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For: Hnisz D, Abraham BJ, Lee TI, Lau A, Saint-André V, Sigova AA, Hoke H, Young RA. Super-enhancers in the control of cell identity and disease. Cell 2013;155:934-47. [PMID: 24119843 PMCID: PMC3841062 DOI: 10.1016/j.cell.2013.09.053] [Citation(s) in RCA: 2630] [Impact Index Per Article: 219.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 09/27/2013] [Accepted: 09/30/2013] [Indexed: 02/07/2023]
Number Cited by Other Article(s)
1
Xie B, Dean A. Noncoding function of super enhancer derived Cpox pre-mRNA in modulating neighbouring gene expression and chromatin interactions. RNA Biol 2025;22:1-17. [PMID: 40051047 PMCID: PMC11913378 DOI: 10.1080/15476286.2025.2475421] [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: 09/24/2024] [Revised: 01/09/2025] [Accepted: 02/17/2025] [Indexed: 03/12/2025]  Open
2
Ang DA, Harmston N, Li Y. ATF4:p52 complex activates oncogenic enhancers in multiple myeloma via p300/CBP recruitment to regulate BACH1. Cancer Lett 2025;623:217727. [PMID: 40250789 DOI: 10.1016/j.canlet.2025.217727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2025] [Revised: 04/03/2025] [Accepted: 04/16/2025] [Indexed: 04/20/2025]
3
Jiang M, Zhang K, Wei G, Qi F, Yu D, Ma J, Zhang X, Chen L, Xie Y, Yu Z, Chen J, Chen D. HDAC4 super-enhancer drives CEBPB-mediated TWIST2 transcription to promote chemoresistance in LUAD. Cancer Lett 2025;623:217716. [PMID: 40222483 DOI: 10.1016/j.canlet.2025.217716] [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: 12/16/2024] [Revised: 04/01/2025] [Accepted: 04/10/2025] [Indexed: 04/15/2025]
4
Zhou X, Zhou X, Li J, He Y, Qiu S, Xu Y, Liu Z, Yao Y, Liu J, Wen Y, Xie S, Chen J, Liu L, Ou Z, Cai C, Lin J, Lei B, Zou F. Bclaf1 mediates super-enhancer-driven activation of POLR2A to enhance chromatin accessibility in nitrosamine-induced esophageal carcinogenesis. JOURNAL OF HAZARDOUS MATERIALS 2025;492:138218. [PMID: 40220379 DOI: 10.1016/j.jhazmat.2025.138218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2025] [Revised: 03/30/2025] [Accepted: 04/07/2025] [Indexed: 04/14/2025]
5
Crump NT, Milne TA. Is Enhancer Function Driven by Protein-Protein Interactions? From Bacteria to Leukemia. Bioessays 2025;47:e70006. [PMID: 40195782 PMCID: PMC12101050 DOI: 10.1002/bies.70006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Revised: 03/23/2025] [Accepted: 03/25/2025] [Indexed: 04/09/2025]
6
Sur I, Zhao W, Zhang J, Kling Pilström M, Webb AT, Cheng H, Ristimäki A, Katajisto P, Enge M, Rannikmae H, de la Roche M, Taipale J. Shared requirement for MYC upstream super-enhancer region in tissue regeneration and cancer. Life Sci Alliance 2025;8:e202403090. [PMID: 40180576 PMCID: PMC11969384 DOI: 10.26508/lsa.202403090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2024] [Revised: 03/14/2025] [Accepted: 03/14/2025] [Indexed: 04/05/2025]  Open
7
Chen Q, Wang S, Zhang J, Xie M, Lu B, He J, Zhen Z, Li J, Zhu J, Li R, Li P, Wang H, Vakoc CR, Roeder RG, Chen M. JMJD1C forms condensate to facilitate a RUNX1-dependent gene expression program shared by multiple types of AML cells. Protein Cell 2025;16:338-364. [PMID: 39450904 DOI: 10.1093/procel/pwae059] [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: 04/25/2024] [Accepted: 09/26/2024] [Indexed: 10/26/2024]  Open
8
Mei J, Huang W, Meng Z, Wen S, Ou L, Bai J, Wang X, Yuan H, Li Y, Zhang L, You Y, Chen Y, Zheng X, Li F, Wang S, Zhu X, Wang Z, Zhu D, Nie X, Ma C. Super-Enhancer-Driven HCG20 Promotes Pulmonary Hypertension Through U2AF2 Splicing. Circ Res 2025. [PMID: 40433695 DOI: 10.1161/circresaha.125.326133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2025] [Revised: 05/09/2025] [Accepted: 05/19/2025] [Indexed: 05/29/2025]
9
Arulsamy K, Xia B, Yu Y, Chen H, Pu WT, Zhang L, Chen K. SCIG: Machine learning uncovers cell identity genes in single cells by genetic sequence codes. Nucleic Acids Res 2025;53:gkaf431. [PMID: 40433981 DOI: 10.1093/nar/gkaf431] [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: 08/21/2024] [Revised: 04/09/2025] [Accepted: 05/09/2025] [Indexed: 05/29/2025]  Open
10
Chen L, Li W, Zai W, Zheng X, Meng X, Yao Q, Li W, Liang Y, Ye M, Zhou K, Liu M, Yang Z, Mao Z, Wei H, Yang S, Shi G, Yuan Z, Yu W. HBV sequence integrated to enhancer acting as oncogenic driver epigenetically promotes hepatocellular carcinoma development. J Exp Clin Cancer Res 2025;44:155. [PMID: 40405227 PMCID: PMC12096768 DOI: 10.1186/s13046-025-03413-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2025] [Accepted: 05/09/2025] [Indexed: 05/24/2025]  Open
11
Marsh GP, Cooper MS, Goggins S, Reynolds SJ, Wheeler DF, Cresser-Brown JO, Arnold RE, Babcock EG, Hughes G, Bosnakovski D, Kyba M, Ojeda S, Harrison DA, Ott CJ, Maple HJ. Development of p300-targeting degraders with enhanced selectivity and onset of degradation. RSC Med Chem 2025;16:2049-2060. [PMID: 40093518 PMCID: PMC11905989 DOI: 10.1039/d4md00969j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2024] [Accepted: 02/17/2025] [Indexed: 03/19/2025]  Open
12
Ye Z, Hu QX, Wei ML, Chen JD, Shi J, Yang NR, Jiang L, Chen J, Chen ZY, Yu WM, Xiao Y, Qian KY, Xu Z, Wang Z, Qi WL, Xiao XY, Duan YY, Xiao Y, Li LY, Ju LG, Chen MK, Wu M. A Feedback Loop Between Fatty Acid Metabolism and Epigenetics in Clear Cell Renal Carcinoma. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025:e04532. [PMID: 40391655 DOI: 10.1002/advs.202504532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2025] [Revised: 04/15/2025] [Indexed: 05/22/2025]
13
Mizutani A, Tan C, Sugita Y, Takada S. Heterogeneous condensates of transcription factors in embryonic stem cells: Molecular simulations. Biophys J 2025;124:1587-1598. [PMID: 40195119 DOI: 10.1016/j.bpj.2025.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2024] [Revised: 02/18/2025] [Accepted: 04/02/2025] [Indexed: 04/09/2025]  Open
14
Shinkai N, Asada K, Machino H, Takasawa K, Takahashi S, Kouno N, Komatsu M, Hamamoto R, Kaneko S. SEgene identifies links between super enhancers and gene expression across cell types. NPJ Syst Biol Appl 2025;11:49. [PMID: 40389443 PMCID: PMC12089303 DOI: 10.1038/s41540-025-00533-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2025] [Accepted: 05/11/2025] [Indexed: 05/21/2025]  Open
15
Huang H, Baxter AE, Zhang Z, Good CR, Alexander KA, Chen Z, Garcia PAA, Samareh P, Collins SM, Glastad KM, Wang L, Donahue G, Manne S, Giles JR, Shi J, Berger SL, Wherry EJ. Deciphering the role of histone modifications in memory and exhausted CD8 T cells. Sci Rep 2025;15:17359. [PMID: 40389726 PMCID: PMC12089470 DOI: 10.1038/s41598-025-99804-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2024] [Accepted: 04/23/2025] [Indexed: 05/21/2025]  Open
16
Sun Y, Li M, Ning C, Gao L, Liu Z, Zhong S, Lv J, Ke Y, Wang X, Ma Q, Liu Z, Wu S, Yu H, Zhao F, Zhang J, Gong Q, Liu J, Wu Q, Wang X, Chen X. Spatiotemporal 3D chromatin organization across multiple brain regions during human fetal development. Cell Discov 2025;11:50. [PMID: 40374600 DOI: 10.1038/s41421-025-00798-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 02/21/2025] [Indexed: 05/17/2025]  Open
17
Ojo OA, Shen H, Ingram JT, Bonner JA, Welner RS, Lacaud G, Zajac AJ, Shi LZ. Gfi1 controls the formation of effector-like CD8+ T cells during chronic infection and cancer. Nat Commun 2025;16:4542. [PMID: 40374625 PMCID: PMC12081725 DOI: 10.1038/s41467-025-59784-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 05/02/2025] [Indexed: 05/17/2025]  Open
18
Nagel M, Taatjes DJ. Regulation of RNA polymerase II transcription through re-initiation and bursting. Mol Cell 2025;85:1907-1919. [PMID: 40378829 DOI: 10.1016/j.molcel.2025.04.011] [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: 12/20/2024] [Revised: 03/13/2025] [Accepted: 04/07/2025] [Indexed: 05/19/2025]
19
Ogikubo K, Nishida J, Takahashi-Yamashiro K, Morikawa M, Ehata S, Watabe T, Miyazono K, Koinuma D. OCT-2 Is Associated With Pro-Metastatic Epigenomic Properties of Triple-Negative Breast Cancer Cells. Cancer Sci 2025. [PMID: 40364745 DOI: 10.1111/cas.70093] [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: 01/11/2025] [Revised: 04/18/2025] [Accepted: 04/26/2025] [Indexed: 05/15/2025]  Open
20
Fu H, Itoh Y, Sawaguchi T, Otake S, Omata C, Saitoh M, Miyazawa K. Identification of a Distal Enhancer That Regulates TGF-β-Induced SNAI1 Expression. Cancer Sci 2025. [PMID: 40364580 DOI: 10.1111/cas.70091] [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: 11/15/2024] [Revised: 04/14/2025] [Accepted: 04/23/2025] [Indexed: 05/15/2025]  Open
21
Chen QS, Cai RZ, Wang Y, Liang GH, Zhang KM, Yang XY, Yang D, Zhao DC, Zhu XF, Deng R, Tang J. Profiling triple-negative breast cancer-specific super-enhancers identifies high-risk mesenchymal development subtype and BETi-Targetable vulnerabilities. Mol Cancer 2025;24:141. [PMID: 40361105 PMCID: PMC12070678 DOI: 10.1186/s12943-025-02342-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2024] [Accepted: 04/23/2025] [Indexed: 05/15/2025]  Open
22
Wang W, Han F, Qi Z, Yan C, Su B, Wang J. Phase Separation: Orchestrating Biological Adaptations to Environmental Fluctuations. Int J Mol Sci 2025;26:4614. [PMID: 40429758 DOI: 10.3390/ijms26104614] [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: 03/24/2025] [Revised: 04/23/2025] [Accepted: 05/08/2025] [Indexed: 05/29/2025]  Open
23
Verhagen PGA, Hansen MMK. Exploring the central dogma through the lens of gene expression noise. J Mol Biol 2025:169202. [PMID: 40354878 DOI: 10.1016/j.jmb.2025.169202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2025] [Revised: 04/30/2025] [Accepted: 05/07/2025] [Indexed: 05/14/2025]
24
Umphred-Wilson K, Ratnayake S, Tang Q, Wang R, Chaudhary SG, Ballachanda DN, Trichka J, Wisniewski J, Zhou L, Chen Q, Meerzaman D, Singer DS, Adoro S. The ESCRT protein CHMP5 promotes T cell leukemia by enabling BRD4-p300-dependent transcription. Nat Commun 2025;16:4133. [PMID: 40319015 PMCID: PMC12049546 DOI: 10.1038/s41467-025-59504-9] [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: 02/23/2024] [Accepted: 04/24/2025] [Indexed: 05/07/2025]  Open
25
Alrouji M, Alshammari MS, Anwar S, Venkatesan K, Shamsi A. Mechanistic Roles of Transcriptional Cyclin-Dependent Kinases in Oncogenesis: Implications for Cancer Therapy. Cancers (Basel) 2025;17:1554. [PMID: 40361480 PMCID: PMC12071579 DOI: 10.3390/cancers17091554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2025] [Revised: 04/27/2025] [Accepted: 04/30/2025] [Indexed: 05/15/2025]  Open
26
Gao J, Zhao D, Nouri HR, Chu HW, Huang H. Transcriptional Regulation of Mouse Mast Cell Differentiation and the Role of Human Lung Mast Cells in Airway Inflammation. Immunol Rev 2025;331:e70026. [PMID: 40211768 PMCID: PMC12017346 DOI: 10.1111/imr.70026] [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: 09/16/2024] [Revised: 03/12/2025] [Accepted: 03/21/2025] [Indexed: 04/25/2025]
27
Yamamoto T, Yamazaki T, Ninomiya K, Nakagawa S, Hirose T. Biophysical Aspect of Assembly and Regulation of Nuclear Bodies Scaffolded by Architectural RNA. J Mol Biol 2025;437:169016. [PMID: 39978724 DOI: 10.1016/j.jmb.2025.169016] [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: 11/15/2024] [Revised: 02/03/2025] [Accepted: 02/14/2025] [Indexed: 02/22/2025]
28
Guo S, Zhang L, Ren J, Lu Z, Ma X, Liu X, Jin H, Li J. The roles of enhancer, especially super-enhancer-driven genes in tumor metabolism and immunity. Int J Biol Macromol 2025;308:142414. [PMID: 40132720 DOI: 10.1016/j.ijbiomac.2025.142414] [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: 10/16/2024] [Revised: 03/19/2025] [Accepted: 03/20/2025] [Indexed: 03/27/2025]
29
Xu M, Jiang SY, Tang S, Zhu M, Hu Y, Li J, Yan J, Qin C, Tan D, An Y, Qu Y, Song BL, Ma H, Qi W. Nuclear SREBP2 condensates regulate the transcriptional activation of lipogenic genes and cholesterol homeostasis. Nat Metab 2025;7:1034-1051. [PMID: 40394324 DOI: 10.1038/s42255-025-01291-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 03/25/2025] [Indexed: 05/22/2025]
30
Chen YJ, Zhao Y, Yao MY, Wang YF, Ma M, Yu CC, Jiang HL, Wei W, Shen J, Xu XW, Xie CY. Concurrent inhibition of p300/CBP and FLT3 enhances cytotoxicity and overcomes resistance in acute myeloid leukemia. Acta Pharmacol Sin 2025;46:1390-1403. [PMID: 39885312 PMCID: PMC12032420 DOI: 10.1038/s41401-025-01479-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2024] [Accepted: 12/22/2024] [Indexed: 02/01/2025]
31
Mondal S, Liu PY, Seneviratne J, De Weck A, Venkat P, Mayoh C, Wu J, Maag J, Chen J, Wong M, Bartonicek N, Khoo P, Jin L, Ludlow LE, Ziegler DS, Trahair T, Mestdagh P, Cheung BB, Li J, Dinger ME, Street I, Zhang XD, Marshall GM, Liu T. The Super Enhancer-Driven Long Noncoding RNA PRKCQ-AS1 Promotes Neuroblastoma Tumorigenesis by Interacting With MSI2 Protein and Is Targetable by Small Molecule Compounds. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025;12:e2412520. [PMID: 40103284 PMCID: PMC12079515 DOI: 10.1002/advs.202412520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2024] [Revised: 01/24/2025] [Indexed: 03/20/2025]
32
Lai PH, Tyrer JP, Pharoah P, Gayther SA, Jones MR, Peng PC. Characterizing somatic mutations in ovarian cancer germline risk regions. Commun Biol 2025;8:676. [PMID: 40301634 PMCID: PMC12041368 DOI: 10.1038/s42003-025-08072-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2024] [Accepted: 04/10/2025] [Indexed: 05/01/2025]  Open
33
Higuchi Y, Teo JL, Yi D, Kahn M. Safely Targeting Cancer, the Wound That Never Heals, Utilizing CBP/Beta-Catenin Antagonists. Cancers (Basel) 2025;17:1503. [PMID: 40361430 PMCID: PMC12071182 DOI: 10.3390/cancers17091503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2025] [Revised: 04/25/2025] [Accepted: 04/25/2025] [Indexed: 05/15/2025]  Open
34
Cheng Z, Wang H, Zhang Y, Ren B, Fu Z, Li Z, Tu C. Deciphering the role of liquid-liquid phase separation in sarcoma: Implications for pathogenesis and treatment. Cancer Lett 2025;616:217585. [PMID: 39999920 DOI: 10.1016/j.canlet.2025.217585] [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: 12/10/2024] [Revised: 02/04/2025] [Accepted: 02/21/2025] [Indexed: 02/27/2025]
35
Morrison TA, Vigee J, Tovar KA, Talley TA, Mujal AM, Kono M, Philips R, Nagashima H, Brooks SR, Dada H, Rozich I, Hudspeth K, Lau CM, Yao C, Sciumè G, Sun HW, Bonifacino JS, Kanno Y, Dustin ML, Randazzo D, Proia RL, Sun JC, Shih HY, O'Shea JJ. Selective requirement of glycosphingolipid synthesis for natural killer and cytotoxic T cells. Cell 2025:S0092-8674(25)00409-X. [PMID: 40306279 DOI: 10.1016/j.cell.2025.04.007] [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: 12/22/2024] [Revised: 03/11/2025] [Accepted: 04/03/2025] [Indexed: 05/02/2025]
36
Dhar SS, Brown C, Rizvi A, Reed L, Kotla S, Zod C, Abraham J, Abe JI, Rajaram V, Chen K, Lee MG. Heterozygous Kmt2d loss diminishes enhancers to render medulloblastoma cells vulnerable to combinatory inhibition of LSD1 and OXPHOS. Cell Rep 2025;44:115619. [PMID: 40286267 DOI: 10.1016/j.celrep.2025.115619] [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: 07/10/2024] [Revised: 02/17/2025] [Accepted: 04/04/2025] [Indexed: 04/29/2025]  Open
37
Xiao L, Jin H, Dang Y, Zhao P, Li S, Shi Y, Wang S, Zhang K. DUX-mediated configuration of p300/CBP drives minor zygotic genome activation independent of its catalytic activity. Cell Rep 2025;44:115544. [PMID: 40202846 DOI: 10.1016/j.celrep.2025.115544] [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: 12/03/2024] [Revised: 02/18/2025] [Accepted: 03/19/2025] [Indexed: 04/11/2025]  Open
38
Gao C, Gao A, Jiang Y, Gao R, Guo Y, Peng Z, Jiang W, Zhang M, Zhou Z, Yan C, Fang W, Hu H, Zhu G, Zhang J. Hypoxia-induced phase separation of ZHX2 alters chromatin looping to drive cancer metastasis. Mol Cell 2025;85:1525-1542.e10. [PMID: 40185097 DOI: 10.1016/j.molcel.2025.03.009] [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: 05/14/2024] [Revised: 01/12/2025] [Accepted: 03/07/2025] [Indexed: 04/07/2025]
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Li F, Wang S, Chen L, Jiang N, Chen X, Li J. Systemic genome-epigenome analysis captures a lineage-specific super-enhancer for MYB in gastrointestinal adenocarcinoma. Mol Syst Biol 2025:10.1038/s44320-025-00098-1. [PMID: 40234694 DOI: 10.1038/s44320-025-00098-1] [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: 12/02/2024] [Revised: 03/26/2025] [Accepted: 03/31/2025] [Indexed: 04/17/2025]  Open
40
Liu SQ, Cheng XX, He S, Xia T, Li YQ, Peng W, Zhou YQ, Xu ZH, He MS, Liu Y, Wei PP, Yuan SH, Liu C, Sun SL, Zou DL, Zheng M, Lan CY, Luo CL, Bei JX. Super-enhancer-driven EFNA1 fuels tumor progression in cervical cancer via the FOSL2-Src/AKT/STAT3 axis. J Clin Invest 2025;135:e177599. [PMID: 39964764 PMCID: PMC11996870 DOI: 10.1172/jci177599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/13/2025] [Indexed: 02/20/2025]  Open
41
Renatino Canevarolo R, Sudalagunta PR, Meads MB, Silva M, Zhao X, Magaletti D, Alugubelli RR, DeAvila G, Persi E, Maura F, Bell ET, Bishop RT, Cubitt CL, Sansil SS, Zhang W, Teer JK, Teng M, Yoder SJ, Siegel EM, Shah BD, Nishihori T, Hazlehurst LA, Lynch CC, Landgren O, Hampton O, Gatenby RA, Sullivan DM, Brayer JB, Dalton WS, Cleveland JL, Alsina M, Baz R, Shain KH, Silva AS. Epigenetic Plasticity Drives Carcinogenesis and Multi-Therapy Resistance in Multiple Myeloma. RESEARCH SQUARE 2025:rs.3.rs-6306816. [PMID: 40321765 PMCID: PMC12048002 DOI: 10.21203/rs.3.rs-6306816/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/09/2025]
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Rosario GX, Brown S, Karmakar S, Rumi MAK, Nayak NR. Super-Enhancers in Placental Development and Diseases. J Dev Biol 2025;13:11. [PMID: 40265369 PMCID: PMC12015882 DOI: 10.3390/jdb13020011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2025] [Revised: 03/24/2025] [Accepted: 04/03/2025] [Indexed: 04/24/2025]  Open
43
Liu J, Huang H, An F, Wu S, Guo H, Wang B, Han Z, Tan J, Lin Z, Fang Y, Liu J, Ye H, Du Y, Mo K, Huang Y, Li M, Wang L, Mao Z, Ouyang H. FOXO4-SP6 axis controls surface epithelium commitment by mediating epigenomic remodeling. Stem Cell Reports 2025;20:102445. [PMID: 40086444 PMCID: PMC12069900 DOI: 10.1016/j.stemcr.2025.102445] [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: 11/01/2024] [Revised: 02/10/2025] [Accepted: 02/11/2025] [Indexed: 03/16/2025]  Open
44
Betti MJ, Lin P, Aldrich MC, Gamazon ER. Genetically regulated eRNA expression predicts chromatin contact frequency and reveals genetic mechanisms at GWAS loci. Nat Commun 2025;16:3193. [PMID: 40180945 PMCID: PMC11968980 DOI: 10.1038/s41467-025-58023-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 02/18/2025] [Indexed: 04/05/2025]  Open
45
Altendorfer E, Mundlos S, Mayer A. A transcription coupling model for how enhancers communicate with their target genes. Nat Struct Mol Biol 2025;32:598-606. [PMID: 40217119 DOI: 10.1038/s41594-025-01523-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Accepted: 02/27/2025] [Indexed: 04/16/2025]
46
Tanwar VS, Reddy MA, Dey S, Malek V, Lanting L, Chen Z, Ganguly R, Natarajan R. Palmitic acid alters enhancers/super-enhancers near inflammatory and efferocytosis-associated genes in human monocytes. J Lipid Res 2025;66:100774. [PMID: 40068774 PMCID: PMC12002881 DOI: 10.1016/j.jlr.2025.100774] [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: 12/07/2024] [Revised: 02/20/2025] [Accepted: 03/07/2025] [Indexed: 04/07/2025]  Open
47
Tan X, Li Y, Song M, Yuan L, Zhao Z, Liu Y, Meng Q, Huang X, Ma Y, Xu Z. The Molecular Mechanism of Interaction Between SEPALLATA3 and APETALA1 in Arabidopsis thaliana. PLANT DIRECT 2025;9:e70052. [PMID: 40166359 PMCID: PMC11955279 DOI: 10.1002/pld3.70052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Revised: 10/31/2024] [Accepted: 02/06/2025] [Indexed: 04/02/2025]
48
Sasse SK, Dahlin A, Sanford L, Gruca MA, Gupta A, Gally F, Wu AC, Iribarren C, Dowell RD, Weiss ST, Gerber AN. Enhancer RNA transcription pinpoints functional genetic variants linked to asthma. Nat Commun 2025;16:2750. [PMID: 40164603 PMCID: PMC11958640 DOI: 10.1038/s41467-025-57693-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/28/2025] [Indexed: 04/02/2025]  Open
49
Benhassoun R, Morel AP, Jacquot V, Puisieux A, Ouzounova M. The epipliancy journey: Tumor initiation at the mercy of identity crisis and epigenetic drift. Biochim Biophys Acta Rev Cancer 2025;1880:189307. [PMID: 40174706 DOI: 10.1016/j.bbcan.2025.189307] [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: 10/25/2024] [Revised: 03/05/2025] [Accepted: 03/27/2025] [Indexed: 04/04/2025]
50
Inagaki T, Kumar A, Wang KH, Komaki S, Espera JM, Bautista CSA, Nakajima KI, Izumiya C, Izumiya Y. Studies on Gene Enhancer with KSHV mini-chromatin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.24.644916. [PMID: 40196677 PMCID: PMC11974746 DOI: 10.1101/2025.03.24.644916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2025]
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