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Shan L, Wang W, Du L, Li D, Wang Y, Xie Y, Li H, Wang J, Shi Z, Zhou Y, Zhu D, Sui G, Liu F. SP1 undergoes phase separation and activates RGS20 expression through super-enhancers to promote lung adenocarcinoma progression. Proc Natl Acad Sci U S A 2024; 121:e2401834121. [PMID: 38976739 DOI: 10.1073/pnas.2401834121] [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: 01/28/2024] [Accepted: 05/28/2024] [Indexed: 07/10/2024] Open
Abstract
Lung adenocarcinoma (LUAD) is the leading cause of cancer-related death worldwide, but the underlying molecular mechanisms remain largely unclear. The transcription factor (TF) specificity protein 1 (SP1) plays a crucial role in the development of various cancers, including LUAD. Recent studies have indicated that master TFs may form phase-separated macromolecular condensates to promote super-enhancer (SE) assembly and oncogene expression. In this study, we demonstrated that SP1 undergoes phase separation and that its zinc finger 3 in the DNA-binding domain is essential for this process. Through Cleavage Under Targets & Release Using Nuclease (CUT&RUN) using antibodies against SP1 and H3K27ac, we found a significant correlation between SP1 enrichment and SE elements, identified the regulator of the G protein signaling 20 (RGS20) gene as the most likely target regulated by SP1 through SE mechanisms, and verified this finding using different approaches. The oncogenic activity of SP1 relies on its phase separation ability and RGS20 gene activation, which can be abolished by glycogen synthase kinase J4 (GSK-J4), a demethylase inhibitor. Together, our findings provide evidence that SP1 regulates its target oncogene expression through phase separation and SE mechanisms, thereby promoting LUAD cell progression. This study also revealed an innovative target for LUAD therapies through intervening in SP1-mediated SE formation.
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Affiliation(s)
- Liying Shan
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Wenmeng Wang
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Lijuan Du
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Dangdang Li
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yunxuan Wang
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Yuyan Xie
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Hongyan Li
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Jiale Wang
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Zhihao Shi
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Yang Zhou
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Daling Zhu
- College of Pharmacy, Harbin Medical University (Daqing), Daqing 163319, China
| | - Guangchao Sui
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Fang Liu
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, China
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2
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Mian Y, Wang L, Keikhosravi A, Guo K, Misteli T, Arda HE, Finn EH. Cell type- and transcription-independent spatial proximity between enhancers and promoters. Mol Biol Cell 2024; 35:ar96. [PMID: 38717453 DOI: 10.1091/mbc.e24-02-0082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024] Open
Abstract
Cell type-specific enhancers are critically important for lineage specification. The mechanisms that determine cell-type specificity of enhancer activity, however, are not fully understood. Most current models for how enhancers function invoke physical proximity between enhancer elements and their target genes. Here, we use an imaging-based approach to examine the spatial relationship of cell type-specific enhancers and their target genes with single-cell resolution. Using high-throughput microscopy, we measure the spatial distance from target promoters to their cell type-specific active and inactive enhancers in individual pancreatic cells derived from distinct lineages. We find increased proximity of all promoter-enhancer pairs relative to non-enhancer pairs separated by similar genomic distances. Strikingly, spatial proximity between enhancers and target genes was unrelated to tissue-specific enhancer activity. Furthermore, promoter-enhancer proximity did not correlate with the expression status of target genes. Our results suggest that promoter-enhancer pairs exist in a distinctive chromatin environment but that genome folding is not a universal driver of cell-type specificity in enhancer function.
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Affiliation(s)
- Yasmine Mian
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Li Wang
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Adib Keikhosravi
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Konnie Guo
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - H Efsun Arda
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Elizabeth H Finn
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104
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3
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Lu Z, Wang Y, Assumpção ALFV, Liu P, Kopp A, Saka S, Mcilwain SJ, Viny AD, Brand M, Pan X. Yin Yang 1 regulates cohesin complex protein SMC3 in mouse hematopoietic stem cells. Blood Adv 2024; 8:3076-3091. [PMID: 38531064 PMCID: PMC11222949 DOI: 10.1182/bloodadvances.2023011411] [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: 08/09/2023] [Revised: 02/16/2024] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
ABSTRACT Yin Yang 1 (YY1) and structural maintenance of chromosomes 3 (SMC3) are 2 critical chromatin structural factors that mediate long-distance enhancer-promoter interactions and promote developmentally regulated changes in chromatin architecture in hematopoietic stem/progenitor cells (HSPCs). Although YY1 has critical functions in promoting hematopoietic stem cell (HSC) self-renewal and maintaining HSC quiescence, SMC3 is required for proper myeloid lineage differentiation. However, many questions remain unanswered regarding how YY1 and SMC3 interact with each other and affect hematopoiesis. We found that YY1 physically interacts with SMC3 and cooccupies with SMC3 at a large cohort of promoters genome wide, and YY1 deficiency deregulates the genetic network governing cell metabolism. YY1 occupies the Smc3 promoter and represses SMC3 expression in HSPCs. Although deletion of 1 Smc3 allele partially restores HSC numbers and quiescence in YY1 knockout mice, Yy1-/-Smc3+/- HSCs fail to reconstitute blood after bone marrow transplant. YY1 regulates HSC metabolic pathways and maintains proper intracellular reactive oxygen species levels in HSCs, and this regulation is independent of the YY1-SMC3 axis. Our results establish a distinct YY1-SMC3 axis and its impact on HSC quiescence and metabolism.
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Affiliation(s)
- Zhanping Lu
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI
- Carbone Cancer Center, University of Wisconsin, Madison, WI
- Wisconsin Blood Cancer Research Institute, University of Wisconsin, Madison, WI
| | - Yinghua Wang
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI
- Carbone Cancer Center, University of Wisconsin, Madison, WI
- Wisconsin Blood Cancer Research Institute, University of Wisconsin, Madison, WI
| | - Anna L. F. V. Assumpção
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI
- Carbone Cancer Center, University of Wisconsin, Madison, WI
- Wisconsin Blood Cancer Research Institute, University of Wisconsin, Madison, WI
| | - Peng Liu
- Carbone Cancer Center, University of Wisconsin, Madison, WI
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Audrey Kopp
- Wisconsin Blood Cancer Research Institute, University of Wisconsin, Madison, WI
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Sahitya Saka
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI
- Carbone Cancer Center, University of Wisconsin, Madison, WI
- Wisconsin Blood Cancer Research Institute, University of Wisconsin, Madison, WI
| | - Sean J. Mcilwain
- Carbone Cancer Center, University of Wisconsin, Madison, WI
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Aaron D. Viny
- Division of Hematology & Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY
| | - Marjorie Brand
- Wisconsin Blood Cancer Research Institute, University of Wisconsin, Madison, WI
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Xuan Pan
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI
- Carbone Cancer Center, University of Wisconsin, Madison, WI
- Wisconsin Blood Cancer Research Institute, University of Wisconsin, Madison, WI
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4
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Tang G, Xia H, Huang Y, Guo Y, Chen Y, Ma Z, Liu W. Liquid-liquid phase separation of H3K27me3 reader BP1 regulates transcriptional repression. Genome Biol 2024; 25:67. [PMID: 38468348 PMCID: PMC10926671 DOI: 10.1186/s13059-024-03209-7] [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: 08/04/2023] [Accepted: 03/04/2024] [Indexed: 03/13/2024] Open
Abstract
BACKGROUND Bromo-adjacent homology-plant homeodomain domain containing protein 1 (BP1) is a reader of histone post-translational modifications in fungi. BP1 recognizes trimethylation of lysine 27 in histone H3 (H3K27me3), an epigenetic hallmark of gene silencing. However, whether and how BP1 participates in transcriptional repression remains poorly understood. RESULTS We report that BP1 forms phase-separated liquid condensates to modulate its biological function in Fusarium graminearum. Deletion assays reveal that intrinsically disordered region 2 (IDR2) of BP1 mediates its liquid-liquid phase separation. The phase separation of BP1 is indispensable for its interaction with suppressor of Zeste 12, a component of polycomb repressive complex 2. Furthermore, IDR2 deletion abolishes BP1-H3K27me3 binding and alleviates the transcriptional repression of secondary metabolism-related genes, especially deoxynivalenol mycotoxin biosynthesis genes. CONCLUSIONS BP1 maintains transcriptional repression by forming liquid-liquid phase-separated condensates, expanding our understanding of the relationship between post-translational modifications and liquid-liquid phase separation.
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Affiliation(s)
- Guangfei Tang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Haoxue Xia
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yufei Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yuanwen Guo
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yun Chen
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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5
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Yan X, Zhang M, Wang D. Interplay between posttranslational modifications and liquid‒liquid phase separation in tumors. Cancer Lett 2024; 584:216614. [PMID: 38246226 DOI: 10.1016/j.canlet.2024.216614] [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: 11/08/2023] [Revised: 12/22/2023] [Accepted: 12/30/2023] [Indexed: 01/23/2024]
Abstract
Liquid‒liquid phase separation (LLPS) is a general phenomenon recently recognized to be critically involved in the regulation of a variety of cellular biological processes, such as transcriptional regulation, heterochromatin formation and signal transduction, through the compartmentalization of proteins or nucleic acids into droplet-like condensates. These processes are directly or indirectly related to tumor initiation and treatment. Posttranslational modifications (PTMs), which represent a rapid and reversible mechanism involved in the functional regulation of proteins, have emerged as key events in modulating LLPS under physiological or pathophysiological conditions, including tumorigenesis and antitumor therapy. In this review, we introduce the biological functions participated in cancer-associated LLPS, discuss the potential roles of LLPS during tumor onset or therapy, and emphasize the mechanistic characteristics of LLPS regulated by PTMs and its effects on tumor progression. We then provide a perspective on further studies on LLPS and its regulation by PTMs in cancer research. This review aims to broaden the understanding of the functions of LLPS and its regulation by PTMs under normal or aberrant cellular conditions.
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Affiliation(s)
- Xiaojun Yan
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Meng Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Donglai Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.
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6
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Wang W, Li D, Xu Q, Cheng J, Yu Z, Li G, Qiao S, Pan J, Wang H, Shi J, Zheng T, Sui G. G-quadruplexes promote the motility in MAZ phase-separated condensates to activate CCND1 expression and contribute to hepatocarcinogenesis. Nat Commun 2024; 15:1045. [PMID: 38316778 PMCID: PMC10844655 DOI: 10.1038/s41467-024-45353-5] [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: 05/03/2023] [Accepted: 01/22/2024] [Indexed: 02/07/2024] Open
Abstract
G-quadruplexes (G4s) can recruit transcription factors to activate gene expression, but detailed mechanisms remain enigmatic. Here, we demonstrate that G4s in the CCND1 promoter propel the motility in MAZ phase-separated condensates and subsequently activate CCND1 transcription. Zinc finger (ZF) 2 of MAZ is a responsible for G4 binding, while ZF3-5, but not a highly disordered region, is critical for MAZ condensation. MAZ nuclear puncta overlaps with signals of G4s and various coactivators including BRD4, MED1, CDK9 and active RNA polymerase II, as well as gene activation histone markers. MAZ mutants lacking either G4 binding or phase separation ability did not form nuclear puncta, and showed deficiencies in promoting hepatocellular carcinoma cell proliferation and xenograft tumor formation. Overall, we unveiled that G4s recruit MAZ to the CCND1 promoter and facilitate the motility in MAZ condensates that compartmentalize coactivators to activate CCND1 expression and subsequently exacerbate hepatocarcinogenesis.
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Affiliation(s)
- Wenmeng Wang
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Dangdang Li
- College of Life Science, Northeast Forestry University, Harbin, 150040, China.
| | - Qingqing Xu
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Jiahui Cheng
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Zhiwei Yu
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Guangyue Li
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Shiyao Qiao
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Jiasong Pan
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Hao Wang
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Jinming Shi
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Tongsen Zheng
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, 150081, China
- Key Laboratory of Molecular Oncology of Heilongjiang Province, Harbin, China
| | - Guangchao Sui
- College of Life Science, Northeast Forestry University, Harbin, 150040, China.
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7
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Meeussen JVW, Lenstra TL. Time will tell: comparing timescales to gain insight into transcriptional bursting. Trends Genet 2024; 40:160-174. [PMID: 38216391 PMCID: PMC10860890 DOI: 10.1016/j.tig.2023.11.003] [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: 09/13/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 01/14/2024]
Abstract
Recent imaging studies have captured the dynamics of regulatory events of transcription inside living cells. These events include transcription factor (TF) DNA binding, chromatin remodeling and modification, enhancer-promoter (E-P) proximity, cluster formation, and preinitiation complex (PIC) assembly. Together, these molecular events culminate in stochastic bursts of RNA synthesis, but their kinetic relationship remains largely unclear. In this review, we compare the timescales of upstream regulatory steps (input) with the kinetics of transcriptional bursting (output) to generate mechanistic models of transcription dynamics in single cells. We highlight open questions and potential technical advances to guide future endeavors toward a quantitative and kinetic understanding of transcription regulation.
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Affiliation(s)
- Joseph V W Meeussen
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, Amsterdam 1066CX, The Netherlands
| | - Tineke L Lenstra
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, Amsterdam 1066CX, The Netherlands.
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8
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Xing YH, Dong R, Lee L, Rengarajan S, Riggi N, Boulay G, Rivera MN. DisP-seq reveals the genome-wide functional organization of DNA-associated disordered proteins. Nat Biotechnol 2024; 42:52-64. [PMID: 37037903 PMCID: PMC10791585 DOI: 10.1038/s41587-023-01737-4] [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: 07/06/2022] [Accepted: 03/07/2023] [Indexed: 04/12/2023]
Abstract
Intrinsically disordered regions (IDRs) in DNA-associated proteins are known to influence gene regulation, but their distribution and cooperative functions in genome-wide regulatory programs remain poorly understood. Here we describe DisP-seq (disordered protein precipitation followed by DNA sequencing), an antibody-independent chemical precipitation assay that can simultaneously map endogenous DNA-associated disordered proteins genome-wide through a combination of biotinylated isoxazole precipitation and next-generation sequencing. DisP-seq profiles are composed of thousands of peaks that are associated with diverse chromatin states, are enriched for disordered transcription factors (TFs) and are often arranged in large lineage-specific clusters with high local concentrations of disordered proteins and different combinations of histone modifications linked to regulatory potential. We use DisP-seq to analyze cancer cells and reveal how disordered protein-associated islands enable IDR-dependent mechanisms that control the binding and function of disordered TFs, including oncogene-dependent sequestration of TFs through long-range interactions and the reactivation of differentiation pathways upon loss of oncogenic stimuli in Ewing sarcoma.
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Affiliation(s)
- Yu-Hang Xing
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Rui Dong
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Lukuo Lee
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Shruthi Rengarajan
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Nicolò Riggi
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Gaylor Boulay
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Miguel N Rivera
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA.
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9
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Liu M, Liu X, Qiao J, Cao B. Silibinin suppresses glioblastoma cell growth, invasion, stemness, and glutamine metabolism by YY1/SLC1A5 pathway. Transl Neurosci 2024; 15:20220333. [PMID: 38410123 PMCID: PMC10896183 DOI: 10.1515/tnsci-2022-0333] [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: 08/12/2023] [Revised: 12/20/2023] [Accepted: 01/03/2024] [Indexed: 02/28/2024] Open
Abstract
Background Silibinin has been found to inhibit glioblastoma (GBM) progression. However, the underlying molecular mechanism by which Silibinin regulates GBM process remains unclear. Methods GBM cell proliferation, apoptosis, invasion, and stemness are assessed by cell counting kit-8 assay, EdU assay, flow cytometry, transwell assay, and sphere formation assay. Western blot is used to measure the protein expression levels of apoptosis-related markers, solute carrier family 1 member 5 (SLC1A5), and Yin Yang-1 (YY1). Glutamine consumption, glutamate production, and α-ketoglutarate production are detected to evaluate glutamine metabolism in cells. Also, SLC1A5 and YY1 mRNA levels are examined using quantitative real-time PCR. Chromatin immunoprecipitation assay and dual-luciferase reporter assay are used to detect the interaction between YY1 and SLC1A5. Mice xenograft models are constructed to explore Silibinin roles in vivo. Results Silibinin inhibits GBM cell proliferation, invasion, stemness, and glutamine metabolism, while promotes apoptosis. SLC1A5 is upregulated in GBM and its expression is decreased by Silibinin. SLC1A5 overexpression abolishes the anti-tumor effect of Silibinin in GBM cells. Transcription factor YY1 binds to SLC1A5 promoter region to induce SLC1A5 expression, and the inhibition effect of YY1 knockdown on GBM cell growth, invasion, stemness, and glutamine metabolism can be reversed by SLC1A5 overexpression. In addition, Silibinin reduces GBM tumor growth by regulating YY1/SLC1A5 pathway. Conclusion Silibinin plays an anti-tumor role in GBM process, which may be achieved via inhibiting YY1/SLC1A5 pathway.
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Affiliation(s)
- Ming Liu
- Department of Neurosurgery, The First Affiliated Hospital of Hebei North University, 12 Changqing Road, Qiaoxi District, Zhangjiakou City, 075000, Hebei Province, China
| | - Xipeng Liu
- Department of Neurosurgery, The First Affiliated Hospital of Hebei North University, 12 Changqing Road, Qiaoxi District, Zhangjiakou City, 075000, Hebei Province, China
| | - Jianxin Qiao
- Department of Neurosurgery, The First Affiliated Hospital of Hebei North University, 12 Changqing Road, Qiaoxi District, Zhangjiakou City, 075000, Hebei Province, China
| | - Bing Cao
- Department of Neurosurgery, The First Affiliated Hospital of Hebei North University, 12 Changqing Road, Qiaoxi District, Zhangjiakou City, 075000, Hebei Province, China
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10
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Yang J, Yu C, Lyn N, Liu L, Li D, Shang Q. Clinical analysis of Gabriele-de Vries caused by YY1 mutations and literature review. Mol Genet Genomic Med 2024; 12:e2281. [PMID: 37658636 PMCID: PMC10767417 DOI: 10.1002/mgg3.2281] [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: 04/18/2023] [Revised: 07/29/2023] [Accepted: 08/22/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND Gabriele-de Vries syndrome is a rare autosomal dominant genetic disease characterized by global development delay/intellectual disability, delayed language development, feeding difficulties, and distinctive facial dysmorphism. It is caused by pathogenic variants in YY1. METHODS The current report describes a female patient with motor delay and a facial dysmorphism phenotype. We identified pathogenic mutations in the patient by whole-exome sequencing and confirmed them by Sanger sequencing. RESULTS A novel heterozygous frameshift mutation NM_003403.5:c.458_476del (p. V153fs*97) in the YY1 gene was detected in the proband. Finally, we provide a case-based review of the clinical features associated with Gabriele-de Vries syndrome. A total of 28 patients with genetic abnormalities and clinical phenotypes have been reported in the literature thus far. CONCLUSIONS The mutation site is reported for the first time, and its discovery would expand the mutation spectrum of the YY1 gene. The main clinical manifestations of Gabriele-de Vries syndrome are developmental delay/intellectual disability, craniofacial dysplasia, intrauterine growth delay, low birth weight, feeding difficulties, and rare congenital malformations. Genetic tests are crucial techniques for its diagnosis because of its nonspecific clinical manifestations.
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Affiliation(s)
- Jingjing Yang
- Department of Pediatric Rehabilitation MedicineChildren's Hospital Affiliated to Zhengzhou UniversityZhengzhouChina
| | - Chaonan Yu
- Department of Pediatric Rehabilitation MedicineChildren's Hospital Affiliated to Zhengzhou UniversityZhengzhouChina
| | - Nan Lyn
- Department of Pediatric Rehabilitation MedicineChildren's Hospital Affiliated to Zhengzhou UniversityZhengzhouChina
| | - Lei Liu
- Henan Neurodevelopment Engineering Research Center for Children, Henan Key Laboratory of Children's Genetics and Metabolic DiseasesChildren's Hospital Affiliated to Zhengzhou UniversityZhengzhouChina
| | - Dongxiao Li
- Henan Neurodevelopment Engineering Research Center for Children, Henan Key Laboratory of Children's Genetics and Metabolic DiseasesChildren's Hospital Affiliated to Zhengzhou UniversityZhengzhouChina
| | - Qing Shang
- Department of Pediatric Rehabilitation MedicineChildren's Hospital Affiliated to Zhengzhou UniversityZhengzhouChina
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11
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Mann R, Notani D. Transcription factor condensates and signaling driven transcription. Nucleus 2023; 14:2205758. [PMID: 37129580 PMCID: PMC10155639 DOI: 10.1080/19491034.2023.2205758] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/10/2023] [Accepted: 04/19/2023] [Indexed: 05/03/2023] Open
Abstract
Transcription Factor (TF) condensates are a heterogenous mix of RNA, DNA, and multiple co-factor proteins capable of modulating the transcriptional response of the cell. The dynamic nature and the spatial location of TF-condensates in the 3D nuclear space is believed to provide a fast response, which is on the same pace as the signaling cascade and yet ever-so-specific in the crowded environment of the nucleus. However, the current understanding of how TF-condensates can achieve these feet so quickly and efficiently is still unclear. In this review, we draw parallels with other protein condensates and share our speculations on how the nucleus uses these TF-condensates to achieve high transcriptional specificity and fidelity. We discuss the various constituents of TF-condensates, their properties, and the known and unknown functions of TF-condensates with a particular focus on steroid signaling-induced transcriptional programs.
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Affiliation(s)
- Rajat Mann
- National Centre for Biological Sciences, TIFR, Bangalore, India
| | - Dimple Notani
- National Centre for Biological Sciences, TIFR, Bangalore, India
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12
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Demmerle J, Hao S, Cai D. Transcriptional condensates and phase separation: condensing information across scales and mechanisms. Nucleus 2023; 14:2213551. [PMID: 37218279 PMCID: PMC10208215 DOI: 10.1080/19491034.2023.2213551] [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: 01/10/2023] [Revised: 04/26/2023] [Accepted: 05/10/2023] [Indexed: 05/24/2023] Open
Abstract
Transcription is the fundamental process of gene expression, which in eukaryotes occurs within the complex physicochemical environment of the nucleus. Decades of research have provided extreme detail in the molecular and functional mechanisms of transcription, but the spatial and genomic organization of transcription remains mysterious. Recent discoveries show that transcriptional components can undergo phase separation and create distinct compartments inside the nucleus, providing new models through which to view the transcription process in eukaryotes. In this review, we focus on transcriptional condensates and their phase separation-like behaviors. We suggest differentiation between physical descriptions of phase separation and the complex and dynamic biomolecular assemblies required for productive gene expression, and we discuss how transcriptional condensates are central to organizing the three-dimensional genome across spatial and temporal scales. Finally, we map approaches for therapeutic manipulation of transcriptional condensates and ask what technical advances are needed to understand transcriptional condensates more completely.
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Affiliation(s)
- Justin Demmerle
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Siyuan Hao
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Danfeng Cai
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
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13
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Donald H, Blane A, Buthelezi S, Naicker P, Stoychev S, Majakwara J, Fanucchi S. Assessing the dynamics and macromolecular interactions of the intrinsically disordered protein YY1. Biosci Rep 2023; 43:BSR20231295. [PMID: 37815922 PMCID: PMC10611921 DOI: 10.1042/bsr20231295] [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: 07/31/2023] [Revised: 09/26/2023] [Accepted: 10/10/2023] [Indexed: 10/12/2023] Open
Abstract
YY1 is a ubiquitously expressed, intrinsically disordered transcription factor involved in neural development. The oligomeric state of YY1 varies depending on the environment. These structural changes may alter its DNA binding ability and hence its transcriptional activity. Just as YY1's oligomeric state can impact its role in transcription, so does its interaction with other proteins such as FOXP2. The aim of this work is to study the structure and dynamics of YY1 so as to determine the influence of oligomerisation and associations with FOXP2 on its DNA binding mechanism. The results confirm that YY1 is primarily a disordered protein, but it does consist of certain specific structured regions. We observed that YY1 quaternary structure is a heterogenous mixture of oligomers, the overall size of which is dependent on ionic strength. Both YY1 oligomerisation and its dynamic behaviour are further subject to changes upon DNA binding, whereby increases in DNA concentration result in a decrease in the size of YY1 oligomers. YY1 and the FOXP2 forkhead domain were found to interact with each other both in isolation and in the presence of YY1-specific DNA. The heterogeneous, dynamic multimerisation of YY1 identified in this work is, therefore likely to be important for its ability to make heterologous associations with other proteins such as FOXP2. The interactions that YY1 makes with itself, FOXP2 and DNA form part of an intricate mechanism of transcriptional regulation by YY1, which is vital for appropriate neural development.
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Affiliation(s)
- Heather Donald
- Protein Structure-Function Unit, School of molecular and Cell Biology, University of the Witwatersrand, Jan Smuts Ave, Braamfontein, 2050 Johannesburg, Gauteng, South Africa
| | - Ashleigh Blane
- Protein Structure-Function Unit, School of molecular and Cell Biology, University of the Witwatersrand, Jan Smuts Ave, Braamfontein, 2050 Johannesburg, Gauteng, South Africa
| | - Sindisiwe Buthelezi
- CSIR Biosciences, CSIR, Meiring Naude Road, Brummeria, 0001 Pretoria, Gauteng, South Africa
| | - Previn Naicker
- CSIR Biosciences, CSIR, Meiring Naude Road, Brummeria, 0001 Pretoria, Gauteng, South Africa
| | - Stoyan Stoychev
- CSIR Biosciences, CSIR, Meiring Naude Road, Brummeria, 0001 Pretoria, Gauteng, South Africa
| | - Jacob Majakwara
- School of Statistics and Actuarial Science, University of the Witwatersrand, Jan Smuts Ave, Braamfontein, 2050 Johannesburg, Gauteng, South Africa
| | - Sylvia Fanucchi
- Protein Structure-Function Unit, School of molecular and Cell Biology, University of the Witwatersrand, Jan Smuts Ave, Braamfontein, 2050 Johannesburg, Gauteng, South Africa
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14
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Gao Z, Smith AL, Scott JF, Bevington S, Boyes J. Temporal analyses reveal a pivotal role for sense and antisense enhancer RNAs in coordinate immunoglobulin lambda locus activation. Nucleic Acids Res 2023; 51:10344-10363. [PMID: 37702072 PMCID: PMC10602925 DOI: 10.1093/nar/gkad741] [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: 03/16/2023] [Revised: 08/24/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023] Open
Abstract
Transcription enhancers are essential activators of V(D)J recombination that orchestrate non-coding transcription through complementary, unrearranged gene segments. How transcription is coordinately increased at spatially distinct promoters, however, remains poorly understood. Using the murine immunoglobulin lambda (Igλ) locus as model, we find that three enhancer-like elements in the 3' Igλ domain, Eλ3-1, HSCλ1 and HSE-1, show strikingly similar transcription factor binding dynamics and close spatial proximity, suggesting that they form an active enhancer hub. Temporal analyses show coordinate recruitment of complementary V and J gene segments to this hub, with comparable transcription factor binding dynamics to that at enhancers. We find further that E2A, p300, Mediator and Integrator bind to enhancers as early events, whereas YY1 recruitment and eRNA synthesis occur later, corresponding to transcription activation. Remarkably, the interplay between sense and antisense enhancer RNA is central to both active enhancer hub formation and coordinate Igλ transcription: Antisense Eλ3-1 eRNA represses Igλ activation whereas temporal analyses demonstrate that accumulating levels of sense eRNA boost YY1 recruitment to stabilise enhancer hub/promoter interactions and lead to coordinate transcription activation. These studies therefore demonstrate for the first time a critical role for threshold levels of sense versus antisense eRNA in locus activation.
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Affiliation(s)
- Zeqian Gao
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Alastair L Smith
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - James N F Scott
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Sarah L Bevington
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Joan Boyes
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
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15
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Neville N, Lehotsky K, Yang Z, Klupt KA, Denoncourt A, Downey M, Jia Z. Modification of histidine repeat proteins by inorganic polyphosphate. Cell Rep 2023; 42:113082. [PMID: 37660293 DOI: 10.1016/j.celrep.2023.113082] [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: 04/10/2023] [Revised: 06/29/2023] [Accepted: 08/16/2023] [Indexed: 09/05/2023] Open
Abstract
Inorganic polyphosphate (polyP) is a linear polymer of orthophosphate that is present in nearly all organisms studied to date. A remarkable function of polyP involves its attachment to lysine residues via non-enzymatic post-translational modification (PTM), which is presumed to be covalent. Here, we show that proteins containing tracts of consecutive histidine residues exhibit a similar modification by polyP, which confers an electrophoretic mobility shift on NuPAGE gels. Our screen uncovers 30 human and yeast histidine repeat proteins that undergo histidine polyphosphate modification (HPM). This polyP modification is histidine dependent and non-covalent in nature, although remarkably it withstands harsh denaturing conditions-a hallmark of covalent PTMs. Importantly, we show that HPM disrupts phase separation and the phosphorylation activity of the human protein kinase DYRK1A, and inhibits the activity of the transcription factor MafB, highlighting HPM as a potential protein regulatory mechanism.
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Affiliation(s)
- Nolan Neville
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Kirsten Lehotsky
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Zhiyun Yang
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Kody A Klupt
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Alix Denoncourt
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Ottawa Institute of Systems Biology, Ottawa, ON K1H 8M5, Canada
| | - Michael Downey
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; Ottawa Institute of Systems Biology, Ottawa, ON K1H 8M5, Canada
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.
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16
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Figiel M, Górka AK, Górecki A. Zinc Ions Modulate YY1 Activity: Relevance in Carcinogenesis. Cancers (Basel) 2023; 15:4338. [PMID: 37686614 PMCID: PMC10487186 DOI: 10.3390/cancers15174338] [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: 07/27/2023] [Revised: 08/17/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
YY1 is widely recognized as an intrinsically disordered transcription factor that plays a role in development of many cancers. In most cases, its overexpression is correlated with tumor progression and unfavorable patient outcomes. Our latest research focusing on the role of zinc ions in modulating YY1's interaction with DNA demonstrated that zinc enhances the protein's multimeric state and affinity to its operator. In light of these findings, changes in protein concentration appear to be just one element relevant to modulating YY1-dependent processes. Thus, alterations in zinc ion concentration can directly and specifically impact the regulation of gene expression by YY1, in line with reports indicating a correlation between zinc ion levels and advancement of certain tumors. This review concentrates on other potential consequences of YY1 interaction with zinc ions that may act by altering charge distribution, conformational state distribution, or oligomerization to influence its interactions with molecular partners that can disrupt gene expression patterns.
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Affiliation(s)
| | | | - Andrzej Górecki
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Physical Biochemistry, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland; (M.F.); (A.K.G.)
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17
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Simpson-Lavy K, Kupiec M. Glucose Inhibits Yeast AMPK (Snf1) by Three Independent Mechanisms. BIOLOGY 2023; 12:1007. [PMID: 37508436 PMCID: PMC10376661 DOI: 10.3390/biology12071007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/13/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023]
Abstract
Snf1, the fungal homologue of mammalian AMP-dependent kinase (AMPK), is a key protein kinase coordinating the response of cells to a shortage of glucose. In fungi, the response is to activate respiratory gene expression and metabolism. The major regulation of Snf1 activity has been extensively investigated: In the absence of glucose, it becomes activated by phosphorylation of its threonine at position 210. This modification can be erased by phosphatases when glucose is restored. In the past decade, two additional independent mechanisms of Snf1 regulation have been elucidated. In response to glucose (or, surprisingly, also to DNA damage), Snf1 is SUMOylated by Mms21 at lysine 549. This inactivates Snf1 and leads to Snf1 degradation. More recently, glucose-induced proton export has been found to result in Snf1 inhibition via a polyhistidine tract (13 consecutive histidine residues) at the N-terminus of the Snf1 protein. Interestingly, the polyhistidine tract plays also a central role in the response to iron scarcity. This review will present some of the glucose-sensing mechanisms of S. cerevisiae, how they interact, and how their interplay results in Snf1 inhibition by three different, and independent, mechanisms.
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Affiliation(s)
- Kobi Simpson-Lavy
- The Shmunis School of Biomedicine & Cancer Research, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Martin Kupiec
- The Shmunis School of Biomedicine & Cancer Research, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
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18
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Gao Z, Yuan J, He X, Wang H, Wang Y. Phase Separation Modulates the Formation and Stabilities of DNA Guanine Quadruplex. JACS AU 2023; 3:1650-1657. [PMID: 37388701 PMCID: PMC10301798 DOI: 10.1021/jacsau.3c00106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 07/01/2023]
Abstract
In the presence of monovalent alkali metal ions, G-rich DNA sequences containing four runs of contiguous guanines can fold into G-quadruplex (G4) structures. Recent studies showed that these structures are located in critical regions of the human genome and assume important functions in many essential DNA metabolic processes, including replication, transcription, and repair. However, not all potential G4-forming sequences are actually folded into G4 structures in cells, where G4 structures are known to be dynamic and modulated by G4-binding proteins as well as helicases. It remains unclear whether there are other factors influencing the formation and stability of G4 structures in cells. Herein, we showed that DNA G4s can undergo phase separation in vitro. In addition, immunofluorescence microscopy and ChIP-seq experiments with the use of BG4, a G4 structure-specific antibody, revealed that disruption of phase separation could result in global destabilization of G4 structures in cells. Together, our work revealed phase separation as a new determinant in modulating the formation and stability of G4 structures in human cells.
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Affiliation(s)
- Zi Gao
- Department
of Chemistry, University of California Riverside, Riverside, California, 92521-0403, United
States
| | - Jun Yuan
- Environmental
Toxicology Graduate Program, University
of California Riverside, Riverside, California, 92521-0403, United States
| | - Xiaomei He
- Department
of Chemistry, University of California Riverside, Riverside, California, 92521-0403, United
States
| | - Handing Wang
- Department
of Chemistry, University of California Riverside, Riverside, California, 92521-0403, United
States
| | - Yinsheng Wang
- Department
of Chemistry, University of California Riverside, Riverside, California, 92521-0403, United
States
- Environmental
Toxicology Graduate Program, University
of California Riverside, Riverside, California, 92521-0403, United States
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19
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Meeussen JVW, Pomp W, Brouwer I, de Jonge WJ, Patel HP, Lenstra TL. Transcription factor clusters enable target search but do not contribute to target gene activation. Nucleic Acids Res 2023; 51:5449-5468. [PMID: 36987884 PMCID: PMC10287935 DOI: 10.1093/nar/gkad227] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/06/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Many transcription factors (TFs) localize in nuclear clusters of locally increased concentrations, but how TF clustering is regulated and how it influences gene expression is not well understood. Here, we use quantitative microscopy in living cells to study the regulation and function of clustering of the budding yeast TF Gal4 in its endogenous context. Our results show that Gal4 forms clusters that overlap with the GAL loci. Cluster number, density and size are regulated in different growth conditions by the Gal4-inhibitor Gal80 and Gal4 concentration. Gal4 truncation mutants reveal that Gal4 clustering is facilitated by, but does not completely depend on DNA binding and intrinsically disordered regions. Moreover, we discover that clustering acts as a double-edged sword: self-interactions aid TF recruitment to target genes, but recruited Gal4 molecules that are not DNA-bound do not contribute to, and may even inhibit, transcription activation. We propose that cells need to balance the different effects of TF clustering on target search and transcription activation to facilitate proper gene expression.
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Affiliation(s)
- Joseph V W Meeussen
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, The Netherlands
| | - Wim Pomp
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, The Netherlands
| | - Ineke Brouwer
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, The Netherlands
| | - Wim J de Jonge
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, The Netherlands
| | - Heta P Patel
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, The Netherlands
| | - Tineke L Lenstra
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, The Netherlands
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20
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Ma S, Liao K, Li M, Wang X, Lv J, Zhang X, Huang H, Li L, Huang T, Guo X, Lin Y, Rong Z. Phase-separated DropCRISPRa platform for efficient gene activation in mammalian cells and mice. Nucleic Acids Res 2023; 51:5271-5284. [PMID: 37094074 PMCID: PMC10250237 DOI: 10.1093/nar/gkad301] [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: 06/27/2022] [Revised: 04/05/2023] [Accepted: 04/21/2023] [Indexed: 04/26/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) plays a critical role in regulating gene transcription via the formation of transcriptional condensates. However, LLPS has not been reported to be engineered as a tool to activate endogenous gene expression in mammalian cells or in vivo. Here, we developed a droplet-forming CRISPR (clustered regularly interspaced short palindromic repeats) gene activation system (DropCRISPRa) to activate transcription with high efficiency via combining the CRISPR-SunTag system with FETIDR-AD fusion proteins, which contain an N-terminal intrinsically disordered region (IDR) of a FET protein (FUS or TAF15) and a transcription activation domain (AD, VP64/P65/VPR). In this system, the FETIDR-AD fusion protein formed phase separation condensates at the target sites, which could recruit endogenous BRD4 and RNA polymerase II with an S2 phosphorylated C-terminal domain (CTD) to enhance transcription elongation. IDR-FUS9Y>S and IDR-FUSG156E, two mutants with deficient and aberrant phase separation respectively, confirmed that appropriate phase separation was required for efficient gene activation. Further, the DropCRISPRa system was compatible with a broad set of CRISPR-associated (Cas) proteins and ADs, including dLbCas12a, dAsCas12a, dSpCas9 and the miniature dUnCas12f1, and VP64, P65 and VPR. Finally, the DropCRISPRa system could activate target genes in mice. Therefore, this study provides a robust tool to activate gene expression for foundational research and potential therapeutics.
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Affiliation(s)
- Shufeng Ma
- Department of Nephrology, Shenzhen Hospital, Southern Medical University, Shenzhen 518110, China
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
| | - Kaitong Liao
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
| | - Mengrao Li
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
| | - Xinlong Wang
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
| | - Jie Lv
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
| | - Xin Zhang
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
- Affiliated Dongguan Hospital, Southern Medical University, (Dongguan People's Hospital), Dongguan 523058, China
| | - Hongxin Huang
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Lian Li
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
| | - Tao Huang
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Xiaohua Guo
- Department of Nephrology, Shenzhen Hospital, Southern Medical University, Shenzhen 518110, China
| | - Ying Lin
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
- Experimental Education/Administration Center, School of Basic Medical Science, Southern Medical University, Guangzhou 510515, China
| | - Zhili Rong
- Cancer Research Institute, School of Basic Medical Sciences, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Key Laboratory of Organ Failure Research (Ministry of Education), Southern Medical University, Guangzhou 510515, China
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
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21
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Li C, Li Z, Wu Z, Lu H. Phase separation in gene transcription control. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1052-1063. [PMID: 37265348 PMCID: PMC10415188 DOI: 10.3724/abbs.2023099] [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: 03/15/2023] [Accepted: 04/28/2023] [Indexed: 06/03/2023] Open
Abstract
Phase separation provides a general mechanism for the formation of biomolecular condensates, and it plays a vital role in regulating diverse cellular processes, including gene expression. Although the role of transcription factors and coactivators in regulating transcription has long been understood, how phase separation is involved in this process is just beginning to be explored. In this review, we highlight recent advance in elucidating the molecular mechanisms and functions of transcriptional condensates in gene expression control. We discuss the different condensates formed at each stage of the transcription cycle and how they are dynamically regulated in response to diverse cellular and extracellular cues that cause rapid changes in gene expression. Furthermore, we present new findings regarding the dysregulation of transcription condensates and their implications in human diseases.
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Affiliation(s)
- Chengyu Li
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell BiologyLife Sciences InstituteZhejiang UniversityHangzhou310058China
| | - Zhuo Li
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell BiologyLife Sciences InstituteZhejiang UniversityHangzhou310058China
| | - Zhibing Wu
- Department of OncologyAffiliated Zhejiang HospitalZhejiang University School of MedicineHangzhou310058China
| | - Huasong Lu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell BiologyLife Sciences InstituteZhejiang UniversityHangzhou310058China
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22
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Bacabac M, Xu W. Oncogenic super-enhancers in cancer: mechanisms and therapeutic targets. Cancer Metastasis Rev 2023; 42:471-480. [PMID: 37059907 PMCID: PMC10527203 DOI: 10.1007/s10555-023-10103-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/05/2023] [Indexed: 04/16/2023]
Abstract
Activation of oncogenes to sustain proliferative signaling and initiate metastasis are important hallmarks of cancer. Oncogenes are amplified or overexpressed in cancer cells and overexpression is often controlled at the level of transcription. Gene expression is tightly controlled by many cis-regulatory elements and trans-acting factors. Large clusters of enhancers known as "super-enhancers" drive robust expression of cell-fate determining transcription factors in cell identity. Cancer cells can take advantage of super-enhancers and become transcriptionally addicted to them leading to tumorigenesis and metastasis. Additionally, the cis-regulatory landscape of cancer includes aberrant super-enhancers that are not present in normal cells. The landscape of super-enhancers in cancer is characterized by high levels of histone H3K27 acetylation and bromodomain-containing protein 4 (BRD4), and Mediator complex. These chromatin features facilitate the identification of cancer type-specific and cell-type-specific super-enhancers that control the expression of important oncogenes to stimulate their growth. Disruption of super-enhancers via inhibiting BRD4 or other epigenetic proteins is a potential therapeutic option. Here, we will describe the discovery of super-enhancers and their unique characteristics compared to typical enhancers. Then, we will highlight how super-enhancer-associated genes contribute to cancer progression in different solid tumor types. Lastly, we will cover therapeutic targets and their epigenetic modulators.
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Affiliation(s)
- Megan Bacabac
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, 1111 Highland Ave, Madison, WI, 53705, USA
- School of Medicine and Public Health, UW Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Wei Xu
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, 1111 Highland Ave, Madison, WI, 53705, USA.
- School of Medicine and Public Health, UW Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA.
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23
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Shi Y, Liao Y, Liu Q, Ni Z, Zhang Z, Shi M, Li P, Li H, Rao Y. BRD4-targeting PROTAC as a unique tool to study biomolecular condensates. Cell Discov 2023; 9:47. [PMID: 37156794 PMCID: PMC10167318 DOI: 10.1038/s41421-023-00544-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/14/2023] [Indexed: 05/10/2023] Open
Abstract
Biomolecular condensates play key roles in various biological processes. However, specific condensation modulators are currently lacking. PROTAC is a new technology that can use small molecules to degrade target proteins specifically. PROTAC molecules are expected to regulate biomolecular condensates dynamically by degrading/recovering key molecules in biomolecular condensates. In this study, we employed a BRD4-targeting PROTAC molecule to regulate the super-enhancer (SE) condensate and monitored the changes of SE condensate under PROTAC treatment using live-cell imaging and high-throughput sequencing technologies. As a result, we found that BRD4-targeting PROTACs can significantly reduce the BRD4 condensates, and we established a quantitative method for tracking BRD4 condensates by PROTAC and cellular imaging. Surprisingly and encouragingly, BRD4 condensates were observed to preferentially form and play specialized roles in biological process regulation for the first time. Additionally, BRD4 PROTAC makes it possible to observe the dynamics of other condensate components under the continued disruption of BRD4 condensates. Together, these results shed new light on research methods for liquid-liquid phase separation (LLPS), and specifically demonstrate that PROTAC presents a powerful and distinctive tool for the study of biomolecular condensates.
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Affiliation(s)
- Yi Shi
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Yuan Liao
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Beijing, China
| | - Qianlong Liu
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Zhihao Ni
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, China
| | - Zhenzhen Zhang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Minglei Shi
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, BNRist, School of Medicine, Tsinghua University, Beijing, China
| | - Pilong Li
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Haitao Li
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.
| | - Yu Rao
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, China.
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Chen S, Lu K, Hou Y, You Z, Shu C, Wei X, Wu T, Shi N, Zhang G, Wu J, Chen S, Zhang L, Li W, Zhang D, Ju S, Chen M, Xu B. YY1 complex in M2 macrophage promotes prostate cancer progression by upregulating IL-6. J Immunother Cancer 2023; 11:jitc-2022-006020. [PMID: 37094986 PMCID: PMC10152059 DOI: 10.1136/jitc-2022-006020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND Tumor-associated macrophages are mainly polarized into the M2 phenotype, remodeling the tumor microenvironment and promoting tumor progression by secreting various cytokines. METHODS Tissue microarray consisting of prostate cancer (PCa), normal prostate, and lymph node metastatic samples from patients with PCa were stained with Yin Yang 1 (YY1) and CD163. Transgenic mice overexpressing YY1 were constructed to observe PCa tumorigenesis. Furthermore, in vivo and in vitro experiments, including CRISPR-Cas9 knock-out, RNA sequencing, chromatin immunoprecipitation (ChIP) sequencing, and liquid-liquid phase separation (LLPS) assays, were performed to investigate the role and mechanism of YY1 in M2 macrophages and PCa tumor microenvironment. RESULTS YY1 was highly expressed in M2 macrophages in PCa and was associated with poorer clinical outcomes. The proportion of tumor-infiltrated M2 macrophages increased in transgenic mice overexpressing YY1. In contrast, the proliferation and activity of anti-tumoral T lymphocytes were suppressed. Treatment targeting YY1 on M2 macrophages using an M2-targeting peptide-modified liposome carrier suppressed PCa cell lung metastasis and generated synergistic anti-tumoral effects with PD-1 blockade. IL-4/STAT6 pathway regulated YY1, and YY1 increased the macrophage-induced PCa progression by upregulating IL-6. Furthermore, by conducting H3K27ac-ChIP-seq in M2 macrophages and THP-1, we found that thousands of enhancers were gained during M2 macrophage polarization, and these M2-specific enhancers were enriched in YY1 ChIP-seq signals. In addition, an M2-specific IL-6 enhancer upregulated IL-6 expression through long-range chromatin interaction with IL-6 promoter in M2 macrophages. During M2 macrophage polarization, YY1 formed an LLPS, in which p300, p65, and CEBPB acted as transcriptional cofactors. CONCLUSIONS Phase separation of the YY1 complex in M2 macrophages upregulated IL-6 by promoting IL-6 enhancer-promoter interactions, thereby increasing PCa progression.
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Affiliation(s)
- Saisai Chen
- Department of Urology, Southeast University Zhongda Hospital, Nanjing, Jiangsu, China
- Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
| | - Kai Lu
- Department of Urology, Southeast University Zhongda Hospital, Nanjing, Jiangsu, China
- Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
| | - Yue Hou
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Zonghao You
- Department of Urology, Southeast University Zhongda Hospital, Nanjing, Jiangsu, China
- Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
| | - Chuanjun Shu
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiaoying Wei
- Department of Pathology, Southeast University Zhongda Hospital, Nanjing, China
| | - Tiange Wu
- Department of Urology, Southeast University Zhongda Hospital, Nanjing, Jiangsu, China
- Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
| | - Naipeng Shi
- Department of Urology, Southeast University Zhongda Hospital, Nanjing, Jiangsu, China
- Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
| | - Guangyuan Zhang
- Department of Urology, Southeast University Zhongda Hospital, Nanjing, Jiangsu, China
- Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
| | - Jianping Wu
- Department of Urology, Southeast University Zhongda Hospital, Nanjing, Jiangsu, China
- Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
| | - Shuqiu Chen
- Department of Urology, Southeast University Zhongda Hospital, Nanjing, Jiangsu, China
- Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
| | - Lihua Zhang
- Department of Pathology, Southeast University Zhongda Hospital, Nanjing, China
| | - Wenchao Li
- Department of Urology, Southeast University Zhongda Hospital, Nanjing, Jiangsu, China
- Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
| | - Dingxiao Zhang
- School of Biomedical Sciences, Hunan University, Changsha, Hunan, China
| | - Shenghong Ju
- Department of Radiology, Southeast University Zhongda Hospital, Nanjing, China
| | - Ming Chen
- Department of Urology, Southeast University Zhongda Hospital, Nanjing, Jiangsu, China
- Surgical Research Center, Institute of Urology, Southeast University Medical School, Nanjing, China
| | - Bin Xu
- Department of Urology, Southeast University Zhongda Hospital, Nanjing, Jiangsu, China
- Institute of Medical Phenomics Research, Southeast University Zhongda Hospital, Nanjing, Jiangsu, China
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25
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van Mierlo G, Pushkarev O, Kribelbauer JF, Deplancke B. Chromatin modules and their implication in genomic organization and gene regulation. Trends Genet 2023; 39:140-153. [PMID: 36549923 DOI: 10.1016/j.tig.2022.11.003] [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: 06/08/2022] [Revised: 11/04/2022] [Accepted: 11/27/2022] [Indexed: 12/24/2022]
Abstract
Regulation of gene expression is a complex but highly guided process. While genomic technologies and computational approaches have allowed high-throughput mapping of cis-regulatory elements (CREs) and their interactions in 3D, their precise role in regulating gene expression remains obscure. Recent complementary observations revealed that interactions between CREs frequently result in the formation of small-scale functional modules within topologically associating domains. Such chromatin modules likely emerge from a complex interplay between regulatory machineries assembled at CREs, including site-specific binding of transcription factors. Here, we review the methods that allow identifying chromatin modules, summarize possible mechanisms that steer CRE interactions within these modules, and discuss outstanding challenges to uncover how chromatin modules fit in our current understanding of the functional 3D genome.
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Affiliation(s)
- Guido van Mierlo
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Olga Pushkarev
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Judith F Kribelbauer
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
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26
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Ling X, Liu X, Jiang S, Fan L, Ding J. The dynamics of three-dimensional chromatin organization and phase separation in cell fate transitions and diseases. CELL REGENERATION (LONDON, ENGLAND) 2022; 11:42. [PMID: 36539553 PMCID: PMC9768101 DOI: 10.1186/s13619-022-00145-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 10/18/2022] [Indexed: 12/24/2022]
Abstract
Cell fate transition is a fascinating process involving complex dynamics of three-dimensional (3D) chromatin organization and phase separation, which play an essential role in cell fate decision by regulating gene expression. Phase separation is increasingly being considered a driving force of chromatin folding. In this review, we have summarized the dynamic features of 3D chromatin and phase separation during physiological and pathological cell fate transitions and systematically analyzed recent evidence of phase separation facilitating the chromatin structure. In addition, we discuss current advances in understanding how phase separation contributes to physical and functional enhancer-promoter contacts. We highlight the functional roles of 3D chromatin organization and phase separation in cell fate transitions, and more explorations are required to study the regulatory relationship between 3D chromatin organization and phase separation. 3D chromatin organization (shown by Hi-C contact map) and phase separation are highly dynamic and play functional roles during early embryonic development, cell differentiation, somatic reprogramming, cell transdifferentiation and pathogenetic process. Phase separation can regulate 3D chromatin organization directly, but whether 3D chromatin organization regulates phase separation remains unclear.
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Affiliation(s)
- Xiaoru Ling
- grid.12981.330000 0001 2360 039XAdvanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XRNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XCenter for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China
| | - Xinyi Liu
- grid.12981.330000 0001 2360 039XAdvanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XRNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XCenter for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China
| | - Shaoshuai Jiang
- grid.12981.330000 0001 2360 039XAdvanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XRNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XCenter for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China
| | - Lili Fan
- grid.258164.c0000 0004 1790 3548Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Jinan University, Guangzhou, Guangdong China
| | - Junjun Ding
- grid.12981.330000 0001 2360 039XAdvanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XRNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.12981.330000 0001 2360 039XCenter for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong China ,grid.410737.60000 0000 8653 1072Department of Histology and Embryology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 511436 China ,grid.13291.380000 0001 0807 1581West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041 China
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HDAC1/3-dependent moderate liquid-liquid phase separation of YY1 promotes METTL3 expression and AML cell proliferation. Cell Death Dis 2022; 13:992. [PMID: 36424383 PMCID: PMC9691727 DOI: 10.1038/s41419-022-05435-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/25/2022]
Abstract
Methyltransferase-like protein 3 (METTL3) plays critical roles in acute myeloid leukemia (AML) progression, however, the mechanism of abnormal overexpression of METTL3 in AML remain elusive. In the current study, we uncovered that Yin Yang 1 (YY1) binds to the promoter region of METTL3 as a transcription factor and promotes its expression, which in turn enhances the proliferation of AML cells. Mechanistically, YY1 binds to HDAC1/3 and regulates METTL3 expression in a moderate liquid-liquid phase separation (LLPS) manner. After mutation of the HDAC-binding site of YY1 or HDAC inhibitor (HDACi) treatment, YY1 was separated from HDAC1/3, which resulted in an excessive LLPS state, thereby inhibiting the expression of METTL3 and the proliferation of AML cells. In conclusion, our study clarified the regulatory mechanism of the abnormal expression of METTL3 in AML, revealed the precise "Yin-Yang" regulatory mechanism of YY1 from the perspective of LLPS degree, and provided new ideas for the precise diagnosis and treatment of AML.
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28
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Vicioso-Mantis M, Balbás MAM. Spatial genome organization, TGFβ, and biomolecular condensates: Do they talk during development? Bioessays 2022; 44:e2200145. [PMID: 36253122 DOI: 10.1002/bies.202200145] [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: 07/22/2022] [Revised: 09/08/2022] [Accepted: 09/26/2022] [Indexed: 11/08/2022]
Abstract
Cis-regulatory elements govern gene expression programs to determine cell identity during development. Recently, the possibility that multiple enhancers are orchestrated in clusters of enhancers has been suggested. How these elements are arranged in the 3D space to control the activation of a specific promoter remains unclear. Our recent work revealed that the TGFβ pathway drives the assembly of enhancer clusters and precise gene activation during neurogenesis. We discovered that the TGFβ pathway coactivator JMJD3 was essential in maintaining these structures in the 3D space. To do that, JMJD3 required an intrinsically disordered region involved in forming phase-separated biomolecular condensates found in the enhancer clusters. Our data support the existence of a relationship between 3D-conformation of the chromatin, biomolecular condensates, and TGFβ-driven response during mammalian neurogenesis. In this review, we discuss how signaling (TGFβ), epigenetics (JMJD3), and biochemical properties (biomolecular condensates nucleation) are coordinated to modulate the genome structure to guarantee proper neural development. Moreover, we comment on the potential underlying mechanisms and implications of the enhancer-mediated regulation. Finally, we point out the knowledge gaps that still need to be addressed.
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Affiliation(s)
- Marta Vicioso-Mantis
- Department of Molecular Genomics. Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Marian A Martínez Balbás
- Department of Molecular Genomics. Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
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29
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Wang Y, Zhang C, Wang Y, Liu X, Zhang Z. Enhancer RNA (eRNA) in Human Diseases. Int J Mol Sci 2022; 23:ijms231911582. [PMID: 36232885 PMCID: PMC9569849 DOI: 10.3390/ijms231911582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 11/16/2022] Open
Abstract
Enhancer RNAs (eRNAs), a class of non-coding RNAs (ncRNAs) transcribed from enhancer regions, serve as a type of critical regulatory element in gene expression. There is increasing evidence demonstrating that the aberrant expression of eRNAs can be broadly detected in various human diseases. Some studies also revealed the potential clinical utility of eRNAs in these diseases. In this review, we summarized the recent studies regarding the pathological mechanisms of eRNAs as well as their potential utility across human diseases, including cancers, neurodegenerative disorders, cardiovascular diseases and metabolic diseases. It could help us to understand how eRNAs are engaged in the processes of diseases and to obtain better insight of eRNAs in diagnosis, prognosis or therapy. The studies we reviewed here indicate the enormous therapeutic potency of eRNAs across human diseases.
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Affiliation(s)
- Yunzhe Wang
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Chenyang Zhang
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yuxiang Wang
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Xiuping Liu
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- Correspondence: author: (X.L.); (Z.Z.); Tel.: +86-21-5423-7896 (Z.Z.)
| | - Zhao Zhang
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- Correspondence: author: (X.L.); (Z.Z.); Tel.: +86-21-5423-7896 (Z.Z.)
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30
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Ng WS, Sielaff H, Zhao ZW. Phase Separation-Mediated Chromatin Organization and Dynamics: From Imaging-Based Quantitative Characterizations to Functional Implications. Int J Mol Sci 2022; 23:ijms23148039. [PMID: 35887384 PMCID: PMC9316379 DOI: 10.3390/ijms23148039] [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: 06/20/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 12/14/2022] Open
Abstract
As an effective and versatile strategy to compartmentalize cellular components without the need for lipid membranes, phase separation has been found to underpin a wide range of intranuclear processes, particularly those involving chromatin. Many of the unique physico-chemical properties of chromatin-based phase condensates are harnessed by the cell to accomplish complex regulatory functions in a spatially and temporally controlled manner. Here, we survey key recent findings on the mechanistic roles of phase separation in regulating the organization and dynamics of chromatin-based molecular processes across length scales, packing states and intranuclear functions, with a particular emphasis on quantitative characterizations of these condensates enabled by advanced imaging-based approaches. By illuminating the complex interplay between chromatin and various chromatin-interacting molecular species mediated by phase separation, this review sheds light on an emerging multi-scale, multi-modal and multi-faceted landscape that hierarchically regulates the genome within the highly crowded and dynamic nuclear space. Moreover, deficiencies in existing studies also highlight the need for mechanism-specific criteria and multi-parametric approaches for the characterization of chromatin-based phase separation using complementary techniques and call for greater efforts to correlate the quantitative features of these condensates with their functional consequences in close-to-native cellular contexts.
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Affiliation(s)
- Woei Shyuan Ng
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore 119543, Singapore; (W.S.N.); (H.S.)
- Centre for BioImaging Sciences (CBIS), Faculty of Science, National University of Singapore, Singapore 117557, Singapore
| | - Hendrik Sielaff
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore 119543, Singapore; (W.S.N.); (H.S.)
- Centre for BioImaging Sciences (CBIS), Faculty of Science, National University of Singapore, Singapore 117557, Singapore
| | - Ziqing Winston Zhao
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore 119543, Singapore; (W.S.N.); (H.S.)
- Centre for BioImaging Sciences (CBIS), Faculty of Science, National University of Singapore, Singapore 117557, Singapore
- Mechanobiology Institute (MBI), National University of Singapore, Singapore 117411, Singapore
- Correspondence:
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