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Liu X, Zhang B, Hua Y, Li C, Li X, Kong D. Nucleosomes represent a crucial target for the intra-S phase checkpoint in response to replication stress. SCIENCE ADVANCES 2025; 11:eadr3673. [PMID: 40378213 PMCID: PMC12083529 DOI: 10.1126/sciadv.adr3673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Accepted: 04/17/2025] [Indexed: 05/18/2025]
Abstract
The intra-S phase checkpoint is essential for stability of stalled DNA replication forks. However, the mechanisms underlying checkpoint regulation remain poorly understood. This study identifies a critical checkpoint target-the ubiquitin E3 ligase Brl2, revealing a new dimension of checkpoint regulation. Upon replication fork stalling, Brl2 undergoes phosphorylation at five serine residues by Cds1Chk2 kinase, resulting in the loss of its ligase activity and a marked reduction in H2BK119ub1 levels. In the brl2-5D (the five serine residues are replaced with aspartic acid) and htb-K119R mutants, chromatin becomes highly compacted. Furthermore, the rates of stalled replication fork collapse, and dsDNA breaks are significantly reduced in brl2-5D cds1Chk2∆ cells compared to cds1Chk2∆ cells. Thus, this study demonstrates that nucleosomes are targeted by the intra-S phase checkpoint and highlights the checkpoint's critical role in configuring compact chromatin structures at replication fork stalling sites. These findings may explain why ATR and Chk1 are essential for cell proliferation and embryonic development, while ATM is not.
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Affiliation(s)
- Xiaoqin Liu
- Peking-Tsinghua Center for Life Sciences, The National Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
- Institute of Brain Science, College of Medicine, Shanxi Datong University, Datong 037009, China
| | - Bo Zhang
- Peking-Tsinghua Center for Life Sciences, The National Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Yu Hua
- Peking-Tsinghua Center for Life Sciences, The National Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Chuanqi Li
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou 215123, China
| | - Xizhou Li
- Department of Breast and Thyroid Surgery, Changhai Hospital, The Naval Military Medical University, Shanghai, China
| | - Daochun Kong
- Peking-Tsinghua Center for Life Sciences, The National Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
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2
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Ahmad JN, Modrak M, Fajfrova M, Sotoca BMB, Benada O, Sebo P. Bordetella adenylate cyclase toxin elicits chromatin remodeling and transcriptional reprogramming that blocks differentiation of monocytes into macrophages. mBio 2025; 16:e0013825. [PMID: 40105369 PMCID: PMC11980580 DOI: 10.1128/mbio.00138-25] [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: 01/28/2025] [Accepted: 02/18/2025] [Indexed: 03/20/2025] Open
Abstract
Bordetella pertussis infects human upper airways and deploys an array of immunosuppressive virulence factors, among which the adenylate cyclase toxin (CyaA) plays a prominent role in disarming host phagocytes. CyaA binds the complement receptor-3 (CR3 aka αMβ2 integrin CD11b/CD18 or Mac-1) of myeloid cells and delivers into their cytosol an adenylyl cyclase enzyme that hijacks cellular signaling through unregulated conversion of cytosolic ATP to cAMP. We found that the action of as little CyaA as 22 pM (4 ng/mL) blocks macrophage colony-stimulating factor (M-CSF)-driven transition of migratory human CD14+ monocytes into macrophages. Global transcriptional profiling (RNAseq) revealed that exposure of monocytes to 22 pM CyaA for 40 hours in culture with 20 ng/mL of M-CSF led to upregulation of genes that exert negative control of monocyte to macrophage differentiation (e.g., SERPINB2, DLL1, and CSNK1E). The sustained CyaA action yielded downregulation of numerous genes involved in processes crucial for host defense, such as myeloid cell differentiation, chemotaxis of inflammatory cells, antigen presentation, phagocytosis, and bactericidal activities. CyaA-elicited signaling also promoted deacetylation and trimethylation of lysines 9 and 27 of histone 3 (H3K9me3 and H3K27me3) and triggered the formation of transcriptionally repressive heterochromatin patches in the nuclei of CyaA-exposed monocytes. These effects were partly reversed by the G9a methyltransferase inhibitor UNC 0631 and by the pleiotropic HDAC inhibitor Trichostatin-A, revealing that CyaA-elicited epigenetic alterations mediate transcriptional reprogramming of monocytes and play a role in CyaA-triggered block of monocyte differentiation into bactericidal macrophage cells.IMPORTANCETo proliferate on host airway mucosa and evade elimination by patrolling sentinel cells, the whooping cough agent Bordetella pertussis produces a potently immunosubversive adenylate cyclase toxin (CyaA) that blocks opsonophagocytic killing of bacteria by phagocytes like neutrophils and macrophages. Indeed, chemotactic migration of CD14+ monocytes to the infection site and their transition into bactericidal macrophages, thus replenishing the exhausted mucosa-patrolling macrophages, represents one of the key mechanisms of innate immune defense to infection. We show that the cAMP signaling action of CyaA already at a very low toxin concentration triggers massive transcriptional reprogramming of monocytes that is accompanied by chromatin remodeling and epigenetic histone modifications, which block the transition of migratory monocytes into bactericidal macrophage cells. This reveals a novel layer of toxin action-mediated hijacking of functional differentiation of innate immune cells for the sake of mucosal pathogen proliferation and transmission to new hosts.
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Affiliation(s)
- Jawid Nazir Ahmad
- Institute of Microbiology of Czech Academy of Sciences, Prague, Czechia
| | - Martin Modrak
- Institute of Microbiology of Czech Academy of Sciences, Prague, Czechia
| | - Marketa Fajfrova
- Institute of Microbiology of Czech Academy of Sciences, Prague, Czechia
| | | | - Oldrich Benada
- Institute of Microbiology of Czech Academy of Sciences, Prague, Czechia
| | - Peter Sebo
- Institute of Microbiology of Czech Academy of Sciences, Prague, Czechia
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3
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Furth N, Cohen N, Spitzer A, Salame TM, Dassa B, Mehlman T, Brandis A, Moussaieff A, Friedmann-Morvinski D, Castro MG, Fortin J, Suvà ML, Tirosh I, Erez A, Ron G, Shema E. Oncogenic IDH1 mut drives robust loss of histone acetylation and increases chromatin heterogeneity. Proc Natl Acad Sci U S A 2025; 122:e2403862122. [PMID: 39793065 PMCID: PMC11725805 DOI: 10.1073/pnas.2403862122] [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: 11/15/2024] [Indexed: 01/12/2025] Open
Abstract
Malignant gliomas are heterogeneous tumors, mostly incurable, arising in the central nervous system (CNS) driven by genetic, epigenetic, and metabolic aberrations. Mutations in isocitrate dehydrogenase (IDH1/2mut) enzymes are predominantly found in low-grade gliomas and secondary high-grade gliomas, with IDH1 mutations being more prevalent. Mutant-IDH1/2 confers a gain-of-function activity that favors the conversion of a-ketoglutarate (α-KG) to the oncometabolite 2-hydroxyglutarate (2-HG), resulting in an aberrant hypermethylation phenotype. Yet, the complete depiction of the epigenetic alterations in IDHmut cells has not been thoroughly explored. Here, we applied an unbiased approach, leveraging epigenetic-focused cytometry by time-of-flight (CyTOF) analysis, to systematically profile the effect of mutant-IDH1 expression on a broad panel of histone modifications at single-cell resolution. This analysis revealed extensive remodeling of chromatin patterns by mutant-IDH1, with the most prominent being deregulation of histone acetylation marks. The loss of histone acetylation occurs rapidly following mutant-IDH1 induction and affects acetylation patterns over enhancers and intergenic regions. Notably, the changes in acetylation are not predominantly driven by 2-HG, can be rescued by pharmacological inhibition of mutant-IDH1, and reversed by acetate supplementations. Furthermore, cells expressing mutant-IDH1 show higher epigenetic and transcriptional heterogeneity and upregulation of oncogenes such as KRAS and MYC, highlighting its tumorigenic potential. Our study underscores the tight interaction between chromatin and metabolism dysregulation in glioma and highlights epigenetic and oncogenic pathways affected by mutant-IDH1-driven metabolic rewiring.
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Affiliation(s)
- Noa Furth
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Niv Cohen
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Avishay Spitzer
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot7610001, Israel
- Oncology Institute, Tel Aviv Sourasky Medical Center, Tel Aviv6423906, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv6997801, Israel
| | - Tomer-Meir Salame
- Mass Cytometry Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Bareket Dassa
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Tevie Mehlman
- Targeted Metabolomics Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Alexander Brandis
- Targeted Metabolomics Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Arieh Moussaieff
- The Institute for Drug Research, Faculty of Medicine, Hebrew University, Jerusalem9112102, Israel
| | - Dinorah Friedmann-Morvinski
- Sagol School of Neurobiology, Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv6997801, Israel
| | - Maria G. Castro
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI48109
| | - Jerome Fortin
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, QCH3A 2B4, Canada
| | - Mario L. Suvà
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA02114
- Broad Institute of Harvard and MIT, Cambridge, MA02142
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Ayelet Erez
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Guy Ron
- Racah Institute of Physics, Hebrew University, Jerusalem9190401, Israel
| | - Efrat Shema
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot7610001, Israel
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4
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Sun F, Ali NN, Londoño-Vásquez D, Simintiras CA, Qiao H, Ortega MS, Agca Y, Takahashi M, Rivera RM, Kelleher AM, Sutovsky P, Patterson AL, Balboula AZ. Increased DNA damage in full-grown oocytes is correlated with diminished autophagy activation. Nat Commun 2024; 15:9463. [PMID: 39487138 PMCID: PMC11530536 DOI: 10.1038/s41467-024-53559-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/14/2024] [Indexed: 11/04/2024] Open
Abstract
Unlike mild DNA damage exposure, DNA damage repair (DDR) is reported to be ineffective in full-grown mammalian oocytes exposed to moderate or severe DNA damage. The underlying mechanisms of this weakened DDR are unknown. Here, we show that moderate DNA damage in full-grown oocytes leads to aneuploidy. Our data reveal that DNA-damaged oocytes have an altered, closed, chromatin state, and suggest that the failure to repair damaged DNA could be due to the inability of DDR proteins to access damaged loci. Our data also demonstrate that, unlike somatic cells, mouse and porcine oocytes fail to activate autophagy in response to DNA double-strand break-inducing treatment, which we suggest may be the cause of the altered chromatin conformation and inefficient DDR. Importantly, autophagy activity is further reduced in maternally aged oocytes (which harbor severe DNA damage), and its induction is correlated with reduced DNA damage in maternally aged oocytes. Our findings provide evidence that reduced autophagy activation contributes to weakened DDR in oocytes, especially in those from aged females, offering new possibilities to improve assisted reproductive therapy in women with compromised oocyte quality.
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Affiliation(s)
- Fei Sun
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Nourhan Nashat Ali
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
- Department of Physiology, Faculty of Veterinary Medicine, Assiut University, Assiut, Egypt
| | | | - Constantine A Simintiras
- School of Animal Sciences, Agricultural Center, Louisiana State University, Baton Rouge, LA, USA
| | - Huanyu Qiao
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - M Sofia Ortega
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Yuksel Agca
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
| | - Masashi Takahashi
- Research Faculty of Agriculture, Hokkaido University, Hokkaido, Japan
| | - Rocío M Rivera
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Andrew M Kelleher
- Department of Obstetrics, Gynecology and Women's Health, University of Missouri, Columbia, MO, USA
| | - Peter Sutovsky
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
- Department of Obstetrics, Gynecology and Women's Health, University of Missouri, Columbia, MO, USA
| | - Amanda L Patterson
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
- Department of Obstetrics, Gynecology and Women's Health, University of Missouri, Columbia, MO, USA
| | - Ahmed Z Balboula
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA.
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5
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Shen J, He Y, Li S, Chen H. Crosstalk of methylation and tamoxifen in breast cancer (Review). Mol Med Rep 2024; 30:180. [PMID: 39129315 PMCID: PMC11338244 DOI: 10.3892/mmr.2024.13304] [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: 06/02/2024] [Accepted: 07/23/2024] [Indexed: 08/13/2024] Open
Abstract
Tamoxifen is a widely used anti‑estrogen drug in the endocrine therapy of breast cancer (BC). It blocks estrogen signaling by competitively binding to estrogen receptor α (ERα), thereby inhibiting the growth of BC cells. However, with the long‑term application of tamoxifen, a subset of patients with BC have shown resistance to tamoxifen, which leads to low overall survival and progression‑free survival. The molecular mechanism of resistance is mainly due to downregulation of ERα expression and abnormal activation of the PI3K/AKT/mTOR signaling pathway. Moreover, the downregulation of targeted gene expression mediated by DNA methylation is an important regulatory mode to control protein expression. In the present review, methylation and tamoxifen are briefly introduced, followed by a focus on the effect of methylation on tamoxifen resistance and sensitivity. Finally, the clinical application of methylation for tamoxifen is described, including its use as a prognostic indicator. Finally, it is hypothesized that when methylation is used in combination with tamoxifen, it could recover the resistance of tamoxifen.
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Affiliation(s)
- Jin Shen
- Department of Rehabilitation, The Affiliated Zhuzhou Hospital of Xiangya Medical College, Central South University, Zhuzhou, Hunan 412000, P.R. China
| | - Yan He
- Department of Neurology, The Affiliated Zhuzhou Hospital of Xiangya Medical College, Central South University, Zhuzhou, Hunan 412000, P.R. China
| | - Shengpeng Li
- Department of Rehabilitation, The Affiliated Zhuzhou Hospital of Xiangya Medical College, Central South University, Zhuzhou, Hunan 412000, P.R. China
| | - Huimin Chen
- Department of Rehabilitation, The Affiliated Zhuzhou Hospital of Xiangya Medical College, Central South University, Zhuzhou, Hunan 412000, P.R. China
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6
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Ni S, Takada Y, Ando T, Yu S, Yamashita Y, Takahashi Y, Sawada M, Oba M, Itoh Y, Suzuki T. Identification of a novel histone H2A mono-ubiquitination-inhibiting cell-active small molecule. Bioorg Med Chem Lett 2024; 105:129759. [PMID: 38636717 DOI: 10.1016/j.bmcl.2024.129759] [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: 02/27/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
Histone H2A mono-ubiquitination plays important roles in epigenetic gene expression and is also involved in tumorigenesis. Small molecules controlling H2A ubiquitination are of interest as potential chemical tools and anticancer drugs. To identify novel small molecule inhibitors of H2A ubiquitination, we synthesized and evaluated several compounds designed based on PRT4165 (1), which is a reported histone ubiquitin ligase RING1A inhibitor. We found that compound 11b strongly inhibited the viability and reduced histone H2A mono-ubiquitination in human osteosarcoma U2OS cells. Therefore, compound 11b is a promising lead compound for the development of H2A histone ubiquitination-inhibiting small molecules.
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Affiliation(s)
- Siyao Ni
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Yuri Takada
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Takaaki Ando
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Shengwang Yu
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | | | - Yukari Takahashi
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Miho Sawada
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Makoto Oba
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Yukihiro Itoh
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Takayoshi Suzuki
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
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7
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Xu Z, Qin Q, Wang Y, Zhang H, Liu S, Li X, Chen Y, Wang Y, Ruan H, He W, Zhang T, Yan X, Wang C, Xu D, Jiang X. Deubiquitinase Mysm1 regulates neural stem cell proliferation and differentiation by controlling Id4 expression. Cell Death Dis 2024; 15:129. [PMID: 38342917 PMCID: PMC10859383 DOI: 10.1038/s41419-024-06530-y] [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: 09/26/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/13/2024]
Abstract
Neural stem cells (NSCs) are critical for brain development and maintenance of neurogenesis. However, the molecular mechanisms that regulate NSC proliferation and differentiation remain unclear. Mysm1 is a deubiquitinase and is essential for the self-renewal and differentiation of several stem cells. It is unknown whether Mysm1 plays an important role in NSCs. Here, we found that Mysm1 was expressed in NSCs and its expression was increased with age in mice. Mice with Mysm1 knockdown by crossing Mysm1 floxed mice with Nestin-Cre mice exhibited abnormal brain development with microcephaly. Mysm1 deletion promoted NSC proliferation and apoptosis, resulting in depletion of the stem cell pool. In addition, Mysm1-deficient NSCs skewed toward neurogenesis instead of astrogliogenesis. Mechanistic investigations with RNA sequencing and genome-wide CUT&Tag analysis revealed that Mysm1 epigenetically regulated Id4 transcription by regulating histone modification at the promoter region. After rescuing the expression of Id4, the hyperproliferation and imbalance differentiation of Mysm1-deficient NSCs was reversed. Additionally, knockdown Mysm1 in aged mice could promote NSC proliferation. Collectively, the present study identified a new factor Mysm1 which is essential for NSC homeostasis and Mysm1-Id4 axis may be an ideal target for proper NSC proliferation and differentiation.
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Affiliation(s)
- Zhenhua Xu
- Beijing Institute of Basic Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Qiaozhen Qin
- Beijing Institute of Basic Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, 100124, China
| | - Yan Wang
- Beijing Institute of Basic Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China
- Anhui Medical University, Hefei, 230032, Anhui, China
| | - Heyang Zhang
- Beijing Institute of Basic Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Shuirong Liu
- Beijing Institute of Basic Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Xiaotong Li
- Beijing Institute of Basic Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Yue Chen
- Beijing Institute of Basic Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Yuqing Wang
- Beijing Institute of Basic Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Huaqiang Ruan
- Beijing Institute of Basic Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Wenyan He
- China National Clinical Research Center for Neurological Diseases, Jing-Jin Center for Neuroinflammation, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100050, China
| | - Tao Zhang
- Beijing Institute of Basic Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Xinlong Yan
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, 100124, China
| | - Changyong Wang
- Beijing Institute of Basic Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China.
| | - Donggang Xu
- Beijing Institute of Basic Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China.
| | - Xiaoxia Jiang
- Beijing Institute of Basic Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China.
- Anhui Medical University, Hefei, 230032, Anhui, China.
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8
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Goncharov T, Kőműves LG, Kist M, Castellanos ER, Witt A, Fedorova AV, Izrael-Tomasevic A, Yu K, Keir M, Matsumoto ML, Vucic D. Simultaneous substrate and ubiquitin modification recognition by bispecific antibodies enables detection of ubiquitinated RIP1 and RIP2. Sci Signal 2024; 17:eabn1101. [PMID: 38227684 DOI: 10.1126/scisignal.abn1101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/21/2023] [Indexed: 01/18/2024]
Abstract
Ubiquitination is a posttranslational modification that is crucial for the dynamic regulation of diverse signaling pathways. To enhance our understanding of ubiquitination-mediated signaling, we generated a new class of bispecific antibodies that combine recognition of ubiquitination substrates and specific polyubiquitin linkages. RIP1-K63 and RIP1-linear (Lin) linkage polyubiquitin bispecific antibodies detected linkage-specific ubiquitination of the proinflammatory kinase RIP1 in cells and in tissues and revealed RIP1 ubiquitination by immunofluorescence. Similarly, ubiquitination of the RIP1-related kinase RIP2 with K63 or linear linkages was specifically detected with the RIP2-K63 and RIP2-Lin bispecific antibodies, respectively. Furthermore, using the RIP2-K63 and RIP2-Lin bispecific antibodies, we found prominent K63-linked and linear RIP2 ubiquitination in samples from patients with ulcerative colitis and Crohn's disease. We also developed a bispecific antibody (K63-Lin) that simultaneously recognizes K63-linked and linear ubiquitination of components of various signaling pathways. Together, these bispecific antibodies represent a new class of reagents with the potential to be developed for the detection of inflammatory biomarkers.
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Affiliation(s)
- Tatiana Goncharov
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA 94080, USA
- Department of Immunology Discovery, Genentech, South San Francisco, CA 94080, USA
| | - László G Kőműves
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Matthias Kist
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA 94080, USA
- Department of Immunology Discovery, Genentech, South San Francisco, CA 94080, USA
| | - Erick R Castellanos
- Department of Structural Biology, Genentech, South San Francisco, CA 94080, USA
| | - Axel Witt
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA 94080, USA
- Department of Immunology Discovery, Genentech, South San Francisco, CA 94080, USA
| | - Anna V Fedorova
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA 94080, USA
| | - Anita Izrael-Tomasevic
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA 94080, USA
| | - Kebing Yu
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA 94080, USA
| | - Mary Keir
- Department of Human Pathobiology and OMNI Reverse Translation, Genentech, South San Francisco, CA 94080, USA
| | - Marissa L Matsumoto
- Department of Structural Biology, Genentech, South San Francisco, CA 94080, USA
| | - Domagoj Vucic
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA 94080, USA
- Department of Immunology Discovery, Genentech, South San Francisco, CA 94080, USA
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9
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Bondra ER, Rine J. Context-dependent function of the transcriptional regulator Rap1 in gene silencing and activation in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2023; 120:e2304343120. [PMID: 37769255 PMCID: PMC10556627 DOI: 10.1073/pnas.2304343120] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 08/04/2023] [Indexed: 09/30/2023] Open
Abstract
In Saccharomyces cerevisiae, heterochromatin is formed through interactions between site-specific DNA-binding factors, including the transcriptional activator Repressor Activator Protein (Rap1), and Sir proteins. Despite an understanding of the establishment and maintenance of Sir-silenced chromatin, the mechanism of gene silencing by Sir proteins has remained a mystery. Utilizing high-resolution chromatin immunoprecipitation, we found that Rap1, the native activator of the bidirectional HMLα promoter, bound its recognition sequence in silenced chromatin, and its binding was enhanced by the presence of Sir proteins. In contrast to prior results, various components of transcription machinery were not able to access HMLα in the silenced state. These findings disproved the long-standing model of indiscriminate steric occlusion by Sir proteins and led to investigation of the role of the transcriptional activator Rap1 in Sir-silenced chromatin. Using a highly sensitive assay that monitors loss-of-silencing events, we identified a role for promoter-bound Rap1 in the maintenance of silent chromatin through interactions with the Sir complex. We also found that promoter-bound Rap1 activated HMLα when in an expressed state, and aided in the transition from transcription initiation to elongation. Highlighting the importance of epigenetic context in transcription factor function, these results point toward a model in which the duality of Rap1 function was mediated by local chromatin environment rather than binding-site availability.
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Affiliation(s)
- Eliana R. Bondra
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
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10
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Bondra ER, Rine J. Context dependent function of the transcriptional regulator Rap1 in gene silencing and activation in Saccharomyces cerevisiae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539937. [PMID: 37214837 PMCID: PMC10197613 DOI: 10.1101/2023.05.08.539937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In Saccharomyces cerevisiae, heterochromatin is formed through interactions between site-specific DNA-binding factors, including the transcriptional activator Rap1, and Sir proteins. Despite a vast understanding of the establishment and maintenance of Sir-silenced chromatin, the mechanism of gene silencing by Sir proteins has remained a mystery. Utilizing high resolution chromatin immunoprecipitation, we found that Rap1, the native activator of the bi-directional HML α promoter, bound its recognition sequence in silenced chromatin and its binding was enhanced by the presence of Sir proteins. In contrast to prior results, various components of transcription machinery were not able to access HML α in the silenced state. These findings disproved the long-standing model of indiscriminate steric occlusion by Sir proteins and led to investigation of the transcriptional activator Rap1 in Sir-silenced chromatin. Using a highly sensitive assay that monitors loss-of-silencing events, we identified a novel role for promoter-bound Rap1 in the maintenance of silent chromatin through interactions with the Sir complex. We also found that promoter-bound Rap1 activated HML α when in an expressed state, and aided in the transition from transcription initiation to elongation. Highlighting the importance of epigenetic context in transcription factor function, these results point toward a model in which the duality of Rap1 function was mediated by local chromatin environment rather than binding-site availability. Significance Statement The coarse partitioning of the genome into regions of active euchromatin and repressed heterochromatin is an important, and conserved, level gene expression regulation in eukaryotes. Repressor Activator Protein (Rap1) is a transcription factor that promotes the activation of genes when recruited to promoters, and aids in the establishment of heterochromatin through interactions with silencer elements. Here, we investigate the role of Rap1 when bound to a promoter in silent chromatin and dissect the context-specific epigenetic cues that regulate the dual properties of this transcription factor. Together, our data highlight the importance of protein-protein interactions and local chromatin state on transcription factor function.
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Affiliation(s)
- Eliana R Bondra
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, United States
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