Y, Wang C, Chen F, Di CX, Dong SS, Cao QL, Guo J, Rong Y, Yao S, Zhu DL, Chen YX, Chen H, Yang TL. Lineage-specific rearrangement of chromatin loops and epigenomic features during adipocytes and osteoblasts commitment. Cell Death Differ 2022; 29:2503-2518. [PMID: 35906483 PMCID: PMC9751090 DOI: 10.1038/s41418-022-01035-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 06/09/2022] [Accepted: 06/13/2022] [Indexed: 01/31/2023] Open
Abstract
Human mesenchymal stem cells (hMSCs) can be differentiated into adipocytes and osteoblasts. The processes are driven by the rewiring of chromatin architectures and transcriptomic/epigenomic changes. Here, we induced hMSCs to adipogenic and osteogenic differentiation, and performed 2 kb resolution Hi-C experiments for chromatin loops detection. We also generated matched RNA-seq, ChIP-seq and ATAC-seq data for integrative analysis. After comprehensively comparing adipogenesis and osteogenesis, we quantitatively identified lineage-specific loops and screened out lineage-specific enhancers and open chromatin. We reveal that lineage-specific loops can activate gene expression and facilitate cell commitment through combining enhancers and accessible chromatin in a lineage-specific manner. We finally proposed loop-mediated regulatory networks and identified the controlling factors for adipocytes and osteoblasts determination. Functional experiments validated the lineage-specific regulation networks towards IRS2 and RUNX2 that are associated with adipogenesis and osteogenesis, respectively. These results are expected to help better understand the chromatin conformation determinants of hMSCs fate commitment.
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Affiliation(s)
- Ruo-Han Hao
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Yan Guo
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Chen Wang
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Fei Chen
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Chen-Xi Di
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Shan-Shan Dong
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Qi-Long Cao
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
- Research and Development Department, Qingdao Haier Biotech Co. Ltd, Qingdao, Shandong, 266109, P. R. China
| | - Jing Guo
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Yu Rong
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Shi Yao
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
- National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, P. R. China
| | - Dong-Li Zhu
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Yi-Xiao Chen
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
- National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, P. R. China
| | - Hao Chen
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Tie-Lin Yang
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China.
- National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, P. R. China.
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16
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Liu S, Cao Y, Cui K, Tang Q, Zhao K. Hi-TrAC reveals division of labor of transcription factors in organizing chromatin loops. Nat Commun 2022; 13:6679. [PMID: 36335136 PMCID: PMC9637178 DOI: 10.1038/s41467-022-34276-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 10/20/2022] [Indexed: 11/08/2022] Open
Abstract
The three-dimensional genomic structure plays a critical role in gene expression, cellular differentiation, and pathological conditions. It is pivotal to elucidate fine-scale chromatin architectures, especially interactions of regulatory elements, to understand the temporospatial regulation of gene expression. In this study, we report Hi-TrAC as a proximity ligation-free, robust, and sensitive technique to profile genome-wide chromatin interactions at high-resolution among regulatory elements. Hi-TrAC detects chromatin looping among accessible regions at single nucleosome resolution. With almost half-million identified loops, we reveal a comprehensive interaction network of regulatory elements across the genome. After integrating chromatin binding profiles of transcription factors, we discover that cohesin complex and CTCF are responsible for organizing long-range chromatin loops, related to domain formation; whereas ZNF143 and HCFC1 are involved in structuring short-range chromatin loops between regulatory elements, which directly regulate gene expression. Thus, we introduce a methodology to identify a delicate and comprehensive network of cis-regulatory elements, revealing the complexity and a division of labor of transcription factors in organizing chromatin loops for genome organization and gene expression.
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Affiliation(s)
- Shuai Liu
- grid.94365.3d0000 0001 2297 5165Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD USA
| | - Yaqiang Cao
- grid.94365.3d0000 0001 2297 5165Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD USA
| | - Kairong Cui
- grid.94365.3d0000 0001 2297 5165Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD USA
| | - Qingsong Tang
- grid.94365.3d0000 0001 2297 5165Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD USA
| | - Keji Zhao
- grid.94365.3d0000 0001 2297 5165Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD USA
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17
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Ito S, Das ND, Umehara T, Koseki H. Factors and Mechanisms That Influence Chromatin-Mediated Enhancer–Promoter Interactions and Transcriptional Regulation. Cancers (Basel) 2022; 14:cancers14215404. [PMID: 36358822 PMCID: PMC9659172 DOI: 10.3390/cancers14215404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/28/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Simple Summary The physical interactions between enhancers and promoters create chromatin conformations involved in gene regulation. In cancer cells, the chromatin conformations can be altered with uncontrolled deposition of histone marks resulting in varied gene expression. Although it is not entirely comprehensive how chromatin-mediated enhancer–promoter (E–P) interactions with various histone marks can affect gene expression, this proximity has been observed in multiple systems at multiple loci and is thought to be essential to control gene expression. In this review, we focus on emerging views of chromatin conformations associated with the E–P interactions and factors that establish or maintain such interactions, which may regulate gene expression. Abstract Eukaryotic gene expression is regulated through chromatin conformation, in which enhancers and promoters physically interact (E–P interactions). How such chromatin-mediated E–P interactions affect gene expression is not yet fully understood, but the roles of histone acetylation and methylation, pioneer transcription factors, and architectural proteins such as CCCTC binding factor (CTCF) and cohesin have recently attracted attention. Moreover, accumulated data suggest that E–P interactions are mechanistically involved in biophysical events, including liquid–liquid phase separation, and in biological events, including cancers. In this review, we discuss various mechanisms that regulate eukaryotic gene expression, focusing on emerging views regarding chromatin conformations that are involved in E–P interactions and factors that establish and maintain them.
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Affiliation(s)
- Shinsuke Ito
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Correspondence: ; Tel.: +81-45-503-9690
| | - Nando Dulal Das
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan
| | - Takashi Umehara
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Immune Regulation, Advanced Research Departments, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan
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18
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Witkowski MT, Lee S, Wang E, Lee AK, Talbot A, Ma C, Tsopoulidis N, Brumbaugh J, Zhao Y, Roberts KG, Hogg SJ, Nomikou S, Ghebrechristos YE, Thandapani P, Mullighan CG, Hochedlinger K, Chen W, Abdel-Wahab O, Eyquem J, Aifantis I. NUDT21 limits CD19 levels through alternative mRNA polyadenylation in B cell acute lymphoblastic leukemia. Nat Immunol 2022; 23:1424-1432. [PMID: 36138187 PMCID: PMC9611506 DOI: 10.1038/s41590-022-01314-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 08/11/2022] [Indexed: 02/04/2023]
Abstract
B cell progenitor acute lymphoblastic leukemia (B-ALL) treatment has been revolutionized by T cell-based immunotherapies-including chimeric antigen receptor T cell therapy (CAR-T) and the bispecific T cell engager therapeutic, blinatumomab-targeting surface glycoprotein CD19. Unfortunately, many patients with B-ALL will fail immunotherapy due to 'antigen escape'-the loss or absence of leukemic CD19 targeted by anti-leukemic T cells. In the present study, we utilized a genome-wide CRISPR-Cas9 screening approach to identify modulators of CD19 abundance on human B-ALL blasts. These studies identified a critical role for the transcriptional activator ZNF143 in CD19 promoter activation. Conversely, the RNA-binding protein, NUDT21, limited expression of CD19 by regulating CD19 messenger RNA polyadenylation and stability. NUDT21 deletion in B-ALL cells increased the expression of CD19 and the sensitivity to CD19-specific CAR-T and blinatumomab. In human B-ALL patients treated with CAR-T and blinatumomab, upregulation of NUDT21 mRNA coincided with CD19 loss at disease relapse. Together, these studies identify new CD19 modulators in human B-ALL.
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Affiliation(s)
- Matthew T Witkowski
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA.
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, USA.
| | - Soobeom Lee
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
- Department of Biology, New York University (NYU), New York, NY, USA
| | - Eric Wang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, USA
| | - Anna K Lee
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Alexis Talbot
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Chao Ma
- Department of Mechanical and Aerospace Engineering, New York University, New York, NY, USA
- Department of Biomedical Engineering, New York University, New York, NY, USA
| | - Nikolaos Tsopoulidis
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Justin Brumbaugh
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Yaqi Zhao
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kathryn G Roberts
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Simon J Hogg
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sofia Nomikou
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Yohana E Ghebrechristos
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Palaniraja Thandapani
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Konrad Hochedlinger
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Weiqiang Chen
- Department of Mechanical and Aerospace Engineering, New York University, New York, NY, USA
- Department of Biomedical Engineering, New York University, New York, NY, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Justin Eyquem
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
- Parker Institute of Cancer Immunotherapy, University of California San Francisco, San Francisco, CA, USA
| | - Iannis Aifantis
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA.
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19
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Cuartero S, Stik G, Stadhouders R. Three-dimensional genome organization in immune cell fate and function. Nat Rev Immunol 2022; 23:206-221. [PMID: 36127477 DOI: 10.1038/s41577-022-00774-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2022] [Indexed: 11/09/2022]
Abstract
Immune cell development and activation demand the precise and coordinated control of transcriptional programmes. Three-dimensional (3D) organization of the genome has emerged as an important regulator of chromatin state, transcriptional activity and cell identity by facilitating or impeding long-range genomic interactions among regulatory elements and genes. Chromatin folding thus enables cell type-specific and stimulus-specific transcriptional responses to extracellular signals, which are essential for the control of immune cell fate, for inflammatory responses and for generating a diverse repertoire of antigen receptor specificities. Here, we review recent findings connecting 3D genome organization to the control of immune cell differentiation and function, and discuss how alterations in genome folding may lead to immune dysfunction and malignancy.
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Affiliation(s)
- Sergi Cuartero
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain. .,Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.
| | - Grégoire Stik
- Centre for Genomic Regulation (CRG), Institute of Science and Technology (BIST), Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Ralph Stadhouders
- Department of Pulmonary Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands. .,Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
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20
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Rao P, Li C, Wang L, Jiang Y, Yang L, Li H, Yang P, Tao J, Lu D, Sun L. ZNF143 regulates autophagic flux to alleviate myocardial ischemia/reperfusion injury through Raptor. Cell Signal 2022; 99:110444. [PMID: 35988805 DOI: 10.1016/j.cellsig.2022.110444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 08/06/2022] [Accepted: 08/16/2022] [Indexed: 11/03/2022]
Abstract
The exact role of autophagy in myocardial ischemia/reperfusion (I/R) injury is still controversial. Excessive or insufficient autophagy may lead to cell death. Therefore, how to regulate autophagic balance during myocardial ischemia/reperfusion is critical to the treatment of myocardial I/R injury. Raptor is an mTOR regulatory related protein and closely related to the induction of autophagy. ZNF143 is widely expressed in various cells and acts as a transcription factor, which is involved in the regulation of autophagy, cell growth and development. In this study, we aimed to explore the mechanism by which ZNF143 regulated autophagy in myocardial I/R injury and the relationship between ZNF143 and Raptor. In our results, we found that ZNF143 expression was down-regulated in myocardial I/R. Inhibition of ZNF143 expression further enhanced autophagy and restored the deficiency of autophagic flux caused by myocardial I/R, subsequently alleviating myocardial I/R injury. On the other hand, overexpression of ZNF143 up-regulated Raptor expression and reduced autophagic activity, consequently exacerbating myocardial I/R injury. Taken together, our study revealed that ZNF143 might be a key target of the regulation of autophagy and a novel therapeutic target of myocardial I/R injury.
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Affiliation(s)
- Peng Rao
- Department of Cardiology, The Second Affiliated Hospital, Kunming Medical University, Kunming 650101, China
| | - Changyan Li
- Science and Technology Achievement Incubation Center, Kunming Medical University, Kunming 650500, China
| | - Limeiting Wang
- Science and Technology Achievement Incubation Center, Kunming Medical University, Kunming 650500, China
| | - Yongliang Jiang
- Department of Cardiology, The Second Affiliated Hospital, Kunming Medical University, Kunming 650101, China
| | - Lin Yang
- Department of Cardiology, The Second Affiliated Hospital, Kunming Medical University, Kunming 650101, China
| | - Hao Li
- Department of Cardiology, The Second Affiliated Hospital, Kunming Medical University, Kunming 650101, China
| | - Ping Yang
- Department of Cardiology, The Second Affiliated Hospital, Kunming Medical University, Kunming 650101, China
| | - Jun Tao
- Science and Technology Achievement Incubation Center, Kunming Medical University, Kunming 650500, China
| | - Di Lu
- Science and Technology Achievement Incubation Center, Kunming Medical University, Kunming 650500, China.
| | - Lin Sun
- Department of Cardiology, The Second Affiliated Hospital, Kunming Medical University, Kunming 650101, China.
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21
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Cobo I, Tanaka TN, Chandra Mangalhara K, Lana A, Yeang C, Han C, Schlachetzki J, Challcombe J, Fixsen BR, Sakai M, Li RZ, Fields H, Mokry M, Tsai RG, Bejar R, Prange K, de Winther M, Shadel GS, Glass CK. DNA methyltransferase 3 alpha and TET methylcytosine dioxygenase 2 restrain mitochondrial DNA-mediated interferon signaling in macrophages. Immunity 2022; 55:1386-1401.e10. [PMID: 35931086 PMCID: PMC9718507 DOI: 10.1016/j.immuni.2022.06.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/29/2022] [Accepted: 06/28/2022] [Indexed: 12/15/2022]
Abstract
Deleterious somatic mutations in DNA methyltransferase 3 alpha (DNMT3A) and TET mehtylcytosine dioxygenase 2 (TET2) are associated with clonal expansion of hematopoietic cells and higher risk of cardiovascular disease (CVD). Here, we investigated roles of DNMT3A and TET2 in normal human monocyte-derived macrophages (MDM), in MDM isolated from individuals with DNMT3A or TET2 mutations, and in macrophages isolated from human atherosclerotic plaques. We found that loss of function of DNMT3A or TET2 resulted in a type I interferon response due to impaired mitochondrial DNA integrity and activation of cGAS signaling. DNMT3A and TET2 normally maintained mitochondrial DNA integrity by regulating the expression of transcription factor A mitochondria (TFAM) dependent on their interactions with RBPJ and ZNF143 at regulatory regions of the TFAM gene. These findings suggest that targeting the cGAS-type I IFN pathway may have therapeutic value in reducing risk of CVD in patients with DNMT3A or TET2 mutations.
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Affiliation(s)
- Isidoro Cobo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Tiffany N Tanaka
- University of California San Diego, Moores Cancer Center, La Jolla, CA, USA
| | | | - Addison Lana
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Calvin Yeang
- University of California San Diego, Sulpizio Cardiovascular Center, La Jolla, CA, USA
| | - Claudia Han
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Johannes Schlachetzki
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jean Challcombe
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Bethany R Fixsen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mashito Sakai
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo, Japan
| | - Rick Z Li
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Hannah Fields
- University of California San Diego, Moores Cancer Center, La Jolla, CA, USA
| | - Michal Mokry
- Department of Pediatric Gastroenterology, Wilhelmina Children's Hospital, 3584 EA Utrecht, the Netherlands
| | - Randy G Tsai
- University of California San Diego, Moores Cancer Center, La Jolla, CA, USA
| | - Rafael Bejar
- University of California San Diego, Moores Cancer Center, La Jolla, CA, USA
| | - Koen Prange
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Amsterdam Infection and Immunity, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Menno de Winther
- Department of Medical Biochemistry, Amsterdam Cardiovascular Sciences, Amsterdam Infection and Immunity, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
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22
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Sun X, Zhang J, Cao C. CTCF and Its Partners: Shaper of 3D Genome during Development. Genes (Basel) 2022; 13:genes13081383. [PMID: 36011294 PMCID: PMC9407368 DOI: 10.3390/genes13081383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 02/06/2023] Open
Abstract
The 3D genome organization and its dynamic modulate genome function, playing a pivotal role in cell differentiation and development. CTCF and cohesin, acting as the core architectural components involved in chromatin looping and genome folding, can also recruit other protein or RNA partners to fine-tune genome structure during development. Moreover, systematic screening for partners of CTCF has been performed through high-throughput approaches. In particular, several novel protein and RNA partners, such as BHLHE40, WIZ, MAZ, Aire, MyoD, YY1, ZNF143, and Jpx, have been identified, and these partners are mostly implicated in transcriptional regulation and chromatin remodeling, offering a unique opportunity for dissecting their roles in higher-order chromatin organization by collaborating with CTCF and cohesin. Here, we review the latest advancements with an emphasis on features of CTCF partners and also discuss the specific functions of CTCF-associated complexes in chromatin structure modulation, which may extend our understanding of the functions of higher-order chromatin architecture in developmental processes.
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Affiliation(s)
- Xiaoyue Sun
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China; (X.S.); (J.Z.)
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Jing Zhang
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China; (X.S.); (J.Z.)
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Chunwei Cao
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China; (X.S.); (J.Z.)
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Guangzhou Laboratory, Guangzhou 510320, China
- Correspondence:
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23
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Ye B, Shen W, Zhang C, Yu M, Ding X, Yin M, Wang Y, Guo X, Bai G, Lin K, Shi S, Li P, Zhang Y, Yu G, Zhao Z. The role of ZNF143 overexpression in rat liver cell proliferation. BMC Genomics 2022; 23:483. [PMID: 35780101 PMCID: PMC9250731 DOI: 10.1186/s12864-022-08714-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/21/2022] [Indexed: 11/10/2022] Open
Abstract
Background Zinc finger protein 143(ZNF143), a member of the Krüppel C2H2-type zinc finger protein family, is strongly associated with cell cycle regulation and cancer development. A recent study suggested that ZNF143 plays as a transcriptional activator that promotes hepatocellular cancer (HCC) cell proliferation and cell cycle transition. However, the exact biological role of ZNF143 in liver regeneration and normal liver cell proliferation has not yet been investigated. Methods In our study, we constructed a stable rat liver cell line (BRL-3A) overexpressing ZNF143 and then integrated RNA-seq and Cleavage Under Targets and Tagmentation (CUT&Tag) data to identify the mechanism underlying differential gene expression. Results Our results show that ZNF143 expression is upregulated during the proliferation phase of liver regeneration after 2/3 partial hepatectomy (PH). The cell counting kit-8 (CCK-8) assay, EdU staining and RNA-seq data analyses revealed that ZNF143 overexpression (OE) significantly inhibited BRL-3A cell proliferation and cell cycle progression. We then performed CUT&Tag assays and found that approximately 10% of ZNF143-binding sites (BSs) were significantly changed genome-wide by ZNF143 OE. However, CCCTC-binding factor (CTCF) binding to chromatin was not affected. Interestingly, the integration analysis of RNA-seq and CUT&Tag data showed that some of genes affected by ZNF143 differential BSs are in the center of each gene regulation module. Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that these genes are critical in the maintenance of cell identity. Conclusion These results indicated that the expression level of ZNF143 in the liver is important for the maintenance of cell identity. ZNF143 plays different roles in HCC and normal liver cells and may be considered as a potential therapeutic target in liver disease. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08714-2.
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Affiliation(s)
- Bingyu Ye
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.,Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China
| | - Wenlong Shen
- Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China
| | - Chunyan Zhang
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Mengli Yu
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Xinru Ding
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Man Yin
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yahao Wang
- Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China
| | - Xinjie Guo
- Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China
| | - Ge Bai
- Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China
| | - Kailin Lin
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.,Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China
| | - Shu Shi
- Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China
| | - Ping Li
- Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China
| | - Yan Zhang
- Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China
| | - Guoying Yu
- State Key Laboratory of Cell Differentiation and Regulation, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
| | - Zhihu Zhao
- Fengtai District, Beijing Institute of Biotechnology, No. 20, Dongdajie Street, Beijing, 100071, China.
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24
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Bentsen M, Heger V, Schultheis H, Kuenne C, Looso M. TF-COMB - discovering grammar of transcription factor binding sites. Comput Struct Biotechnol J 2022; 20:4040-4051. [PMID: 35983231 PMCID: PMC9358416 DOI: 10.1016/j.csbj.2022.07.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/12/2022] [Indexed: 02/07/2023] Open
Abstract
Cooperativity between transcription factors is important to regulate target gene expression. In particular, the binding grammar of TFs in relation to each other, as well as in the context of other genomic elements, is crucial for TF functionality. However, tools to easily uncover co-occurrence between DNA-binding proteins, and investigate the regulatory modules of TFs, are limited. Here we present TF-COMB (Transcription Factor Co-Occurrence using Market Basket analysis) - a tool to investigate co-occurring TFs and binding grammar within regulatory regions. We found that TF-COMB can accurately identify known co-occurring TFs from ChIP-seq data, as well as uncover preferential localization to other genomic elements. With the use of ATAC-seq footprinting and TF motif locations, we found that TFs exhibit both preferred orientation and distance in relation to each other, and that these are biologically significant. Finally, we extended the analysis to not only investigate individual TF pairs, but also TF pairs in the context of networks, which enabled the investigation of TF complexes and TF hubs. In conclusion, TF-COMB is a flexible tool to investigate various aspects of TF binding grammar.
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Affiliation(s)
- Mette Bentsen
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Vanessa Heger
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Hendrik Schultheis
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Carsten Kuenne
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mario Looso
- Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- Cardio-Pulmonary Institute (CPI), Bad Nauheim, Germany
- Corresponding author at: Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
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25
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Super-Enhancers, Phase-Separated Condensates, and 3D Genome Organization in Cancer. Cancers (Basel) 2022; 14:cancers14122866. [PMID: 35740532 PMCID: PMC9221043 DOI: 10.3390/cancers14122866] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 01/27/2023] Open
Abstract
3D chromatin organization plays an important role in transcription regulation and gene expression. The 3D genome is highly maintained by several architectural proteins, such as CTCF, Yin Yang 1, and cohesin complex. This structural organization brings regulatory DNA elements in close proximity to their target promoters. In this review, we discuss the 3D chromatin organization of super-enhancers and their relationship to phase-separated condensates. Super-enhancers are large clusters of DNA elements. They can physically contact with their target promoters by chromatin looping during transcription. Multiple transcription factors can bind to enhancer and promoter sequences and recruit a complex array of transcriptional co-activators and RNA polymerase II to effect transcriptional activation. Phase-separated condensates of transcription factors and transcriptional co-activators have been implicated in assembling the transcription machinery at particular enhancers. Cancer cells can hijack super-enhancers to drive oncogenic transcription to promote cell survival and proliferation. These dysregulated transcriptional programs can cause cancer cells to become highly dependent on transcriptional regulators, such as Mediator and BRD4. Moreover, the expression of oncogenes that are driven by super-enhancers is sensitive to transcriptional perturbation and often occurs in phase-separated condensates, supporting therapeutic rationales of targeting SE components, 3D genome organization, or dysregulated condensates in cancer.
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26
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Deng S, Feng Y, Pauklin S. 3D chromatin architecture and transcription regulation in cancer. J Hematol Oncol 2022; 15:49. [PMID: 35509102 PMCID: PMC9069733 DOI: 10.1186/s13045-022-01271-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/21/2022] [Indexed: 12/18/2022] Open
Abstract
Chromatin has distinct three-dimensional (3D) architectures important in key biological processes, such as cell cycle, replication, differentiation, and transcription regulation. In turn, aberrant 3D structures play a vital role in developing abnormalities and diseases such as cancer. This review discusses key 3D chromatin structures (topologically associating domain, lamina-associated domain, and enhancer-promoter interactions) and corresponding structural protein elements mediating 3D chromatin interactions [CCCTC-binding factor, polycomb group protein, cohesin, and Brother of the Regulator of Imprinted Sites (BORIS) protein] with a highlight of their associations with cancer. We also summarise the recent development of technologies and bioinformatics approaches to study the 3D chromatin interactions in gene expression regulation, including crosslinking and proximity ligation methods in the bulk cell population (ChIA-PET and HiChIP) or single-molecule resolution (ChIA-drop), and methods other than proximity ligation, such as GAM, SPRITE, and super-resolution microscopy techniques.
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Affiliation(s)
- Siwei Deng
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK
| | - Yuliang Feng
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK
| | - Siim Pauklin
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Old Road, Headington, Oxford, OX3 7LD, UK.
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27
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Magnitov MD, Garaev AK, Tyakht AV, Ulianov SV, Razin SV. Pentad: a tool for distance-dependent analysis of Hi-C interactions within and between chromatin compartments. BMC Bioinformatics 2022; 23:116. [PMID: 35366792 PMCID: PMC8976968 DOI: 10.1186/s12859-022-04654-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/25/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Understanding the role of various factors in 3D genome organization is essential to determine their impact on shaping large-scale chromatin units such as euchromatin (A) and heterochromatin (B) compartments. At this level, chromatin compaction is extensively modulated when transcription and epigenetic profiles change upon cell differentiation and response to various external impacts. However, detailed analysis of chromatin contact patterns within and between compartments is complicated because of a lack of suitable computational methods.
Results
We developed a tool, Pentad, to perform calculation, visualisation and quantitative analysis of the average chromatin compartment from the Hi-C matrices in cis, trans, and specified genomic distances. As we demonstrated by applying Pentad to publicly available Hi-C datasets, it helps to reliably detect redistribution of contact frequency in the chromatin compartments and assess alterations in the compartment strength.
Conclusions
Pentad is a simple tool for the analysis of changes in chromatin compartmentalization in various biological conditions. Pentad is freely available at https://github.com/magnitov/pentad.
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28
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Owens DDG, Anselmi G, Oudelaar AM, Downes DJ, Cavallo A, Harman JR, Schwessinger R, Bucakci A, Greder L, de Ornellas S, Jeziorska D, Telenius J, Hughes JR, de Bruijn MFTR. Dynamic Runx1 chromatin boundaries affect gene expression in hematopoietic development. Nat Commun 2022; 13:773. [PMID: 35140205 PMCID: PMC8828719 DOI: 10.1038/s41467-022-28376-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 01/12/2022] [Indexed: 01/22/2023] Open
Abstract
The transcription factor RUNX1 is a critical regulator of developmental hematopoiesis and is frequently disrupted in leukemia. Runx1 is a large, complex gene that is expressed from two alternative promoters under the spatiotemporal control of multiple hematopoietic enhancers. To dissect the dynamic regulation of Runx1 in hematopoietic development, we analyzed its three-dimensional chromatin conformation in mouse embryonic stem cell (ESC) differentiation cultures. Runx1 resides in a 1.1 Mb topologically associating domain (TAD) demarcated by convergent CTCF motifs. As ESCs differentiate to mesoderm, chromatin accessibility, Runx1 enhancer-promoter (E-P) interactions, and CTCF-CTCF interactions increase in the TAD, along with initiation of Runx1 expression from the P2 promoter. Differentiation to hematopoietic progenitor cells is associated with the formation of tissue-specific sub-TADs over Runx1, a shift in E-P interactions, P1 promoter demethylation, and robust expression from both Runx1 promoters. Deletion of promoter-proximal CTCF sites at the sub-TAD boundaries has no obvious effects on E-P interactions but leads to partial loss of domain structure, mildly affects gene expression, and delays hematopoietic development. Together, our analysis of gene regulation at a large multi-promoter developmental gene reveals that dynamic sub-TAD chromatin boundaries play a role in establishing TAD structure and coordinated gene expression.
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Affiliation(s)
- Dominic D G Owens
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Giorgio Anselmi
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - A Marieke Oudelaar
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Damien J Downes
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Alessandro Cavallo
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Joe R Harman
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Ron Schwessinger
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Akin Bucakci
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Lucas Greder
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Sara de Ornellas
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Physical and Theoretical Chemistry Building, Department of Chemistry, University of Oxford, Oxford, UK
| | - Danuta Jeziorska
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jelena Telenius
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jim R Hughes
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
| | - Marella F T R de Bruijn
- MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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Batut PJ, Bing XY, Sisco Z, Raimundo J, Levo M, Levine MS. Genome organization controls transcriptional dynamics during development. Science 2022; 375:566-570. [PMID: 35113722 PMCID: PMC10368186 DOI: 10.1126/science.abi7178] [Citation(s) in RCA: 90] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Past studies offer contradictory claims for the role of genome organization in the regulation of gene activity. Here, we show through high-resolution chromosome conformation analysis that the Drosophila genome is organized by two independent classes of regulatory sequences, tethering elements and insulators. Quantitative live imaging and targeted genome editing demonstrate that this two-tiered organization is critical for the precise temporal dynamics of Hox gene transcription during development. Tethering elements mediate long-range enhancer-promoter interactions and foster fast activation kinetics. Conversely, the boundaries of topologically associating domains (TADs) prevent spurious interactions with enhancers and silencers located in neighboring TADs. These two levels of genome organization operate independently of one another to ensure precision of transcriptional dynamics and the reliability of complex patterning processes.
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Affiliation(s)
- Philippe J Batut
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Xin Yang Bing
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Zachary Sisco
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - João Raimundo
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Michal Levo
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Michael S Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
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30
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Ortabozkoyun H, Huang PY, Cho H, Narendra V, LeRoy G, Gonzalez-Buendia E, Skok JA, Tsirigos A, Mazzoni EO, Reinberg D. CRISPR and biochemical screens identify MAZ as a cofactor in CTCF-mediated insulation at Hox clusters. Nat Genet 2022; 54:202-212. [PMID: 35145304 PMCID: PMC8837555 DOI: 10.1038/s41588-021-01008-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 12/22/2021] [Indexed: 12/14/2022]
Abstract
CCCTC-binding factor (CTCF) is critical to three-dimensional genome organization. Upon differentiation, CTCF insulates active and repressed genes within Hox gene clusters. We conducted a genome-wide CRISPR knockout (KO) screen to identify genes required for CTCF-boundary activity at the HoxA cluster, complemented by biochemical approaches. Among the candidates, we identified Myc-associated zinc-finger protein (MAZ) as a cofactor in CTCF insulation. MAZ colocalizes with CTCF at chromatin borders and, similar to CTCF, interacts with the cohesin subunit RAD21. MAZ KO disrupts gene expression and local contacts within topologically associating domains. Similar to CTCF motif deletions, MAZ motif deletions lead to derepression of posterior Hox genes immediately after CTCF boundaries upon differentiation, giving rise to homeotic transformations in mouse. Thus, MAZ is a factor contributing to appropriate insulation, gene expression and genomic architecture during development.
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Affiliation(s)
- Havva Ortabozkoyun
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Pin-Yao Huang
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Hyunwoo Cho
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA.,Applied Bioinformatics Laboratories, NYU Grossman School of Medicine, New York, NY, USA.,Department of Radiation Oncology, NYU Grossman School of Medicine, New York, NY, USA
| | - Varun Narendra
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gary LeRoy
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Edgar Gonzalez-Buendia
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Jane A Skok
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA.,Applied Bioinformatics Laboratories, NYU Grossman School of Medicine, New York, NY, USA.,Institute for Computational Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | | | - Danny Reinberg
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA. .,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA.
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31
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Li J, Hlavka-Zhang J, Shrimp JH, Piper C, Dupéré-Richér D, Roth JS, Jing D, Casellas Román HL, Troche C, Swaroop A, Kulis M, Oyer JA, Will CM, Shen M, Riva A, Bennett RL, Ferrando AA, Hall MD, Lock RB, Licht JD. PRC2 Inhibitors Overcome Glucocorticoid Resistance Driven by NSD2 Mutation in Pediatric Acute Lymphoblastic Leukemia. Cancer Discov 2022; 12:186-203. [PMID: 34417224 DOI: 10.1158/2159-8290.cd-20-1771] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 07/21/2021] [Accepted: 08/18/2021] [Indexed: 01/05/2023]
Abstract
Mutations in epigenetic regulators are common in relapsed pediatric acute lymphoblastic leukemia (ALL). Here, we uncovered the mechanism underlying the relapse of ALL driven by an activating mutation of the NSD2 histone methyltransferase (p.E1099K). Using high-throughput drug screening, we found that NSD2-mutant cells were specifically resistant to glucocorticoids. Correction of this mutation restored glucocorticoid sensitivity. The transcriptional response to glucocorticoids was blocked in NSD2-mutant cells due to depressed glucocorticoid receptor (GR) levels and the failure of glucocorticoids to autoactivate GR expression. Although H3K27me3 was globally decreased by NSD2 p.E1099K, H3K27me3 accumulated at the NR3C1 (GR) promoter. Pretreatment of NSD2 p.E1099K cell lines and patient-derived xenograft samples with PRC2 inhibitors reversed glucocorticoid resistance in vitro and in vivo. PRC2 inhibitors restored NR3C1 autoactivation by glucocorticoids, increasing GR levels and allowing GR binding and activation of proapoptotic genes. These findings suggest a new therapeutic approach to relapsed ALL associated with NSD2 mutation. SIGNIFICANCE: NSD2 histone methyltransferase mutations observed in relapsed pediatric ALL drove glucocorticoid resistance by repression of the GR and abrogation of GR gene autoactivation due to accumulation of K3K27me3 at its promoter. Pretreatment with PRC2 inhibitors reversed resistance, suggesting a new therapeutic approach to these patients with ALL.This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Jianping Li
- Division of Hematology/Oncology, University of Florida Health Cancer Center, Gainesville, Florida
| | - Julia Hlavka-Zhang
- Children's Cancer Institute, School of Women's and Children's Health, University of New South Wales Sydney, Sydney, Australia
| | - Jonathan H Shrimp
- National Center for Advancing Translational Sciences, NIH, Rockville, Maryland
| | - Crissandra Piper
- Division of Hematology/Oncology, University of Florida Health Cancer Center, Gainesville, Florida
| | - Daphne Dupéré-Richér
- Division of Hematology/Oncology, University of Florida Health Cancer Center, Gainesville, Florida
| | - Jacob S Roth
- National Center for Advancing Translational Sciences, NIH, Rockville, Maryland
| | - Duohui Jing
- Children's Cancer Institute, School of Women's and Children's Health, University of New South Wales Sydney, Sydney, Australia
| | - Heidi L Casellas Román
- Division of Hematology/Oncology, University of Florida Health Cancer Center, Gainesville, Florida
| | - Catalina Troche
- Division of Hematology/Oncology, University of Florida Health Cancer Center, Gainesville, Florida
| | - Alok Swaroop
- Division of Hematology/Oncology, University of Florida Health Cancer Center, Gainesville, Florida
| | - Marta Kulis
- Fundació Clínic per a la Recerca Biomèdica, Barcelona, Spain
| | - Jon A Oyer
- Pfizer Inc., Oncology Research and Development, San Diego, California
| | - Christine M Will
- Division of Hematology/Oncology, University of Florida Health Cancer Center, Gainesville, Florida
| | - Min Shen
- National Center for Advancing Translational Sciences, NIH, Rockville, Maryland
| | - Alberto Riva
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida
| | - Richard L Bennett
- Division of Hematology/Oncology, University of Florida Health Cancer Center, Gainesville, Florida
| | - Adolfo A Ferrando
- Institute of Cancer Genetics, Columbia University, New York, New York
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, NIH, Rockville, Maryland
| | - Richard B Lock
- Children's Cancer Institute, School of Women's and Children's Health, University of New South Wales Sydney, Sydney, Australia
| | - Jonathan D Licht
- Division of Hematology/Oncology, University of Florida Health Cancer Center, Gainesville, Florida.
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32
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Cao Y, Liu S, Ren G, Tang Q, Zhao K. cLoops2: a full-stack comprehensive analytical tool for chromatin interactions. Nucleic Acids Res 2021; 50:57-71. [PMID: 34928392 DOI: 10.1093/nar/gkab1233] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 11/18/2021] [Accepted: 12/02/2021] [Indexed: 12/21/2022] Open
Abstract
Investigating chromatin interactions between regulatory regions such as enhancer and promoter elements is vital for understanding the regulation of gene expression. Compared to Hi-C and its variants, the emerging 3D mapping technologies focusing on enriched signals, such as TrAC-looping, reduce the sequencing cost and provide higher interaction resolution for cis-regulatory elements. A robust pipeline is needed for the comprehensive interpretation of these data, especially for loop-centric analysis. Therefore, we have developed a new versatile tool named cLoops2 for the full-stack analysis of these 3D chromatin interaction data. cLoops2 consists of core modules for peak-calling, loop-calling, differentially enriched loops calling and loops annotation. It also contains multiple modules for interaction resolution estimation, data similarity estimation, features quantification, feature aggregation analysis, and visualization. cLoops2 with documentation and example data are open source and freely available at GitHub: https://github.com/KejiZhaoLab/cLoops2.
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Affiliation(s)
- Yaqiang Cao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Shuai Liu
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Gang Ren
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Qingsong Tang
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
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33
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Liu Y, Wu Z, Zhou J, Ramadurai DKA, Mortenson KL, Aguilera-Jimenez E, Yan Y, Yang X, Taylor AM, Varley KE, Gertz J, Choi PS, Cherniack AD, Chen X, Bass AJ, Bailey SD, Zhang X. A predominant enhancer co-amplified with the SOX2 oncogene is necessary and sufficient for its expression in squamous cancer. Nat Commun 2021; 12:7139. [PMID: 34880227 PMCID: PMC8654995 DOI: 10.1038/s41467-021-27055-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 11/01/2021] [Indexed: 02/05/2023] Open
Abstract
Amplification and overexpression of the SOX2 oncogene represent a hallmark of squamous cancers originating from diverse tissue types. Here, we find that squamous cancers selectively amplify a 3' noncoding region together with SOX2, which harbors squamous cancer-specific chromatin accessible regions. We identify a single enhancer e1 that predominantly drives SOX2 expression. Repression of e1 in SOX2-high cells causes collapse of the surrounding enhancers, remarkable reduction in SOX2 expression, and a global transcriptional change reminiscent of SOX2 knockout. The e1 enhancer is driven by a combination of transcription factors including SOX2 itself and the AP-1 complex, which facilitates recruitment of the co-activator BRD4. CRISPR-mediated activation of e1 in SOX2-low cells is sufficient to rebuild the e1-SOX2 loop and activate SOX2 expression. Our study shows that squamous cancers selectively amplify a predominant enhancer to drive SOX2 overexpression, uncovering functional links among enhancer activation, chromatin looping, and lineage-specific copy number amplifications of oncogenes.
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Affiliation(s)
- Yanli Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, Shanxi, China
| | - Zhong Wu
- Department of Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jin Zhou
- Department of Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Dinesh K A Ramadurai
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Katelyn L Mortenson
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Estrella Aguilera-Jimenez
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Yifei Yan
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Departments of Surgery and Human Genetics, McGill University, Montreal, QC, Canada
| | - Xiaojun Yang
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, Shanxi, China
| | - Alison M Taylor
- Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Katherine E Varley
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Jason Gertz
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Peter S Choi
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew D Cherniack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xingdong Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Fudan University Taizhou Institute of Health Sciences, Taizhou, Jiangsu, China
- Yiwu Research Institute of Fudan University, Yiwu, Zhejiang, China
| | - Adam J Bass
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Swneke D Bailey
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.
- Departments of Surgery and Human Genetics, McGill University, Montreal, QC, Canada.
| | - Xiaoyang Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
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34
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Ray-Jones H, Spivakov M. Transcriptional enhancers and their communication with gene promoters. Cell Mol Life Sci 2021; 78:6453-6485. [PMID: 34414474 PMCID: PMC8558291 DOI: 10.1007/s00018-021-03903-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 12/13/2022]
Abstract
Transcriptional enhancers play a key role in the initiation and maintenance of gene expression programmes, particularly in metazoa. How these elements control their target genes in the right place and time is one of the most pertinent questions in functional genomics, with wide implications for most areas of biology. Here, we synthesise classic and recent evidence on the regulatory logic of enhancers, including the principles of enhancer organisation, factors that facilitate and delimit enhancer-promoter communication, and the joint effects of multiple enhancers. We show how modern approaches building on classic insights have begun to unravel the complexity of enhancer-promoter relationships, paving the way towards a quantitative understanding of gene control.
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Affiliation(s)
- Helen Ray-Jones
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, W12 0NN, UK
| | - Mikhail Spivakov
- MRC London Institute of Medical Sciences, London, W12 0NN, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, W12 0NN, UK.
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