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For: Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods 2013;10:1213-8. [PMID: 24097267 DOI: 10.1038/nmeth.2688] [Citation(s) in RCA: 4398] [Impact Index Per Article: 366.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 08/29/2013] [Indexed: 12/11/2022]
Number Cited by Other Article(s)
1
Chowdhury SR, Shilpi A, Felsenfeld G. RNA Pol-II transcripts in nucleolar associated domains of cancer cell nucleoli. Nucleus 2025;16:2468597. [PMID: 39987497 PMCID: PMC11849958 DOI: 10.1080/19491034.2025.2468597] [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: 04/14/2023] [Revised: 01/03/2025] [Accepted: 02/13/2025] [Indexed: 02/25/2025]  Open
2
Santosa EK, Zhang JM, Sauter JC, Lee ME, Ng BD, Stulz SV, Takizawa M, Grassmann S, Weizman OE, Adams NM, Chaligné R, Oxenius A, Gasteiger G, Lau CM, Sun JC. Defining molecular circuits of CD8+ T cell responses in tissues during latent viral infection. J Exp Med 2025;222:e20242078. [PMID: 40387857 DOI: 10.1084/jem.20242078] [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: 11/05/2024] [Revised: 03/18/2025] [Accepted: 04/29/2025] [Indexed: 05/20/2025]  Open
3
Pouncey L, Mok GF. Unravelling early hematoendothelial development through the chick model: Insights and future perspectives. Dev Biol 2025;523:20-31. [PMID: 40228783 DOI: 10.1016/j.ydbio.2025.04.008] [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: 10/25/2024] [Revised: 03/31/2025] [Accepted: 04/10/2025] [Indexed: 04/16/2025]
4
Begeman IJ, Guyer ME, Kang J. Cardiac enhancers: Gateway to the regulatory mechanisms of heart regeneration. Semin Cell Dev Biol 2025;170:103610. [PMID: 40215762 PMCID: PMC12064385 DOI: 10.1016/j.semcdb.2025.103610] [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: 10/14/2024] [Revised: 02/17/2025] [Accepted: 03/31/2025] [Indexed: 05/10/2025]
5
Yamamoto K. How to analyze and understand the human immune system. Semin Arthritis Rheum 2025;72S:152696. [PMID: 40037996 DOI: 10.1016/j.semarthrit.2025.152696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2025] [Accepted: 02/12/2025] [Indexed: 03/06/2025]
6
Kadagandla S, Gunamalai L, Lee D, Kapoor A. Identification and Functional Assessment of Candidate Causal Cis-Regulatory Variants Underlying Electrocardiographic QT Interval GWAS Loci. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2025:e005032. [PMID: 40421528 DOI: 10.1161/circgen.124.005032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2024] [Accepted: 04/17/2025] [Indexed: 05/28/2025]
7
Saeki K, Ozato K. Transcription factors that define the epigenome structures and transcriptomes in microglia. Exp Hematol 2025:104814. [PMID: 40425139 DOI: 10.1016/j.exphem.2025.104814] [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: 02/28/2025] [Revised: 05/08/2025] [Accepted: 05/10/2025] [Indexed: 05/29/2025]
8
Fu Y, Okawa H, Vinaikosol N, Mori S, Limraksasin P, Nattasit P, Tahara Y, Egusa H. Shaking culture attenuates circadian rhythms in induced pluripotent stem cells during osteogenic differentiation through the TEAD-Fbxl3-CRY axis. Cell Death Discov 2025;11:252. [PMID: 40413171 PMCID: PMC12103599 DOI: 10.1038/s41420-025-02533-6] [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: 12/04/2024] [Revised: 05/04/2025] [Accepted: 05/13/2025] [Indexed: 05/27/2025]  Open
9
Kraft M, Schoofs H, Petkova M, Andrade J, Grosso AR, Benedito R, De Roo AK, Boon LM, Vikkula M, Kapp FG, Hägerling R, Potente M, Mäkinen T. Angiopoietin-TIE2 feedforward circuit promotes PIK3CA-driven venous malformations. NATURE CARDIOVASCULAR RESEARCH 2025:10.1038/s44161-025-00655-9. [PMID: 40410415 DOI: 10.1038/s44161-025-00655-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/11/2025] [Indexed: 05/25/2025]
10
Kosicki M, Laboy Cintrón D, Keukeleire P, Schubach M, Page NF, Georgakopoulos-Soares I, Akiyama JA, Plajzer-Frick I, Novak CS, Kato M, Hunter RD, von Maydell K, Barton S, Godfrey P, Beckman E, Sanders SJ, Kircher M, Pennacchio LA, Ahituv N. Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity. Nat Commun 2025;16:4786. [PMID: 40404660 PMCID: PMC12098896 DOI: 10.1038/s41467-025-60064-1] [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: 04/16/2024] [Accepted: 05/13/2025] [Indexed: 05/24/2025]  Open
11
Prince NH, Hamamura M, Zhou Y, Fujita Y. An ATAC-seq protocol for neuroscience research. Anat Sci Int 2025:10.1007/s12565-025-00850-5. [PMID: 40402346 DOI: 10.1007/s12565-025-00850-5] [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: 03/20/2025] [Accepted: 05/02/2025] [Indexed: 05/23/2025]
12
Wang Y, Yildirim A, Boninsegna L, Christian V, Kang SHL, Zhou XJ, Alber F. 3D genome organization shapes DNA damage susceptibility to platinum-based drugs. Nucleic Acids Res 2025;53:gkaf315. [PMID: 40433977 DOI: 10.1093/nar/gkaf315] [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: 06/25/2024] [Revised: 03/31/2025] [Accepted: 05/23/2025] [Indexed: 05/29/2025]  Open
13
Yang W, Wang XQ, Wei F, Yu J, Liu Y, Dou Y. Revealing long-range heterogeneous organization of nucleoproteins with 6mA footprinting by ipdTrimming. Genome Biol 2025;26:136. [PMID: 40399934 PMCID: PMC12096735 DOI: 10.1186/s13059-025-03592-9] [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: 09/30/2024] [Accepted: 04/27/2025] [Indexed: 05/23/2025]  Open
14
Tang L, Zhang J, Shao Y, Wei Y, Li Y, Tian K, Yan X, Feng C, Zhang QC. Joint analysis of chromatin accessibility and gene expression in the same single cells reveals cancer-specific regulatory programs. Cell Syst 2025;16:101266. [PMID: 40262617 DOI: 10.1016/j.cels.2025.101266] [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: 08/18/2024] [Revised: 01/19/2025] [Accepted: 03/28/2025] [Indexed: 04/24/2025]
15
Mok CH, Hu D, Losa M, Risolino M, Selleri L, Marcucio RS. PBX1 and PBX3 transcription factors regulate SHH expression in the Frontonasal Ectodermal Zone through complementary mechanisms. PLoS Genet 2025;21:e1011315. [PMID: 40397886 DOI: 10.1371/journal.pgen.1011315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 04/22/2025] [Indexed: 05/23/2025]  Open
16
Zhao S, Yang Q, Yu Z, Chu C, Dai S, Li H, Diao M, Feng L, Ke J, Xue Y, Zhou Q, Liu Y, Ma H, Lin CP, Yao YG, Zhong G. Deciphering enhancers of hearing loss genes for efficient and targeted gene therapy of hereditary deafness. Neuron 2025;113:1579-1596.e5. [PMID: 40262614 DOI: 10.1016/j.neuron.2025.03.023] [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: 12/22/2024] [Revised: 02/23/2025] [Accepted: 03/18/2025] [Indexed: 04/24/2025]
17
Auer F, Morcos MNF, Sipola M, Akhtar I, Moisio S, Vogt J, Haag R, Lahnalampi M, Tuononen TJ, Hanel A, Viitasalo A, Friedrich UA, Dahl A, Prexler C, Pandyra AA, Stepensky P, Takagi M, Borkhardt A, Heinäniemi M, Hauer J. Trajectories from single-cells to PAX5-driven leukemia reveal PAX5-MYC interplay in vivo. Leukemia 2025:10.1038/s41375-025-02626-2. [PMID: 40394211 DOI: 10.1038/s41375-025-02626-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 03/31/2025] [Accepted: 04/22/2025] [Indexed: 05/22/2025]
18
Cheng P, Zhao H, Zhang S, Zong Z, Li C, Ming L, Xie W, Yu H. Feedback regulation of m6A modification creates local auxin maxima essential for rice microsporogenesis. Dev Cell 2025;60:1454-1466.e4. [PMID: 39809283 DOI: 10.1016/j.devcel.2024.12.034] [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: 06/25/2024] [Revised: 11/10/2024] [Accepted: 12/17/2024] [Indexed: 01/16/2025]
19
Cui X, Yin Q, Gao Z, Li Z, Chen X, Lv H, Chen S, Liu Q, Zeng W, Jiang R. CREATE: cell-type-specific cis-regulatory element identification via discrete embedding. Nat Commun 2025;16:4607. [PMID: 40382355 PMCID: PMC12085597 DOI: 10.1038/s41467-025-59780-5] [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: 09/10/2024] [Accepted: 05/02/2025] [Indexed: 05/20/2025]  Open
20
Yu Y, Cen C, Shao Z, Wang C, Wang Y, Miao Z, Sun M, Wang C, Xu Q, Liang K, Zhou J, Zhou D, Ji H, Xu G, Du Y. APE1 promotes lung adenocarcinoma through G4-mediated transcriptional reprogramming of urea cycle metabolism. iScience 2025;28:112275. [PMID: 40276763 PMCID: PMC12019196 DOI: 10.1016/j.isci.2025.112275] [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: 01/24/2024] [Revised: 07/17/2024] [Accepted: 03/19/2025] [Indexed: 04/26/2025]  Open
21
Gill ME, Fischer M, De Geyter C, Peters AHFM. Normozoospermic infertile men possess subpopulations of sperm varying in DNA accessibility, relating to differing reproductive outcomes. Hum Reprod 2025:deaf081. [PMID: 40375809 DOI: 10.1093/humrep/deaf081] [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: 09/24/2024] [Revised: 02/19/2025] [Indexed: 05/18/2025]  Open
22
Alfano V, Pascucci GR, Corleone G, Cocca M, De Nicola F, Floriot O, Paturel A, Di Tocco FC, de Fromentel CC, Merle P, Rivoire M, Levrero M, Guerrieri F. HBV-driven host chromatin accessibility changes affect liver metabolic pathways, iron homeostasis and promote a preneoplastic phenotype. J Exp Clin Cancer Res 2025;44:146. [PMID: 40380227 DOI: 10.1186/s13046-025-03414-7] [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: 03/03/2025] [Accepted: 05/09/2025] [Indexed: 05/19/2025]  Open
23
Fu Y, Land M, Kavlashvili T, Cui R, Kim M, DeBitetto E, Lieber T, Ryu KW, Choi E, Masilionis I, Saha R, Takizawa M, Baker D, Tigano M, Lareau CA, Reznik E, Sharma R, Chaligne R, Thompson CB, Pe'er D, Sfeir A. Engineering mtDNA deletions by reconstituting end joining in human mitochondria. Cell 2025;188:2778-2793.e21. [PMID: 40068680 DOI: 10.1016/j.cell.2025.02.009] [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: 08/27/2024] [Revised: 01/22/2025] [Accepted: 02/13/2025] [Indexed: 03/19/2025]
24
Ahmad K, Henikoff S. Profiling regulatory elements in vivo by genome-wide methods. Curr Opin Struct Biol 2025;92:103064. [PMID: 40378608 DOI: 10.1016/j.sbi.2025.103064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2025] [Revised: 04/21/2025] [Accepted: 04/22/2025] [Indexed: 05/19/2025]
25
Bubb KL, Hamm MO, Tullius TW, Min JK, Ramirez-Corona B, Mueth NA, Ranchalis J, Mao Y, Bergstrom EJ, Vollger MR, Trapnell C, Cuperus JT, Stergachis AB, Queitsch C. The regulatory potential of transposable elements in maize. NATURE PLANTS 2025:10.1038/s41477-025-02002-z. [PMID: 40360747 DOI: 10.1038/s41477-025-02002-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Accepted: 04/11/2025] [Indexed: 05/15/2025]
26
Barbadilla-Martínez L, Klaassen N, van Steensel B, de Ridder J. Predicting gene expression from DNA sequence using deep learning models. Nat Rev Genet 2025:10.1038/s41576-025-00841-2. [PMID: 40360798 DOI: 10.1038/s41576-025-00841-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/01/2025] [Indexed: 05/15/2025]
27
Zhang J, Ma L, Deng H, Yi W, Tohtihan A, Tang X, Wu X, Feng X. Multi-omics integration identifies NK cell-mediated cytotoxicity as a therapeutic target in systemic lupus erythematosus. Front Immunol 2025;16:1580540. [PMID: 40433370 PMCID: PMC12106370 DOI: 10.3389/fimmu.2025.1580540] [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: 02/20/2025] [Accepted: 04/18/2025] [Indexed: 05/29/2025]  Open
28
Guichard V, Leão FB, Zhao J, Zhang Y, Ito T, Shirley S, Postler TS, Tian R, Huang Y, Ghosh S. Pre-existing epigenetic state and differential NF-κB activation shape type 2 immune cell responses. Immunity 2025:S1074-7613(25)00179-7. [PMID: 40367949 DOI: 10.1016/j.immuni.2025.04.016] [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: 03/04/2024] [Revised: 12/20/2024] [Accepted: 04/15/2025] [Indexed: 05/16/2025]
29
Tasan I, Eres I, Wei C, Bryant EE, Brisan E, Hubert R. Identification of Loci with High Transgene Expression in CHO Cells. ACS Synth Biol 2025. [PMID: 40357755 DOI: 10.1021/acssynbio.4c00678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2025]
30
Sugata K, Rahman A, Niimura K, Monde K, Ueno T, Rajib SA, Takatori M, Sakhor W, Hossain MB, Sithi SN, Jahan MI, Matsuda K, Ueda M, Yamano Y, Ikeda T, Ueno T, Tsuchiya K, Tanaka Y, Tokunaga M, Maeda K, Utsunomiya A, Okuma K, Ono M, Satou Y. Intragenic viral silencer element regulates HTLV-1 latency via RUNX complex recruitment. Nat Microbiol 2025:10.1038/s41564-025-02006-7. [PMID: 40360701 DOI: 10.1038/s41564-025-02006-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 04/07/2025] [Indexed: 05/15/2025]
31
Hyle J, Qi W, Djekidel MN, Rosikiewicz W, Xu B, Li C. Deciphering the role of RNA in regulating CTCF's DNA binding affinity in leukemia cells. Genome Biol 2025;26:126. [PMID: 40355969 PMCID: PMC12067947 DOI: 10.1186/s13059-025-03582-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: 03/30/2024] [Accepted: 04/20/2025] [Indexed: 05/15/2025]  Open
32
Zahavi EE, Koppel I, Kawaguchi R, Oses-Prieto JA, Briner A, Monavarfeshani A, Dalla Costa I, van Niekerk E, Lee J, Matoo S, Hegarty S, Donahue RJ, Sahoo PK, Ben-Dor S, Feldmesser E, Ryvkin J, Leshkowitz D, Perry RBT, Cheng Y, Farber E, Abraham O, Samra N, Okladnikov N, Alber S, Albus CA, Rishal I, Ulitsky I, Tuszynski MH, Twiss JL, He Z, Burlingame AL, Fainzilber M. Repeat-element RNAs integrate a neuronal growth circuit. Cell 2025:S0092-8674(25)00498-2. [PMID: 40381624 DOI: 10.1016/j.cell.2025.04.030] [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: 03/14/2024] [Revised: 11/12/2024] [Accepted: 04/23/2025] [Indexed: 05/20/2025]
33
Williams RM. Leveraging chicken embryos for studying human enhancers. Dev Biol 2025;524:123-131. [PMID: 40368318 DOI: 10.1016/j.ydbio.2025.05.009] [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: 10/29/2024] [Revised: 04/30/2025] [Accepted: 05/12/2025] [Indexed: 05/16/2025]
34
Shinozaki T, Togasaki K, Hamamoto J, Mitsuishi A, Fukushima T, Sugihara K, Ebisudani T, Okada M, Saito A, Shigematsu L, Takaoka H, Ito F, Ohgino K, Ishioka K, Watanabe K, Hishima T, Kurebayashi Y, Emoto K, Terai H, Ikemura S, Kawada I, Asakura K, Hishida T, Asamura H, Ohta Y, Takahashi S, Oda M, Saito M, Matano M, Soejima K, Fujii M, Fukunaga K, Yasuda H, Sato T. Basal-shift transformation leads to EGFR therapy-resistance in human lung adenocarcinoma. Nat Commun 2025;16:4369. [PMID: 40350470 PMCID: PMC12066730 DOI: 10.1038/s41467-025-59623-3] [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: 12/14/2024] [Accepted: 04/30/2025] [Indexed: 05/14/2025]  Open
35
Liu X, Wang D, Zhang Z, Lin X, Xiao J. Epigenetic perspectives on wheat speciation, adaptation, and development. Trends Genet 2025:S0168-9525(25)00083-6. [PMID: 40348655 DOI: 10.1016/j.tig.2025.04.008] [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: 02/14/2025] [Revised: 04/16/2025] [Accepted: 04/18/2025] [Indexed: 05/14/2025]
36
Dincer TU, Ernst J. ChromActivity: integrative epigenomic and functional characterization assay based annotation of regulatory activity across diverse human cell types. Genome Biol 2025;26:123. [PMID: 40346707 PMCID: PMC12063466 DOI: 10.1186/s13059-025-03579-6] [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: 07/13/2023] [Accepted: 04/15/2025] [Indexed: 05/11/2025]  Open
37
Guo S, Hu X, Cotton JL, Ma L, Li Q, Cui J, Wang Y, Thakare RP, Tao Z, Ip YT, Wu X, Wang J, Mao J. VGLL2 and TEAD1 fusion proteins identified in human sarcoma drive YAP/TAZ-independent tumorigenesis by engaging EP300. eLife 2025;13:RP98386. [PMID: 40338073 PMCID: PMC12061476 DOI: 10.7554/elife.98386] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2025]  Open
38
Jo Y, Greene TT, Chiale C, Zhang K, Fang Z, Dallari S, Marooki N, Wang W, Zuniga EI. Genomic analysis of progenitors in viral infection implicates glucocorticoids as suppressors of plasmacytoid dendritic cell generation. Proc Natl Acad Sci U S A 2025;122:e2410092122. [PMID: 40294270 PMCID: PMC12067256 DOI: 10.1073/pnas.2410092122] [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: 05/20/2024] [Accepted: 02/19/2025] [Indexed: 04/30/2025]  Open
39
Fang J, Singh S, Wells B, Wu Q, Jin H, Janke LJ, Wan S, Steele JA, Connelly JP, Murphy AJ, Wang R, Davidoff A, Ashcroft M, Pruett-Miller SM, Yang J. The context-dependent epigenetic and organogenesis programs determine 3D vs. 2D cellular fitness of MYC-driven murine liver cancer cells. eLife 2025;14:RP101299. [PMID: 40326560 PMCID: PMC12055005 DOI: 10.7554/elife.101299] [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] [Indexed: 05/07/2025]  Open
40
Marinov GK, Greenleaf WJ. Mapping the Simultaneously Accessible and ssDNA-Containing Genome With KAS-ATAC Sequencing. Bio Protoc 2025;15:e5306. [PMID: 40364983 PMCID: PMC12067302 DOI: 10.21769/bioprotoc.5306] [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: 02/01/2025] [Revised: 04/09/2025] [Accepted: 04/11/2025] [Indexed: 05/15/2025]  Open
41
Cheng B, Peng SI, Jia YY, Tong E, Atwood SX, Sun BK. Comprehensive secretome profiling and CRISPR screen identifies SFRP1 as a key inhibitor of epidermal progenitor proliferation. Cell Death Dis 2025;16:360. [PMID: 40319033 PMCID: PMC12049499 DOI: 10.1038/s41419-025-07691-0] [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: 08/01/2024] [Revised: 04/11/2025] [Accepted: 04/23/2025] [Indexed: 05/07/2025]
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Sereti K, Russo AE, Raisner R, Ma TP, Gascoigne KE. PAX8 Interacts with the SWI/SNF Complex at Enhancers to Drive Proliferation in Ovarian Cancer. Mol Cancer Res 2025;23:416-425. [PMID: 39918415 DOI: 10.1158/1541-7786.mcr-24-0710] [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: 08/01/2024] [Revised: 12/23/2024] [Accepted: 02/05/2025] [Indexed: 05/03/2025]
43
Abe K. Dynamic activity changes in transcription factors: Unlocking the mechanisms regulating physiological changes in the brain. Neurosci Res 2025;214:16-22. [PMID: 39134224 DOI: 10.1016/j.neures.2024.08.001] [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: 08/03/2024] [Revised: 07/30/2024] [Accepted: 08/04/2024] [Indexed: 08/18/2024]
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Loft A, Emont MP, Weinstock A, Divoux A, Ghosh A, Wagner A, Hertzel AV, Maniyadath B, Deplancke B, Liu B, Scheele C, Lumeng C, Ding C, Ma C, Wolfrum C, Strieder-Barboza C, Li C, Truong DD, Bernlohr DA, Stener-Victorin E, Kershaw EE, Yeger-Lotem E, Shamsi F, Hui HX, Camara H, Zhong J, Kalucka J, Ludwig JA, Semon JA, Jalkanen J, Whytock KL, Dumont KD, Sparks LM, Muir LA, Fang L, Massier L, Saraiva LR, Beyer MD, Jeschke MG, Mori MA, Boroni M, Walsh MJ, Patti ME, Lynes MD, Blüher M, Rydén M, Hamda N, Solimini NL, Mejhert N, Gao P, Gupta RK, Murphy R, Pirouzpanah S, Corvera S, Tang S, Das SK, Schmidt SF, Zhang T, Nelson TM, O'Sullivan TE, Efthymiou V, Wang W, Tong Y, Tseng YH, Mandrup S, Rosen ED. Towards a consensus atlas of human and mouse adipose tissue at single-cell resolution. Nat Metab 2025;7:875-894. [PMID: 40360756 DOI: 10.1038/s42255-025-01296-9] [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: 11/01/2024] [Accepted: 03/28/2025] [Indexed: 05/15/2025]
45
Xie L, Jakutis G, Dooley CM, Guenther S, Kontarakis Z, Howard SP, Juan T, Stainier DYR. Induction of a transcriptional adaptation response by RNA destabilization events. EMBO Rep 2025;26:2262-2279. [PMID: 40128410 PMCID: PMC12069562 DOI: 10.1038/s44319-025-00427-3] [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: 08/14/2024] [Revised: 03/03/2025] [Accepted: 03/10/2025] [Indexed: 03/26/2025]  Open
46
Miyashita Y, Tajima K, Izumi K, Matsumoto N, Hayakawa D, Nakamura IT, Katayama I, Wibowo A, Matsuda H, Winardi W, Amien BR, Mitsuishi Y, Takahashi F, Nakamura K, Uchibori K, Yanagitani N, Hayashi T, Takamochi K, Suzuki K, Katayama R, Takahashi K. Novel Approach to Overcome Osimertinib Resistance Using Bromodomain and Extra-Terminal Domain Inhibitors. Cancer Sci 2025;116:1392-1404. [PMID: 40036147 PMCID: PMC12044652 DOI: 10.1111/cas.70032] [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: 11/29/2024] [Revised: 02/09/2025] [Accepted: 02/18/2025] [Indexed: 03/06/2025]  Open
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Vicanolo T, Özcan A, Li JL, Huerta-López C, Ballesteros I, Rubio-Ponce A, Dumitru AC, Nicolás-Ávila JÁ, Molina-Moreno M, Reyes-Gutierrez P, Johnston AD, Martone C, Greto E, Quílez-Alvarez A, Calvo E, Bonzon-Kulichenko E, Álvarez-Velez R, Chooi MY, Kwok I, González-Bermúdez B, Malleret B, Espinosa FM, Zhang M, Wang YL, Sun D, Zhen Chong S, El-Armouche A, Kim KK, Udalova IA, Greco V, Garcia R, Vázquez J, Dopazo A, Plaza GR, Alegre-Cebollada J, Uderhardt S, Ng LG, Hidalgo A. Matrix-producing neutrophils populate and shield the skin. Nature 2025;641:740-748. [PMID: 40108463 PMCID: PMC12074881 DOI: 10.1038/s41586-025-08741-5] [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: 08/31/2023] [Accepted: 02/04/2025] [Indexed: 03/22/2025]
48
Fan S, Li X, Xu X, Yin Y, Wang G, Shao A, Wang W, Fu J. Chromatin Accessibility and Translational Landscapes of Bermudagrass (Cynodon dactylon) Under Chilling Stress. PHYSIOLOGIA PLANTARUM 2025;177:e70279. [PMID: 40432571 DOI: 10.1111/ppl.70279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2024] [Revised: 02/25/2025] [Accepted: 03/05/2025] [Indexed: 05/29/2025]
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Chai H, Huang X, Xiong G, Huang J, Pels KK, Meng L, Han J, Tang D, Pan G, Deng L, Xiao Q, Wang X, Zhang M, Banecki K, Plewczynski D, Wei CL, Ruan Y. Tri-omic single-cell mapping of the 3D epigenome and transcriptome in whole mouse brains throughout the lifespan. Nat Methods 2025;22:994-1007. [PMID: 40301621 DOI: 10.1038/s41592-025-02658-7] [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: 11/14/2024] [Accepted: 03/13/2025] [Indexed: 05/01/2025]
50
Hui T, Zhou J, Yao M, Xie Y, Zeng H. Advances in Spatial Omics Technologies. SMALL METHODS 2025;9:e2401171. [PMID: 40099571 DOI: 10.1002/smtd.202401171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 03/03/2025] [Indexed: 03/20/2025]
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