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Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Wolberger C. Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch. Nucleic Acids Res 2024:gkae698. [PMID: 39149911 DOI: 10.1093/nar/gkae698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 07/15/2024] [Accepted: 08/01/2024] [Indexed: 08/17/2024] Open
Abstract
Monoubiquitination of histones H2B-K120 (H2BK120ub) and H2A-K119 (H2AK119ub) play opposing roles in regulating transcription and chromatin compaction. H2BK120ub is a hallmark of actively transcribed euchromatin, while H2AK119ub is highly enriched in transcriptionally repressed heterochromatin. Whereas H2BK120ub is known to stimulate the binding or activity of various chromatin-modifying enzymes, this post-translational modification (PTM) also interferes with the binding of several proteins to the nucleosome H2A/H2B acidic patch via an unknown mechanism. Here, we report cryoEM structures of an H2BK120ub nucleosome showing that ubiquitin adopts discrete positions that occlude the acidic patch. Molecular dynamics simulations show that ubiquitin remains stably positioned over this nucleosome region. By contrast, our cryoEM structures of H2AK119ub nucleosomes show ubiquitin adopting discrete positions that minimally occlude the acidic patch. Consistent with these observations, H2BK120ub, but not H2AK119ub, abrogates nucleosome interactions with acidic patch-binding proteins RCC1 and LANA, and single-domain antibodies specific to this region. Our results suggest a mechanism by which H2BK120ub serves as a gatekeeper to the acidic patch and point to distinct roles for histone H2AK119 and H2BK120 ubiquitination in regulating protein binding to nucleosomes.
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Affiliation(s)
- Chad W Hicks
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA
| | - Sanim Rahman
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA
| | - Susan L Gloor
- EpiCypher Inc., 6 Davis Drive, Suite 755, Durham, NC 27709, USA
| | - James K Fields
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA
| | | | - Anup Vaidya
- EpiCypher Inc., 6 Davis Drive, Suite 755, Durham, NC 27709, USA
| | - Keith E Maier
- EpiCypher Inc., 6 Davis Drive, Suite 755, Durham, NC 27709, USA
| | - Michael Morgan
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA
| | - Cynthia Wolberger
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA
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2
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Bi X. Hmo1: A versatile member of the high mobility group box family of chromosomal architecture proteins. World J Biol Chem 2024; 15:97938. [PMID: 39156122 PMCID: PMC11325855 DOI: 10.4331/wjbc.v15.i1.97938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/21/2024] [Accepted: 08/01/2024] [Indexed: 08/08/2024] Open
Abstract
Eukaryotic chromatin consisting of nucleosomes connected by linker DNA is organized into higher order structures, which is facilitated by linker histone H1. Formation of chromatin compacts and protects the genome, but also hinders DNA transactions. Cells have evolved mechanisms to modify/remodel chromatin resulting in chromatin states suitable for genome functions. The high mobility group box (HMGB) proteins are non-histone chromatin architectural factors characterized by one or more HMGB motifs that bind DNA in a sequence nonspecific fashion. They play a major role in chromatin dynamics. The Saccharomyces cerevisiae (yeast hereafter) HMGB protein Hmo1 contains two HMGB motifs. However, unlike a canonical HMGB protein that has an acidic C-terminus, Hmo1 ends with a lysine rich, basic, C-terminus, resembling linker histone H1. Hmo1 exhibits characteristics of both HMGB proteins and linker histones in its multiple functions. For instance, Hmo1 promotes transcription by RNA polymerases I and II like canonical HMGB proteins but makes chromatin more compact/stable like linker histones. Recent studies have demonstrated that Hmo1 destabilizes/disrupts nucleosome similarly as other HMGB proteins in vitro and acts to maintain a common topological architecture of genes in yeast genome. This minireview reviews the functions of Hmo1 and the underlying mechanisms, highlighting recent discoveries.
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Affiliation(s)
- Xin Bi
- Department of Biology, University of Rochester, Rochester, NY 14627, United States
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3
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Dabin J, Giacomini G, Petit E, Polo SE. New facets in the chromatin-based regulation of genome maintenance. DNA Repair (Amst) 2024; 140:103702. [PMID: 38878564 DOI: 10.1016/j.dnarep.2024.103702] [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: 04/09/2024] [Revised: 05/30/2024] [Accepted: 06/02/2024] [Indexed: 07/13/2024]
Abstract
The maintenance of genome integrity by DNA damage response machineries is key to protect cells against pathological development. In cell nuclei, these genome maintenance machineries operate in the context of chromatin, where the DNA wraps around histone proteins. Here, we review recent findings illustrating how the chromatin substrate modulates genome maintenance mechanisms, focusing on the regulatory role of histone variants and post-translational modifications. In particular, we discuss how the pre-existing chromatin landscape impacts DNA damage formation and guides DNA repair pathway choice, and how DNA damage-induced chromatin alterations control DNA damage signaling and repair, and DNA damage segregation through cell divisions. We also highlight that pathological alterations of histone proteins may trigger genome instability by impairing chromosome segregation and DNA repair, thus defining new oncogenic mechanisms and opening up therapeutic options.
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Affiliation(s)
- Juliette Dabin
- Epigenetics and Cell Fate Centre, UMR7216 CNRS Université Paris Cité, Paris, France
| | - Giulia Giacomini
- Epigenetics and Cell Fate Centre, UMR7216 CNRS Université Paris Cité, Paris, France
| | - Eliane Petit
- Epigenetics and Cell Fate Centre, UMR7216 CNRS Université Paris Cité, Paris, France
| | - Sophie E Polo
- Epigenetics and Cell Fate Centre, UMR7216 CNRS Université Paris Cité, Paris, France.
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4
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Park G, Patel AB, Wu C, Louder RK. Structures of H2A.Z-associated human chromatin remodelers SRCAP and TIP60 reveal divergent mechanisms of chromatin engagement. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.30.605802. [PMID: 39131301 PMCID: PMC11312561 DOI: 10.1101/2024.07.30.605802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
H2A.Z is a conserved histone variant that is localized to specific genomic regions where it plays important roles in transcription, DNA repair, and replication. Central to the biochemistry of human H2A.Z are the SRCAP and TIP60 chromatin remodelers, homologs of yeast SWR1 which catalyzes ATP-dependent H2A.Z exchange. Here, we use cryo-electron microscopy to resolve six structural states of the native SRCAP complex, uncovering conformational intermediates interpreted as a stepwise path to full nucleosome engagement. We also resolve the structure of the native TIP60 complex which consists of a structured core from which flexibly tethered chromatin binding domains emerge. Despite the shared subunit composition, the core of TIP60 displays divergent architectures from SRCAP that structurally disfavor nucleosome engagement, suggesting a distinct biochemical function.
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Affiliation(s)
- Giho Park
- Biochemistry, Cellular and Molecular Graduate Program, Johns Hopkins School of Medicine; Baltimore, MD 21205, USA
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine; Baltimore, MD 21205, USA
| | - Avinash B. Patel
- Department of Biophysics, Johns Hopkins University; Baltimore, MD 21218, USA
| | - Carl Wu
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine; Baltimore, MD 21205, USA
- Department of Biology, Johns Hopkins University; Baltimore, MD 21218, USA
| | - Robert K. Louder
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine; Baltimore, MD 21205, USA
- Department of Biology, Johns Hopkins University; Baltimore, MD 21218, USA
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5
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Khatun S, Prasad Bhagat R, Dutta R, Datta A, Jaiswal A, Halder S, Jha T, Amin SA, Gayen S. Unraveling HDAC11: Epigenetic orchestra in different diseases and structural insights for inhibitor design. Biochem Pharmacol 2024; 225:116312. [PMID: 38788962 DOI: 10.1016/j.bcp.2024.116312] [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: 02/05/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
Abstract
Histone deacetylase 11 (HDAC11), a member of the HDAC family, has emerged as a critical regulator in numerous physiological as well as pathological processes. Due to its diverse roles, HDAC11 has been a focal point of research in recent times. Different non-selective inhibitors are already approved, and research is going on to find selective HDAC11 inhibitors. The objective of this review is to comprehensively explore the role of HDAC11 as a pivotal regulator in a multitude of physiological and pathological processes. It aims to delve into the intricate details of HDAC11's structural and functional aspects, elucidating its molecular interactions and implications in different disease contexts. With a primary focus on elucidating the structure-activity relationships (SARs) of HDAC11 inhibitors, this review also aims to provide a holistic understanding of how its molecular architecture influences its inhibition. Additionally, by integrating both established knowledge and recent research, the review seeks to contribute novel insights into the potential therapeutic applications of HDAC11 inhibitors. Overall, the scope of this review spans from fundamental research elucidating the complexities of HDAC11 biology to the potential of targeting HDAC11 in therapeutic interventions.
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Affiliation(s)
- Samima Khatun
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, West Bengal, India
| | - Rinki Prasad Bhagat
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, West Bengal, India
| | - Ritam Dutta
- Department of Pharmaceutical Technology, JIS University, 81, Nilgunj Road, Agarpara, Kolkata 700109, West Bengal, India
| | - Anwesha Datta
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, West Bengal, India
| | - Abhishek Jaiswal
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, West Bengal, India
| | - Swapnamay Halder
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, West Bengal, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, West Bengal, India.
| | - Sk Abdul Amin
- Department of Pharmaceutical Technology, JIS University, 81, Nilgunj Road, Agarpara, Kolkata 700109, West Bengal, India.
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, West Bengal, India.
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6
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Funaya S, Takahashi Y, Suzuki MG, Suzuki Y, Aoki F. H3.1/3.2 regulate the initial progression of the gene expression program. Nucleic Acids Res 2024; 52:6158-6170. [PMID: 38567720 PMCID: PMC11194095 DOI: 10.1093/nar/gkae214] [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: 11/24/2023] [Revised: 02/07/2024] [Accepted: 03/13/2024] [Indexed: 06/25/2024] Open
Abstract
In mice, transcription from the zygotic genome is initiated at the mid-one-cell stage, and occurs promiscuously in many areas of the genome, including intergenic regions. Regulated transcription from selected genes is established during the two-cell stage. This dramatic change in the gene expression pattern marks the initiation of the gene expression program and is essential for early development. We investigated the involvement of the histone variants H3.1/3.2 in the regulation of changes in gene expression pattern during the two-cell stage. Immunocytochemistry analysis showed low nuclear deposition of H3.1/3.2 in the one-cell stage, followed by a rapid increase in the late two-cell stage. Where chromatin structure is normally closed between the one- and two-cell stages, it remained open until the late two-cell stage when H3.1/3.2 were knocked down by small interfering RNA. Hi-C analysis showed that the formation of the topologically associating domain was disrupted in H3.1/3.2 knockdown (KD) embryos. Promiscuous transcription was also maintained in the late two-cell stage in H3.1/3.2 KD embryos. These results demonstrate that H3.1/3.2 are involved in the initial process of the gene expression program after fertilization, through the formation of a closed chromatin structure to execute regulated gene expression during the two-cell stage.
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Affiliation(s)
- Satoshi Funaya
- Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
| | - Yusuke Takahashi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
| | - Masataka G Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
| | - Fugaku Aoki
- Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
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7
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Gillet N, Dumont E, Bignon E. DNA damage and repair in the nucleosome: insights from computational methods. Biophys Rev 2024; 16:345-356. [PMID: 39099841 PMCID: PMC11297232 DOI: 10.1007/s12551-024-01183-9] [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: 11/01/2023] [Accepted: 03/05/2024] [Indexed: 08/06/2024] Open
Abstract
Cellular DNA is constantly exposed to endogenous or exogenous factors that can induce lesions. Several types of lesions have been described that can result from UV/ionizing irradiations, oxidative stress, or free radicals, among others. In order to overcome the deleterious effects of such damages, i.e., mutagenicity or cytotoxicity, cells possess a highly complex DNA repair machinery, involving repair enzymes targeting specific types of lesions through dedicated cellular pathways. In addition, DNA is highly compacted in the nucleus, the first level of compaction consisting of ~ 147 DNA base pairs wrapped around a core of histones, the so-called nucleosome core particle. In this complex environment, the DNA structure is highly constrained, and fine-tuned mechanisms involving remodeling processes are required to expose the DNA to repair enzymes and to facilitate the damage removal. However, these nucleosome-specific mechanisms remain poorly understood, and computational methods emerged only recently as powerful tools to investigate DNA damages in such complex systems as the nucleosome. In this mini-review, we summarize the latest advances brought out by computational approaches in the field, opening new exciting perspectives for the study of DNA damage and repair in the nucleosome context.
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Affiliation(s)
- Natacha Gillet
- ENS de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, 69342 Lyon, France
| | - Elise Dumont
- Institut de Chimie de Nice, UMR 7272, Université Côte d’Azur, CNRS, 06108 Nice, France
- Institut Universitaire de France, 5 Rue Descartes, 75005 Paris, France
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8
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Alex K, Winkler EC. Comparative ethical evaluation of epigenome editing and genome editing in medicine: first steps and future directions. JOURNAL OF MEDICAL ETHICS 2024; 50:398-406. [PMID: 37527926 PMCID: PMC11137457 DOI: 10.1136/jme-2022-108888] [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: 01/02/2023] [Accepted: 07/17/2023] [Indexed: 08/03/2023]
Abstract
Targeted modifications of the human epigenome, epigenome editing (EE), are around the corner. For EE, techniques similar to genome editing (GE) techniques are used. While in GE the genetic information is changed by directly modifying DNA, intervening in the epigenome requires modifying the configuration of DNA, for example, how it is folded. This does not come with alterations in the base sequence ('genetic code'). To date, there is almost no ethical debate about EE, whereas the discussions about GE are voluminous. Our article introduces EE into bioethics by translating knowledge from science to ethics and by comparing the risks of EE with those of GE. We, first (I), make the case that a broader ethical debate on EE is due, provide scientific background on EE, compile potential use-cases and recap previous debates. We then (II) compare EE and GE and suggest that the severity of risks of novel gene technologies depends on three factors: (i) the choice of an ex vivo versus an in vivo editing approach, (ii) the time of intervention and intervention windows and (iii) the targeted diseases. Moreover, we show why germline EE is not effective and reject the position of strong epigenetic determinism. We conclude that EE is not always ethically preferable to GE in terms of risks, and end with suggestions for next steps in the current ethical debate on EE by briefly introducing ethical challenges of new areas of preventive applications of EE (III).
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Affiliation(s)
- Karla Alex
- Section Translational Medical Ethics, Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
| | - Eva C Winkler
- Section Translational Medical Ethics, Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Medical Faculty, Heidelberg University, Heidelberg, Germany
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9
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Shaban HA, Friman ET, Deluz C, Tollenaere A, Katanayeva N, Suter DM. Individual transcription factors modulate both the micromovement of chromatin and its long-range structure. Proc Natl Acad Sci U S A 2024; 121:e2311374121. [PMID: 38648478 PMCID: PMC11067044 DOI: 10.1073/pnas.2311374121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 03/13/2024] [Indexed: 04/25/2024] Open
Abstract
The control of eukaryotic gene expression is intimately connected to highly dynamic chromatin structures. Gene regulation relies on activator and repressor transcription factors (TFs) that induce local chromatin opening and closing. However, it is unclear how nucleus-wide chromatin organization responds dynamically to the activity of specific TFs. Here, we examined how two TFs with opposite effects on local chromatin accessibility modulate chromatin dynamics nucleus-wide. We combine high-resolution diffusion mapping and dense flow reconstruction and correlation in living cells to obtain an imaging-based, nanometer-scale analysis of local diffusion processes and long-range coordinated movements of both chromatin and TFs. We show that the expression of either an individual transcriptional activator (CDX2) or repressor (SIX6) with large numbers of binding sites increases chromatin mobility nucleus-wide, yet they induce opposite coherent chromatin motions at the micron scale. Hi-C analysis of higher-order chromatin structures shows that induction of the pioneer factor CDX2 leads both to changes in local chromatin interactions and the distribution of A and B compartments, thus relating the micromovement of chromatin with changes in compartmental structures. Given that inhibition of transcription initiation and elongation by RNA Pol II has a partial impact on the global chromatin dynamics induced by CDX2, we suggest that CDX2 overexpression alters chromatin structure dynamics both dependently and independently of transcription. Our biophysical analysis shows that sequence-specific TFs can influence chromatin structure on multiple architectural levels, arguing that local chromatin changes brought by TFs alter long-range chromatin mobility and its organization.
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Affiliation(s)
- Haitham A. Shaban
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
- Spectroscopy Department, Institute of Physics Research, National Research Centre, Cairo12622, Egypt
| | - Elias T. Friman
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, United Kingdom
| | - Cédric Deluz
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - Armelle Tollenaere
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - Natalya Katanayeva
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - David M. Suter
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
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10
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Navarro-Carrasco E, Monte-Serrano E, Campos-Díaz A, Rolfs F, de Goeij-de Haas R, Pham TV, Piersma SR, González-Alonso P, Jiménez CR, Lazo PA. VRK1 Regulates Sensitivity to Oxidative Stress by Altering Histone Epigenetic Modifications and the Nuclear Phosphoproteome in Tumor Cells. Int J Mol Sci 2024; 25:4874. [PMID: 38732093 PMCID: PMC11084957 DOI: 10.3390/ijms25094874] [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: 03/21/2024] [Revised: 04/24/2024] [Accepted: 04/27/2024] [Indexed: 05/13/2024] Open
Abstract
The chromatin organization and its dynamic remodeling determine its accessibility and sensitivity to DNA damage oxidative stress, the main source of endogenous DNA damage. We studied the role of the VRK1 chromatin kinase in the response to oxidative stress. which alters the nuclear pattern of histone epigenetic modifications and phosphoproteome pathways. The early effect of oxidative stress on chromatin was studied by determining the levels of 8-oxoG lesions and the alteration of the epigenetic modification of histones. Oxidative stress caused an accumulation of 8-oxoG DNA lesions that were increased by VRK1 depletion, causing a significant accumulation of DNA strand breaks detected by labeling free 3'-DNA ends. In addition, oxidative stress altered the pattern of chromatin epigenetic marks and the nuclear phosphoproteome pathways that were impaired by VRK1 depletion. Oxidative stress induced the acetylation of H4K16ac and H3K9 and the loss of H3K4me3. The depletion of VRK1 altered all these modifications induced by oxidative stress and resulted in losses of H4K16ac and H3K9ac and increases in the H3K9me3 and H3K4me3 levels. All these changes were induced by the oxidative stress in the epigenetic pattern of histones and impaired by VRK1 depletion, indicating that VRK1 plays a major role in the functional reorganization of chromatin in the response to oxidative stress. The analysis of the nuclear phosphoproteome in response to oxidative stress detected an enrichment of the phosphorylated proteins associated with the chromosome organization and chromatin remodeling pathways, which were significantly decreased by VRK1 depletion. VRK1 depletion alters the histone epigenetic pattern and nuclear phosphoproteome pathways in response to oxidative stress. The enzymes performing post-translational epigenetic modifications are potential targets in synthetic lethality strategies for cancer therapies.
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Affiliation(s)
- Elena Navarro-Carrasco
- Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, E-37007 Salamanca, Spain; (E.N.-C.); (E.M.-S.); (A.C.-D.); (P.G.-A.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, E-37007 Salamanca, Spain
| | - Eva Monte-Serrano
- Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, E-37007 Salamanca, Spain; (E.N.-C.); (E.M.-S.); (A.C.-D.); (P.G.-A.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, E-37007 Salamanca, Spain
| | - Aurora Campos-Díaz
- Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, E-37007 Salamanca, Spain; (E.N.-C.); (E.M.-S.); (A.C.-D.); (P.G.-A.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, E-37007 Salamanca, Spain
| | - Frank Rolfs
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (F.R.); (R.d.G.-d.H.); (T.V.P.); (S.R.P.); (C.R.J.)
| | - Richard de Goeij-de Haas
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (F.R.); (R.d.G.-d.H.); (T.V.P.); (S.R.P.); (C.R.J.)
| | - Thang V. Pham
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (F.R.); (R.d.G.-d.H.); (T.V.P.); (S.R.P.); (C.R.J.)
| | - Sander R. Piersma
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (F.R.); (R.d.G.-d.H.); (T.V.P.); (S.R.P.); (C.R.J.)
| | - Paula González-Alonso
- Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, E-37007 Salamanca, Spain; (E.N.-C.); (E.M.-S.); (A.C.-D.); (P.G.-A.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, E-37007 Salamanca, Spain
| | - Connie R. Jiménez
- OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands; (F.R.); (R.d.G.-d.H.); (T.V.P.); (S.R.P.); (C.R.J.)
| | - Pedro A. Lazo
- Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, E-37007 Salamanca, Spain; (E.N.-C.); (E.M.-S.); (A.C.-D.); (P.G.-A.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, E-37007 Salamanca, Spain
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11
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Bao K, Ma Y, Li Y, Shen X, Zhao J, Tian S, Zhang C, Liang C, Zhao Z, Yang Y, Zhang K, Yang N, Meng FL, Hao J, Yang J, Liu T, Yao Z, Ai D, Shi L. A di-acetyl-decorated chromatin signature couples liquid condensation to suppress DNA end synapsis. Mol Cell 2024; 84:1206-1223.e15. [PMID: 38423014 DOI: 10.1016/j.molcel.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/27/2023] [Accepted: 02/02/2024] [Indexed: 03/02/2024]
Abstract
Appropriate DNA end synapsis, regulated by core components of the synaptic complex including KU70-KU80, LIG4, XRCC4, and XLF, is central to non-homologous end joining (NHEJ) repair of chromatinized DNA double-strand breaks (DSBs). However, it remains enigmatic whether chromatin modifications can influence the formation of NHEJ synaptic complex at DNA ends, and if so, how this is achieved. Here, we report that the mitotic deacetylase complex (MiDAC) serves as a key regulator of DNA end synapsis during NHEJ repair in mammalian cells. Mechanistically, MiDAC removes combinatorial acetyl marks on histone H2A (H2AK5acK9ac) around DSB-proximal chromatin, suppressing hyperaccumulation of bromodomain-containing protein BRD4 that would otherwise undergo liquid-liquid phase separation with KU80 and prevent the proper installation of LIG4-XRCC4-XLF onto DSB ends. This study provides mechanistic insight into the control of NHEJ synaptic complex assembly by a specific chromatin signature and highlights the critical role of H2A hypoacetylation in restraining unscheduled compartmentalization of DNA repair machinery.
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Affiliation(s)
- Kaiwen Bao
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Yanhui Ma
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Yuan Li
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xilin Shen
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Jiao Zhao
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Shanshan Tian
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Chunyong Zhang
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Can Liang
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Ziyan Zhao
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Ying Yang
- Core Facilities Center, Capital Medical University, Beijing, China
| | - Kai Zhang
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Na Yang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin, China
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Jihui Hao
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Jie Yang
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Zhi Yao
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Ding Ai
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.
| | - Lei Shi
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.
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12
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Galanti L, Peritore M, Gnügge R, Cannavo E, Heipke J, Palumbieri MD, Steigenberger B, Symington LS, Cejka P, Pfander B. Dbf4-dependent kinase promotes cell cycle controlled resection of DNA double-strand breaks and repair by homologous recombination. Nat Commun 2024; 15:2890. [PMID: 38570537 PMCID: PMC10991553 DOI: 10.1038/s41467-024-46951-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 03/13/2024] [Indexed: 04/05/2024] Open
Abstract
DNA double-strand breaks (DSBs) can be repaired by several pathways. In eukaryotes, DSB repair pathway choice occurs at the level of DNA end resection and is controlled by the cell cycle. Upon cell cycle-dependent activation, cyclin-dependent kinases (CDKs) phosphorylate resection proteins and thereby stimulate end resection and repair by homologous recombination (HR). However, inability of CDK phospho-mimetic mutants to bypass this cell cycle regulation, suggests that additional cell cycle regulators may be important. Here, we identify Dbf4-dependent kinase (DDK) as a second major cell cycle regulator of DNA end resection. Using inducible genetic and chemical inhibition of DDK in budding yeast and human cells, we show that end resection and HR require activation by DDK. Mechanistically, DDK phosphorylates at least two resection nucleases in budding yeast: the Mre11 activator Sae2, which promotes resection initiation, as well as the Dna2 nuclease, which promotes resection elongation. Notably, synthetic activation of DDK allows limited resection and HR in G1 cells, suggesting that DDK is a key component of DSB repair pathway selection.
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Affiliation(s)
- Lorenzo Galanti
- Cell Biology, Dortmund Life Science Center (DOLCE), TU Dortmund University, Faculty of Chemistry and Chemical Biology, Dortmund, Germany
- Research Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Institute for Genome Stability in Aging and Disease, University of Cologne, Medical Faculty, CECAD Research Center, Cologne, Germany
| | - Martina Peritore
- Research Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Institute for Genome Stability in Aging and Disease, University of Cologne, Medical Faculty, CECAD Research Center, Cologne, Germany
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Robert Gnügge
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Elda Cannavo
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana (USI), Bellinzona, Switzerland
| | - Johannes Heipke
- Cell Biology, Dortmund Life Science Center (DOLCE), TU Dortmund University, Faculty of Chemistry and Chemical Biology, Dortmund, Germany
- Research Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
- Institute for Genome Stability in Aging and Disease, University of Cologne, Medical Faculty, CECAD Research Center, Cologne, Germany
| | - Maria Dilia Palumbieri
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Institute for Genome Stability in Aging and Disease, University of Cologne, Medical Faculty, CECAD Research Center, Cologne, Germany
- Research Group of Proteomics and ADP-Ribosylation Signaling, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Barbara Steigenberger
- Mass Spectrometry Core Facility, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lorraine S Symington
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Petr Cejka
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera Italiana (USI), Bellinzona, Switzerland
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland
| | - Boris Pfander
- Cell Biology, Dortmund Life Science Center (DOLCE), TU Dortmund University, Faculty of Chemistry and Chemical Biology, Dortmund, Germany.
- Research Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany.
- Institute for Genome Stability in Aging and Disease, University of Cologne, Medical Faculty, CECAD Research Center, Cologne, Germany.
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13
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Eustermann S, Patel AB, Hopfner KP, He Y, Korber P. Energy-driven genome regulation by ATP-dependent chromatin remodellers. Nat Rev Mol Cell Biol 2024; 25:309-332. [PMID: 38081975 DOI: 10.1038/s41580-023-00683-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2023] [Indexed: 03/28/2024]
Abstract
The packaging of DNA into chromatin in eukaryotes regulates gene transcription, DNA replication and DNA repair. ATP-dependent chromatin remodelling enzymes (re)arrange nucleosomes at the first level of chromatin organization. Their Snf2-type motor ATPases alter histone-DNA interactions through a common DNA translocation mechanism. Whether remodeller activities mainly catalyse nucleosome dynamics or accurately co-determine nucleosome organization remained unclear. In this Review, we discuss the emerging mechanisms of chromatin remodelling: dynamic remodeller architectures and their interactions, the inner workings of the ATPase cycle, allosteric regulation and pathological dysregulation. Recent mechanistic insights argue for a decisive role of remodellers in the energy-driven self-organization of chromatin, which enables both stability and plasticity of genome regulation - for example, during development and stress. Different remodellers, such as members of the SWI/SNF, ISWI, CHD and INO80 families, process (epi)genetic information through specific mechanisms into distinct functional outputs. Combinatorial assembly of remodellers and their interplay with histone modifications, histone variants, DNA sequence or DNA-bound transcription factors regulate nucleosome mobilization or eviction or histone exchange. Such input-output relationships determine specific nucleosome positions and compositions with distinct DNA accessibilities and mediate differential genome regulation. Finally, remodeller genes are often mutated in diseases characterized by genome dysregulation, notably in cancer, and we discuss their physiological relevance.
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Affiliation(s)
- Sebastian Eustermann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Avinash B Patel
- Department of Molecular Biosciences, Robert H. Lurie Comprehensive Cancer Center, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Karl-Peter Hopfner
- Gene Center and Department of Biochemistry, Faculty of Chemistry and Pharmacy, LMU Munich, Munich, Germany
| | - Yuan He
- Department of Molecular Biosciences, Robert H. Lurie Comprehensive Cancer Center, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.
| | - Philipp Korber
- Biomedical Center (BMC), Molecular Biology, Faculty of Medicine, LMU Munich, Martinsried, Germany.
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14
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Zhu Z, Li S, Yin X, Sun K, Song J, Ren W, Gao L, Zhi K. Review: Protein O-GlcNAcylation regulates DNA damage response: A novel target for cancer therapy. Int J Biol Macromol 2024; 264:130351. [PMID: 38403231 DOI: 10.1016/j.ijbiomac.2024.130351] [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: 01/07/2024] [Revised: 02/02/2024] [Accepted: 02/19/2024] [Indexed: 02/27/2024]
Abstract
The DNA damage response (DDR) safeguards the stable genetic information inheritance by orchestrating a complex protein network in response to DNA damage. However, this mechanism can often hamper the effectiveness of radiotherapy and DNA-damaging chemotherapy in destroying tumor cells, causing cancer resistance. Inhibiting DDR can significantly improve tumor cell sensitivity to radiotherapy and DNA-damaging chemotherapy. Thus, DDR can be a potential target for cancer treatment. Post-translational modifications (PTMs) of DDR-associated proteins profoundly affect their activity and function by covalently attaching new functional groups. O-GlcNAcylation (O-linked-N-acetylglucosaminylation) is an emerging PTM associated with adding and removing O-linked N-acetylglucosamine to serine and threonine residues of proteins. It acts as a dual sensor for nutrients and stress in the cell and is sensitive to DNA damage. However, the explanation behind the specific role of O-GlcNAcylation in the DDR remains remains to be elucidated. To illustrate the complex relationship between O-GlcNAcylation and DDR, this review systematically describes the role of O-GlcNAcylation in DNA repair, cell cycle, and chromatin. We also discuss the defects of current strategies for targeting O-GlcNAcylation-regulated DDR in cancer therapy and suggest potential directions to address them.
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Affiliation(s)
- Zhuang Zhu
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Shaoming Li
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Xiaopeng Yin
- Department of Oral and Maxillofacial Surgery, Central Laboratory of Jinan Stamotological Hospital, Jinan Key Laboratory of Oral Tissue Regeneration, Jinan 250001, Shandong Province, China
| | - Kai Sun
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Jianzhong Song
- Department of Oral and Maxilloafacial Surgery, People's Hospital of Rizhao, Rizhao, Shandong, China
| | - Wenhao Ren
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
| | - Ling Gao
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Key Lab of Oral Clinical Medicine, the Affiliated Hospital of Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
| | - Keqian Zhi
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Key Lab of Oral Clinical Medicine, the Affiliated Hospital of Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
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15
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Roy S, Adhikary H, D’Amours D. The SMC5/6 complex: folding chromosomes back into shape when genomes take a break. Nucleic Acids Res 2024; 52:2112-2129. [PMID: 38375830 PMCID: PMC10954462 DOI: 10.1093/nar/gkae103] [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: 11/13/2023] [Revised: 01/28/2024] [Accepted: 02/01/2024] [Indexed: 02/21/2024] Open
Abstract
High-level folding of chromatin is a key determinant of the shape and functional state of chromosomes. During cell division, structural maintenance of chromosome (SMC) complexes such as condensin and cohesin ensure large-scale folding of chromatin into visible chromosomes. In contrast, the SMC5/6 complex plays more local and context-specific roles in the structural organization of interphase chromosomes with important implications for health and disease. Recent advances in single-molecule biophysics and cryo-electron microscopy revealed key insights into the architecture of the SMC5/6 complex and how interactions connecting the complex to chromatin components give rise to its unique repertoire of interphase functions. In this review, we provide an integrative view of the features that differentiates the SMC5/6 complex from other SMC enzymes and how these enable dramatic reorganization of DNA folding in space during DNA repair reactions and other genome transactions. Finally, we explore the mechanistic basis for the dynamic targeting of the SMC5/6 complex to damaged chromatin and its crucial role in human health.
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Affiliation(s)
- Shamayita Roy
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Roger Guindon Hall, 451 Smyth Rd, Ottawa, ON K1H 8M5, Canada
| | - Hemanta Adhikary
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Roger Guindon Hall, 451 Smyth Rd, Ottawa, ON K1H 8M5, Canada
| | - Damien D’Amours
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Roger Guindon Hall, 451 Smyth Rd, Ottawa, ON K1H 8M5, Canada
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16
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Wang H, Wang Y, Zhang D, Li P. Circulating nucleosomes as potential biomarkers for cancer diagnosis and treatment monitoring. Int J Biol Macromol 2024; 262:130005. [PMID: 38331061 DOI: 10.1016/j.ijbiomac.2024.130005] [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: 11/29/2023] [Revised: 01/03/2024] [Accepted: 02/04/2024] [Indexed: 02/10/2024]
Abstract
Nucleosomes play a crucial role in regulating gene expression through their composition and post-translational modifications. When cells die, intracellular endonucleases are activated and cleave chromatin into oligo- and mono-nucleosomes, which are then released into the body fluids. Studies have shown that the levels of nucleosomes are increased in serum and plasma in various cancer types, suggesting that analysis of circulating nucleosomes can provide an initial assessment of carcinogenesis. However, it should be noted that elevated serum nucleosome levels may not accurately diagnose certain tumor types, as increased cell death may occur in different pathological conditions. Nevertheless, detection of circulating nucleosomes and their histone modifications, along with specific tumor markers, can help diagnose certain types of cancer. Furthermore, monitoring changes in circulating nucleosome levels during chemotherapy or radiotherapy in patients with malignancies can provide valuable insights into clinical outcomes and therapeutic efficacy. The utilization of circulating nucleosomes as biomarkers is an exciting and emerging area of research, with the potential for early detection of various diseases and monitoring of treatment response. Integrating nucleosome-based biomarkers with existing ones may improve the specificity and sensitivity of current assays, offering the possibility of personalized precision medical treatment for patients.
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Affiliation(s)
- Huawei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
| | - Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
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17
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Dong Y, Du J, Deng Y, Cheng M, Shi Z, Zhu H, Sun H, Yu Q, Li M. Reduction of histone proteins dosages increases CFW sensitivity and attenuates virulence of Candida albicans. Microbiol Res 2024; 279:127552. [PMID: 38000336 DOI: 10.1016/j.micres.2023.127552] [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: 08/31/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023]
Abstract
Histone proteins are important components of nucleosomes, which play an important role in regulating the accessibility of DNA and the function of genomes. However, the effect of histone proteins dosages on physiological processes is not clear in the human fungal pathogen Candida albicans. In this study, we found that the deletion of the histone protein H3 coding gene HHT21 and the histone protein H4 coding gene HHF1 resulted in a significant decrease in the expression dosage of the histone proteins H3 and H4, which had a significant impact on the localization of the histone protein H2A and plasmid maintenance. Stress sensitivity experiments showed that the mutants hht21Δ/Δ, hhf1Δ/Δ and hht21Δ/Δhhf1Δ/Δ were more sensitive to cell wall stress induced by Calcofluor White (CFW) than the wild-type strain. Further studies showed that the decrease in the dosage of the histone proteins H3 and H4 led to the change of cell wall components, increased chitin contents, and down-regulated expression of the SAP9, KAR2, and CRH11 genes involved in the cell wall integrity (CWI) pathway. Overexpression of SAP9 could rescue the sensitivity of the mutants to CFW. Moreover, the decrease in the histone protein s dosages affected the FAD-catalyzed oxidation of Ero1 protein, resulting in the obstruction of protein folding in the ER, and thus reduced resistance to CFW. It was also found that CFW induced a large amount of ROS accumulation in the mutants, and the addition of ROS scavengers could restore the growth of the mutants under CFW treatment. In addition, the reduction of the histone proteins dosages greatly weakened systemic infection and kidney fungal burden in mice, and hyphal development was significantly impaired in the mutants under macrophage treatment, indicating that the histone proteins dosages is very important for the virulence of C. albicans. This study revealed that histone proteins dosages play a key role in the cell wall stress response and pathogenicity in C. albicans.
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Affiliation(s)
- Yixuan Dong
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jiawen Du
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Ying Deng
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Mengjuan Cheng
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhishang Shi
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Hangqi Zhu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Hao Sun
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Qilin Yu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Mingchun Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China.
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18
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Leem J, Lee C, Choi DY, Oh JS. Distinct characteristics of the DNA damage response in mammalian oocytes. Exp Mol Med 2024; 56:319-328. [PMID: 38355825 PMCID: PMC10907590 DOI: 10.1038/s12276-024-01178-2] [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: 08/20/2023] [Revised: 11/15/2023] [Accepted: 12/07/2023] [Indexed: 02/16/2024] Open
Abstract
DNA damage is a critical threat that poses significant challenges to all cells. To address this issue, cells have evolved a sophisticated molecular and cellular process known as the DNA damage response (DDR). Among the various cell types, mammalian oocytes, which remain dormant in the ovary for extended periods, are particularly susceptible to DNA damage. The occurrence of DNA damage in oocytes can result in genetic abnormalities, potentially leading to infertility, birth defects, and even abortion. Therefore, understanding how oocytes detect and repair DNA damage is of paramount importance in maintaining oocyte quality and preserving fertility. Although the fundamental concept of the DDR is conserved across various cell types, an emerging body of evidence reveals striking distinctions in the DDR between mammalian oocytes and somatic cells. In this review, we highlight the distinctive characteristics of the DDR in oocytes and discuss the clinical implications of DNA damage in oocytes.
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Affiliation(s)
- Jiyeon Leem
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Crystal Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Da Yi Choi
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Jeong Su Oh
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea.
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19
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Thomson G, Dickinson L, Jacob Y. Genomic consequences associated with Agrobacterium-mediated transformation of plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:342-363. [PMID: 37831618 PMCID: PMC10841553 DOI: 10.1111/tpj.16496] [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: 08/11/2023] [Revised: 09/22/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023]
Abstract
Attenuated strains of the naturally occurring plant pathogen Agrobacterium tumefaciens can transfer virtually any DNA sequence of interest to model plants and crops. This has made Agrobacterium-mediated transformation (AMT) one of the most commonly used tools in agricultural biotechnology. Understanding AMT, and its functional consequences, is of fundamental importance given that it sits at the intersection of many fundamental fields of study, including plant-microbe interactions, DNA repair/genome stability, and epigenetic regulation of gene expression. Despite extensive research and use of AMT over the last 40 years, the extent of genomic disruption associated with integrating exogenous DNA into plant genomes using this method remains underappreciated. However, new technologies like long-read sequencing make this disruption more apparent, complementing previous findings from multiple research groups that have tackled this question in the past. In this review, we cover progress on the molecular mechanisms involved in Agrobacterium-mediated DNA integration into plant genomes. We also discuss localized mutations at the site of insertion and describe the structure of these DNA insertions, which can range from single copy insertions to large concatemers, consisting of complex DNA originating from different sources. Finally, we discuss the prevalence of large-scale genomic rearrangements associated with the integration of DNA during AMT with examples. Understanding the intended and unintended effects of AMT on genome stability is critical to all plant researchers who use this methodology to generate new genetic variants.
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Affiliation(s)
- Geoffrey Thomson
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; New Haven, Connecticut 06511, USA
| | - Lauren Dickinson
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; New Haven, Connecticut 06511, USA
| | - Yannick Jacob
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; New Haven, Connecticut 06511, USA
- Yale Cancer Center, Yale School of Medicine; New Haven, Connecticut 06511, USA
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20
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Zamalloa LG, Pruitt MM, Hermance NM, Gali H, Flynn RL, Manning AL. RB loss sensitizes cells to replication-associated DNA damage after PARP inhibition by trapping. Life Sci Alliance 2023; 6:e202302067. [PMID: 37704395 PMCID: PMC10500056 DOI: 10.26508/lsa.202302067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 09/05/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023] Open
Abstract
The retinoblastoma tumor suppressor protein (RB) interacts physically and functionally with a number of epigenetic modifying enzymes to control transcriptional regulation, respond to replication stress, promote DNA damage response and repair, and regulate genome stability. To better understand how disruption of RB function impacts epigenetic regulation of genome stability and determine whether such changes represent exploitable weaknesses of RB-deficient cancer cells, we performed an imaging-based screen to identify epigenetic inhibitors that promote DNA damage and compromise the viability of RB-deficient cells. We found that loss of RB alone leads to high levels of replication-dependent poly-ADP ribosylation (PARylation) and that preventing PARylation by trapping PARP enzymes on chromatin enables RB-deficient cells to progress to mitosis with unresolved replication stress. These defects contribute to high levels of DNA damage and compromised cell viability. We demonstrate this sensitivity is conserved across a panel of drugs that target both PARP1 and PARP2 and can be suppressed by reexpression of the RB protein. Together, these data indicate that drugs that target PARP1 and PARP2 may be clinically relevant for RB-deficient cancers.
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Affiliation(s)
- Luis Gregory Zamalloa
- https://ror.org/05ejpqr48 Worcester Polytechnic Institute, Department of Biology and Biotechnology, Worcester, MA, USA
| | - Margaret M Pruitt
- https://ror.org/05ejpqr48 Worcester Polytechnic Institute, Department of Biology and Biotechnology, Worcester, MA, USA
| | - Nicole M Hermance
- https://ror.org/05ejpqr48 Worcester Polytechnic Institute, Department of Biology and Biotechnology, Worcester, MA, USA
| | - Himabindu Gali
- Boston University School of Medicine, Pharmacology, Boston, MA, USA
| | - Rachel L Flynn
- Boston University School of Medicine, Pharmacology, Boston, MA, USA
| | - Amity L Manning
- https://ror.org/05ejpqr48 Worcester Polytechnic Institute, Department of Biology and Biotechnology, Worcester, MA, USA
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21
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Melnikova L, Golovnin A. Multiple Roles of dXNP and dADD1- Drosophila Orthologs of ATRX Chromatin Remodeler. Int J Mol Sci 2023; 24:16486. [PMID: 38003676 PMCID: PMC10671109 DOI: 10.3390/ijms242216486] [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: 10/09/2023] [Revised: 11/11/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023] Open
Abstract
The Drosophila melanogaster dADD1 and dXNP proteins are orthologues of the ADD and SNF2 domains of the vertebrate ATRX (Alpha-Thalassemia with mental Retardation X-related) protein. ATRX plays a role in general molecular processes, such as regulating chromatin status and gene expression, while dADD1 and dXNP have similar functions in the Drosophila genome. Both ATRX and dADD1/dXNP interact with various protein partners and participate in various regulatory complexes. Disruption of ATRX expression in humans leads to the development of α-thalassemia and cancer, especially glioma. However, the mechanisms that allow ATRX to regulate various cellular processes are poorly understood. Studying the functioning of dADD1/dXNP in the Drosophila model may contribute to understanding the mechanisms underlying the multifunctional action of ATRX and its connection with various cellular processes. This review provides a brief overview of the currently available information in mammals and Drosophila regarding the roles of ATRX, dXNP, and dADD1. It discusses possible mechanisms of action of complexes involving these proteins.
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Affiliation(s)
- Larisa Melnikova
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
| | - Anton Golovnin
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
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22
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Vasquez PA, Walker B, Bloom K, Kolbin D, Caughman N, Freeman R, Lysy M, Hult C, Newhall KA, Papanikolas M, Edelmaier C, Forest MG. The power of weak, transient interactions across biology: A paradigm of emergent behavior. PHYSICA D. NONLINEAR PHENOMENA 2023; 454:133866. [PMID: 38274029 PMCID: PMC10806540 DOI: 10.1016/j.physd.2023.133866] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
A growing list of diverse biological systems and their equally diverse functionalities provides realizations of a paradigm of emergent behavior. In each of these biological systems, pervasive ensembles of weak, short-lived, spatially local interactions act autonomously to convey functionalities at larger spatial and temporal scales. In this article, a range of diverse systems and functionalities are presented in a cursory manner with literature citations for further details. Then two systems and their properties are discussed in more detail: yeast chromosome biology and human respiratory mucus.
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Affiliation(s)
- Paula A. Vasquez
- Department of Mathematics, University of South Carolina, United States of America
| | - Ben Walker
- Department of Mathematics, University of California at Irvine, United States of America
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, United States of America
| | - Daniel Kolbin
- Department of Biology, University of North Carolina at Chapel Hill, United States of America
| | - Neall Caughman
- Department of Mathematics, University of North Carolina at Chapel Hill, United States of America
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, United States of America
| | - Martin Lysy
- Department of Statistics and Actuarial Science, University of Waterloo, Canada
| | - Caitlin Hult
- Department of Mathematics, Gettysburg College, United States of America
| | - Katherine A. Newhall
- Department of Mathematics, University of North Carolina at Chapel Hill, United States of America
| | - Micah Papanikolas
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, United States of America
| | - Christopher Edelmaier
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, United States of America
- Center for Computational Biology, Flatiron Institute, United States of America
| | - M. Gregory Forest
- Department of Mathematics, University of North Carolina at Chapel Hill, United States of America
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, United States of America
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23
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Wang R, Sun Y, Li C, Xue Y, Ba X. Targeting the DNA Damage Response for Cancer Therapy. Int J Mol Sci 2023; 24:15907. [PMID: 37958890 PMCID: PMC10648182 DOI: 10.3390/ijms242115907] [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: 09/21/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023] Open
Abstract
Over the course of long-term evolution, cells have developed intricate defense mechanisms in response to DNA damage; these mechanisms play a pivotal role in maintaining genomic stability. Defects in the DNA damage response pathways can give rise to various diseases, including cancer. The DNA damage response (DDR) system is instrumental in safeguarding genomic stability. The accumulation of DNA damage and the weakening of DDR function both promote the initiation and progression of tumors. Simultaneously, they offer opportunities and targets for cancer therapeutics. This article primarily elucidates the DNA damage repair pathways and the progress made in targeting key proteins within these pathways for cancer treatment. Among them, poly (ADP-ribose) polymerase 1 (PARP1) plays a crucial role in DDR, and inhibitors targeting PARP1 have garnered extensive attention in anticancer research. By delving into the realms of DNA damage and repair, we aspire to explore more precise and effective strategies for cancer therapy and to seek novel avenues for intervention.
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Affiliation(s)
- Ruoxi Wang
- Center for Cell Structure and Function, Key Laboratory of Animal Resistance Biology of Shandong Province, College of Life Sciences, Shandong Normal University, Jinan 250014, China; (R.W.); (Y.S.)
| | - Yating Sun
- Center for Cell Structure and Function, Key Laboratory of Animal Resistance Biology of Shandong Province, College of Life Sciences, Shandong Normal University, Jinan 250014, China; (R.W.); (Y.S.)
| | - Chunshuang Li
- Key Laboratory of Molecular Epigenetics of Ministry of Education, College of Life Sciences, Northeast Normal University, Changchun 130024, China; (C.L.); (Y.X.)
| | - Yaoyao Xue
- Key Laboratory of Molecular Epigenetics of Ministry of Education, College of Life Sciences, Northeast Normal University, Changchun 130024, China; (C.L.); (Y.X.)
| | - Xueqing Ba
- Key Laboratory of Molecular Epigenetics of Ministry of Education, College of Life Sciences, Northeast Normal University, Changchun 130024, China; (C.L.); (Y.X.)
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24
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Gasser SM, Stutz F. SUMO in the regulation of DNA repair and transcription at nuclear pores. FEBS Lett 2023; 597:2833-2850. [PMID: 37805446 DOI: 10.1002/1873-3468.14751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/06/2023] [Accepted: 09/25/2023] [Indexed: 10/09/2023]
Abstract
Two related post-translational modifications, the covalent linkage of Ubiquitin and the Small Ubiquitin-related MOdifier (SUMO) to lysine residues, play key roles in the regulation of both DNA repair pathway choice and transcription. Whereas ubiquitination is generally associated with proteasome-mediated protein degradation, the impact of sumoylation has been more mysterious. In the cell nucleus, sumoylation effects are largely mediated by the relocalization of the modified targets, particularly in response to DNA damage. This is governed in part by the concentration of SUMO protease at nuclear pores [Melchior, F et al. (2003) Trends Biochem Sci 28, 612-618; Ptak, C and Wozniak, RW (2017) Adv Exp Med Biol 963, 111-126]. We review here the roles of sumoylation in determining genomic locus positioning relative to the nuclear envelope and to nuclear pores, to facilitate repair and regulate transcription.
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Affiliation(s)
- Susan M Gasser
- Department of Fundamental Microbiology, University of Lausanne, Switzerland
- ISREC Foundation, Agora Cancer Research Center, Lausanne, Switzerland
| | - Françoise Stutz
- Department of Molecular and Cellular Biology, University of Geneva, Switzerland
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25
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Murphy PJ, Berger F. The chromatin source-sink hypothesis: a shared mode of chromatin-mediated regulations. Development 2023; 150:dev201989. [PMID: 38771301 PMCID: PMC10629678 DOI: 10.1242/dev.201989] [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: 05/13/2023] [Accepted: 09/12/2023] [Indexed: 11/05/2023]
Abstract
We propose that several chromatin-mediated regulatory processes are dominated by source-sink relationships in which factors operate as 'sources' to produce or provide a resource and compete with each other to occupy separate 'sinks'. In this model, large portions of genomic DNA operate as 'sinks', which are filled by 'sources', such as available histone variants, covalent modifications to histones, the readers of these modifications and non-coding RNAs. Competing occupation for the sinks by different sources leads to distinct states of genomic equilibrium in differentiated cells. During dynamic developmental events, such as sexual reproduction, we propose that dramatic and rapid reconfiguration of source-sink relationships modifies chromatin states. We envision that re-routing of sources could occur by altering the dimensions of the sink, by reconfiguration of existing sink occupation or by varying the size of the source, providing a central mechanism to explain a plethora of epigenetic phenomena, which contribute to phenotypic variegation, zygotic genome activation and nucleolar dominance.
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Affiliation(s)
- Patrick J. Murphy
- University of Rochester, Department of Biomedical Genetics and Department of Biology, 601 Elmwood Ave., Rochester NY 14620, USA
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter; Dr. Bohr-Gasse 3, 1030 Vienna, Austria
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26
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Pabba MK, Ritter C, Chagin VO, Meyer J, Celikay K, Stear JH, Loerke D, Kolobynina K, Prorok P, Schmid AK, Leonhardt H, Rohr K, Cardoso MC. Replisome loading reduces chromatin motion independent of DNA synthesis. eLife 2023; 12:RP87572. [PMID: 37906089 PMCID: PMC10617993 DOI: 10.7554/elife.87572] [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: 11/02/2023] Open
Abstract
Chromatin has been shown to undergo diffusional motion, which is affected during gene transcription by RNA polymerase activity. However, the relationship between chromatin mobility and other genomic processes remains unclear. Hence, we set out to label the DNA directly in a sequence unbiased manner and followed labeled chromatin dynamics in interphase human cells expressing GFP-tagged proliferating cell nuclear antigen (PCNA), a cell cycle marker and core component of the DNA replication machinery. We detected decreased chromatin mobility during the S-phase compared to G1 and G2 phases in tumor as well as normal diploid cells using automated particle tracking. To gain insight into the dynamical organization of the genome during DNA replication, we determined labeled chromatin domain sizes and analyzed their motion in replicating cells. By correlating chromatin mobility proximal to the active sites of DNA synthesis, we showed that chromatin motion was locally constrained at the sites of DNA replication. Furthermore, inhibiting DNA synthesis led to increased loading of DNA polymerases. This was accompanied by accumulation of the single-stranded DNA binding protein on the chromatin and activation of DNA helicases further restricting local chromatin motion. We, therefore, propose that it is the loading of replisomes but not their catalytic activity that reduces the dynamics of replicating chromatin segments in the S-phase as well as their accessibility and probability of interactions with other genomic regions.
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Affiliation(s)
| | - Christian Ritter
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg UniversityHeidelbergGermany
| | - Vadim O Chagin
- Department of Biology, Technical University of DarmstadtDarmstadtGermany
- Institute of Cytology RASSt. PetersburgRussian Federation
| | - Janis Meyer
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg UniversityHeidelbergGermany
| | - Kerem Celikay
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg UniversityHeidelbergGermany
| | - Jeffrey H Stear
- EMBL Australia Node in Single Molecule Science, University of New South WalesSydneyAustralia
| | - Dinah Loerke
- Department of Physics & Astronomy, University of DenverDenverUnited States
| | - Ksenia Kolobynina
- Department of Biology, Technical University of DarmstadtDarmstadtGermany
| | - Paulina Prorok
- Department of Biology, Technical University of DarmstadtDarmstadtGermany
| | - Alice Kristin Schmid
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg UniversityHeidelbergGermany
| | | | - Karl Rohr
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg UniversityHeidelbergGermany
| | - M Cristina Cardoso
- Department of Biology, Technical University of DarmstadtDarmstadtGermany
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27
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Wang X, Zhang C, Dong N, Xu H, Zhou Y, Hou D. E2F1-driven histone demethylase KDM6B enhances thyroid malignancy via manipulating TFEB-dependent autophagy axis. Exp Cell Res 2023; 431:113742. [PMID: 37574036 DOI: 10.1016/j.yexcr.2023.113742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 07/22/2023] [Accepted: 08/08/2023] [Indexed: 08/15/2023]
Abstract
Aberrant epigenetic modifications or events regulate autophagy to influence tumor progression, which has gained increasing attention. KDM6B is an essential histone demethylase that participates in multiple processes of tumors, but its role in thyroid carcinoma (THCA) remains to be unknown. Here, in this study, we used the MTT assay to screen and validate that KDM6B is an essential demethylase for THCA. KDM6B promotes THCA proliferation, migration, invasion in vitro and in vivo. Transcriptional factor E2F1 directly binds to the promoter region of KDM6B and regulates its mRNA levels in THCA. E2F1 partially depended on KDM6B to exert its oncogenic functions. Mechanistically, KDM6B binds to TFEB promoter region and mediates the demethylation of H3K27me3. KDM6B depended on TFEB to activate a series of lysosomal-related genes. KDM6B enhances autophagy process, as evidenced by elevated p62 and Beclin-1 proteins. KDM6B depended on TFEB-driven autophagy activity to accelerate THCA progression. Lastly, targeting autophagy with 3-MA could notably abrogate growth of KDM6Bhigh THCA, but has mild influence on KDM6Blow THCA. Together, this study identified KDM6B as an essential epigenetic regulator for THCA, functioning as an autophagy regulator. The fundamental mechanisms underlying E2F1/KDM6B/TFEB axis provided novel vulnerabilities for THCA treatment.
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Affiliation(s)
- Xiaoyuan Wang
- Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210011, Jiangsu, China
| | - Chi Zhang
- Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210011, Jiangsu, China
| | - Na Dong
- Department of Pediatric Gastroenterology & Nutrition, Children's Medical Centre, Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210011, Jiangsu, China
| | - Hai'e Xu
- Department of Clinical Nutrition, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210011, Jiangsu, China
| | - Yi Zhou
- Department of General Surgery, Yixing Guanlin Hospital, Wuxi, 214000, Jiangsu, China
| | - Dawei Hou
- Department of General Surgery, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210011, Jiangsu, China.
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28
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Aleksandrova Y, Neganova M. Deciphering the Mysterious Relationship between the Cross-Pathogenetic Mechanisms of Neurodegenerative and Oncological Diseases. Int J Mol Sci 2023; 24:14766. [PMID: 37834214 PMCID: PMC10573395 DOI: 10.3390/ijms241914766] [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: 08/10/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
The relationship between oncological pathologies and neurodegenerative disorders is extremely complex and is a topic of concern among a growing number of researchers around the world. In recent years, convincing scientific evidence has accumulated that indicates the contribution of a number of etiological factors and pathophysiological processes to the pathogenesis of these two fundamentally different diseases, thus demonstrating an intriguing relationship between oncology and neurodegeneration. In this review, we establish the general links between three intersecting aspects of oncological pathologies and neurodegenerative disorders, i.e., oxidative stress, epigenetic dysregulation, and metabolic dysfunction, examining each process in detail to establish an unusual epidemiological relationship. We also focus on reviewing the current trends in the research and the clinical application of the most promising chemical structures and therapeutic platforms that have a modulating effect on the above processes. Thus, our comprehensive analysis of the set of molecular determinants that have obvious cross-functional pathways in the pathogenesis of oncological and neurodegenerative diseases can help in the creation of advanced diagnostic tools and in the development of innovative pharmacological strategies.
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Affiliation(s)
- Yulia Aleksandrova
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences, 142432 Chernogolovka, Russia;
| | - Margarita Neganova
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences, 142432 Chernogolovka, Russia;
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, 420088 Kazan, Russia
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29
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Smerdon MJ, Wyrick JJ, Delaney S. A half century of exploring DNA excision repair in chromatin. J Biol Chem 2023; 299:105118. [PMID: 37527775 PMCID: PMC10498010 DOI: 10.1016/j.jbc.2023.105118] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 08/03/2023] Open
Abstract
DNA in eukaryotic cells is packaged into the compact and dynamic structure of chromatin. This packaging is a double-edged sword for DNA repair and genomic stability. Chromatin restricts the access of repair proteins to DNA lesions embedded in nucleosomes and higher order chromatin structures. However, chromatin also serves as a signaling platform in which post-translational modifications of histones and other chromatin-bound proteins promote lesion recognition and repair. Similarly, chromatin modulates the formation of DNA damage, promoting or suppressing lesion formation depending on the chromatin context. Therefore, the modulation of DNA damage and its repair in chromatin is crucial to our understanding of the fate of potentially mutagenic and carcinogenic lesions in DNA. Here, we survey many of the landmark findings on DNA damage and repair in chromatin over the last 50 years (i.e., since the beginning of this field), focusing on excision repair, the first repair mechanism studied in the chromatin landscape. For example, we highlight how the impact of chromatin on these processes explains the distinct patterns of somatic mutations observed in cancer genomes.
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Affiliation(s)
- Michael J Smerdon
- Biochemistry and Biophysics, School of Molecular Biosciences, Washington State University, Pullman, Washington, USA.
| | - John J Wyrick
- Genetics and Cell Biology, School of Molecular Biosciences, Washington State University, Pullman, Washington, USA
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, Rhode Island, USA
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30
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Abini-Agbomson S, Gretarsson K, Shih RM, Hsieh L, Lou T, De Ioannes P, Vasilyev N, Lee R, Wang M, Simon MD, Armache JP, Nudler E, Narlikar G, Liu S, Lu C, Armache KJ. Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1. Mol Cell 2023; 83:2872-2883.e7. [PMID: 37595555 DOI: 10.1016/j.molcel.2023.07.020] [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: 01/18/2023] [Revised: 06/12/2023] [Accepted: 07/20/2023] [Indexed: 08/20/2023]
Abstract
SUV420H1 di- and tri-methylates histone H4 lysine 20 (H4K20me2/H4K20me3) and plays crucial roles in DNA replication, repair, and heterochromatin formation. It is dysregulated in several cancers. Many of these processes were linked to its catalytic activity. However, deletion and inhibition of SUV420H1 have shown distinct phenotypes, suggesting that the enzyme likely has uncharacterized non-catalytic activities. Our cryoelectron microscopy (cryo-EM), biochemical, biophysical, and cellular analyses reveal how SUV420H1 recognizes its nucleosome substrates, and how histone variant H2A.Z stimulates its catalytic activity. SUV420H1 binding to nucleosomes causes a dramatic detachment of nucleosomal DNA from the histone octamer, which is a non-catalytic activity. We hypothesize that this regulates the accessibility of large macromolecular complexes to chromatin. We show that SUV420H1 can promote chromatin condensation, another non-catalytic activity that we speculate is needed for its heterochromatin functions. Together, our studies uncover and characterize the catalytic and non-catalytic mechanisms of SUV420H1, a key histone methyltransferase that plays an essential role in genomic stability.
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Affiliation(s)
- Stephen Abini-Agbomson
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Kristjan Gretarsson
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Rochelle M Shih
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
| | - Laura Hsieh
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Tracy Lou
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Pablo De Ioannes
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Nikita Vasilyev
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Rachel Lee
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Miao Wang
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jean-Paul Armache
- Department of Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Geeta Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Karim-Jean Armache
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA.
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31
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Carnie CJ, Armstrong L, Sebesta M, Ariza A, Wang X, Graham E, Zhu K, Ahel D. ERCC6L2 mitigates replication stress and promotes centromere stability. Cell Rep 2023; 42:112329. [PMID: 37014751 DOI: 10.1016/j.celrep.2023.112329] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 01/26/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
Structurally complex genomic regions, such as centromeres, are inherently difficult to duplicate. The mechanism behind centromere inheritance is not well understood, and one of the key questions relates to the reassembly of centromeric chromatin following DNA replication. Here, we define ERCC6L2 as a key regulator of this process. ERCC6L2 accumulates at centromeres and promotes deposition of core centromeric factors. Interestingly, ERCC6L2-/- cells show unrestrained replication of centromeric DNA, likely caused by the erosion of centromeric chromatin. Beyond centromeres, ERCC6L2 facilitates replication at genomic repeats and non-canonical DNA structures. Notably, ERCC6L2 interacts with the DNA-clamp PCNA through an atypical peptide, presented here in a co-crystal structure. Finally, ERCC6L2 also restricts DNA end resection, acting independently of the 53BP1-REV7-Shieldin complex. We propose a mechanistic model, which reconciles seemingly distinct functions of ERCC6L2 in DNA repair and DNA replication. These findings provide a molecular context for studies linking ERCC6L2 to human disease.
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Affiliation(s)
| | - Lucy Armstrong
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Marek Sebesta
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Antonio Ariza
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Xiaomeng Wang
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Emily Graham
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Kang Zhu
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Dragana Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
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32
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Huang J, Wu C, Kloeber JA, Gao H, Gao M, Zhu Q, Chang Y, Zhao F, Guo G, Luo K, Dai H, Liu S, Huang Q, Kim W, Zhou Q, Zhu S, Wu Z, Tu X, Yin P, Deng M, Wang L, Yuan J, Lou Z. SLFN5-mediated chromatin dynamics sculpt higher-order DNA repair topology. Mol Cell 2023; 83:1043-1060.e10. [PMID: 36854302 PMCID: PMC10467573 DOI: 10.1016/j.molcel.2023.02.004] [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: 05/17/2022] [Revised: 12/23/2022] [Accepted: 02/01/2023] [Indexed: 03/02/2023]
Abstract
Repair of DNA double-strand breaks (DSBs) elicits three-dimensional (3D) chromatin topological changes. A recent finding reveals that 53BP1 assembles into a 3D chromatin topology pattern around DSBs. How this formation of a higher-order structure is configured and regulated remains enigmatic. Here, we report that SLFN5 is a critical factor for 53BP1 topological arrangement at DSBs. Using super-resolution imaging, we find that SLFN5 binds to 53BP1 chromatin domains to assemble a higher-order microdomain architecture by driving damaged chromatin dynamics at both DSBs and deprotected telomeres. Mechanistically, we propose that 53BP1 topology is shaped by two processes: (1) chromatin mobility driven by the SLFN5-LINC-microtubule axis and (2) the assembly of 53BP1 oligomers mediated by SLFN5. In mammals, SLFN5 deficiency disrupts the DSB repair topology and impairs non-homologous end joining, telomere fusions, class switch recombination, and sensitivity to poly (ADP-ribose) polymerase inhibitor. We establish a molecular mechanism that shapes higher-order chromatin topologies to safeguard genomic stability.
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Affiliation(s)
- Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Chenming Wu
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Jake A Kloeber
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA; Medical Scientist Training Program, Mayo Clinic, Rochester, MN 55905, USA
| | - Huanyao Gao
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Ming Gao
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Qian Zhu
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Yiming Chang
- Jinzhou Medical University, Shanghai East Hospital, Shanghai 200120, China
| | - Fei Zhao
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Guijie Guo
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Kuntian Luo
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Haiming Dai
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Sijia Liu
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - Qiru Huang
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Wootae Kim
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Qin Zhou
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Shouhai Zhu
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Zheming Wu
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xinyi Tu
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ping Yin
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Min Deng
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Jian Yuan
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China; Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200092, China.
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA.
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Shi D, Huang Y, Bai C. Studies of the Mechanism of Nucleosome Dynamics: A Review on Multifactorial Regulation from Computational and Experimental Cases. Polymers (Basel) 2023; 15:polym15071763. [PMID: 37050377 PMCID: PMC10096840 DOI: 10.3390/polym15071763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/28/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023] Open
Abstract
The nucleosome, which organizes the long coil of genomic DNA in a highly condensed, polymeric way, is thought to be the basic unit of chromosomal structure. As the most important protein–DNA complex, its structural and dynamic features have been successively revealed in recent years. However, its regulatory mechanism, which is modulated by multiple factors, still requires systemic discussion. This study summarizes the regulatory factors of the nucleosome’s dynamic features from the perspective of histone modification, DNA methylation, and the nucleosome-interacting factors (transcription factors and nucleosome-remodeling proteins and cations) and focuses on the research exploring the molecular mechanism through both computational and experimental approaches. The regulatory factors that affect the dynamic features of nucleosomes are also discussed in detail, such as unwrapping, wrapping, sliding, and stacking. Due to the complexity of the high-order topological structures of nucleosomes and the comprehensive effects of regulatory factors, the research on the functional modulation mechanism of nucleosomes has encountered great challenges. The integration of computational and experimental approaches, the construction of physical modes for nucleosomes, and the application of deep learning techniques will provide promising opportunities for further exploration.
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Affiliation(s)
- Danfeng Shi
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Yuxin Huang
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
| | - Chen Bai
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
- Chenzhu (MoMeD) Biotechnology Co., Ltd., Hangzhou 310005, China
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34
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Feng L, Si J, Yue J, Zhao M, Qi W, Zhu S, Mo J, Wang L, Lan G, Liang J. The Landscape of Accessible Chromatin and Developmental Transcriptome Maps Reveal a Genetic Mechanism of Skeletal Muscle Development in Pigs. Int J Mol Sci 2023; 24:ijms24076413. [PMID: 37047386 PMCID: PMC10094211 DOI: 10.3390/ijms24076413] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/19/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
The epigenetic regulation mechanism of porcine skeletal muscle development relies on the openness of chromatin and is also precisely regulated by transcriptional machinery. However, fewer studies have exploited the temporal changes in gene expression and the landscape of accessible chromatin to reveal the underlying molecular mechanisms controlling muscle development. To address this, skeletal muscle biopsy samples were taken from Landrace pigs at days 0 (D0), 60 (D60), 120 (D120), and 180 (D180) after birth and were then analyzed using RNA-seq and ATAC-seq. The RNA-seq analysis identified 8554 effective differential genes, among which ACBD7, TMEM220, and ATP1A2 were identified as key genes related to the development of porcine skeletal muscle. Some potential cis-regulatory elements identified by ATAC-seq analysis contain binding sites for many transcription factors, including SP1 and EGR1, which are also the predicted transcription factors regulating the expression of ACBD7 genes. Moreover, the omics analyses revealed regulatory regions that become ectopically active after birth during porcine skeletal muscle development after birth and identified 151,245, 53,435, 30,494, and 40,911 peaks. The enriched functional elements are related to the cell cycle, muscle development, and lipid metabolism. In summary, comprehensive high-resolution gene expression maps were developed for the transcriptome and accessible chromatin during postnatal skeletal muscle development in pigs.
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Affiliation(s)
- Lingli Feng
- Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, Guangxi University, Nanning 530004, China (G.L.)
| | - Jinglei Si
- Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, Guangxi University, Nanning 530004, China (G.L.)
| | - Jingwei Yue
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100097, China
| | - Mingwei Zhao
- Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, Guangxi University, Nanning 530004, China (G.L.)
| | - Wenjing Qi
- Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, Guangxi University, Nanning 530004, China (G.L.)
| | - Siran Zhu
- Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, Guangxi University, Nanning 530004, China (G.L.)
| | - Jiayuan Mo
- Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, Guangxi University, Nanning 530004, China (G.L.)
| | - Lixian Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100097, China
| | - Ganqiu Lan
- Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, Guangxi University, Nanning 530004, China (G.L.)
| | - Jing Liang
- Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, Guangxi University, Nanning 530004, China (G.L.)
- Correspondence:
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35
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Zamalloa LG, Pruitt MM, Hermance NM, Gali H, Flynn RL, Manning AL. RB loss sensitizes cells to replication-associated DNA damage by PARP inhibition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.25.532215. [PMID: 36993348 PMCID: PMC10055402 DOI: 10.1101/2023.03.25.532215] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The retinoblastoma tumor suppressor protein (RB) interacts physically and functionally with a number of epigenetic modifying enzymes to control transcriptional regulation, respond to replication stress, promote DNA damage response and repair pathways, and regulate genome stability. To better understand how disruption of RB function impacts epigenetic regulation of genome stability and determine whether such changes may represent exploitable weaknesses of RB-deficient cancer cells, we performed an imaging-based screen to identify epigenetic inhibitors that promote DNA damage and compromise viability of RB-deficient cells. We found that loss of RB alone leads to high levels of replication-dependent poly-ADP ribosylation (PARylation) and that preventing PARylation through inhibition of PARP enzymes enables RB-deficient cells to progress to mitosis with unresolved replication stress and under-replicated DNA. These defects contribute to high levels of DNA damage, decreased proliferation, and compromised cell viability. We demonstrate this sensitivity is conserved across a panel of inhibitors that target both PARP1 and PARP2 and can be suppressed by re-expression of the RB protein. Together, these data indicate that inhibitors of PARP1 and PARP2 may be clinically relevant for RB-deficient cancers.
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36
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Abini-Agbomson S, Gretarsson K, Shih RM, Hsieh L, Lou T, De Ioannes P, Vasilyev N, Lee R, Wang M, Simon M, Armache JP, Nudler E, Narlikar G, Liu S, Lu C, Armache KJ. Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533220. [PMID: 36993485 PMCID: PMC10055266 DOI: 10.1101/2023.03.17.533220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The intricate regulation of chromatin plays a key role in controlling genome architecture and accessibility. Histone lysine methyltransferases regulate chromatin by catalyzing the methylation of specific histone residues but are also hypothesized to have equally important non-catalytic roles. SUV420H1 di- and tri-methylates histone H4 lysine 20 (H4K20me2/me3) and plays crucial roles in DNA replication, repair, and heterochromatin formation, and is dysregulated in several cancers. Many of these processes were linked to its catalytic activity. However, deletion and inhibition of SUV420H1 have shown distinct phenotypes suggesting the enzyme likely has uncharacterized non-catalytic activities. To characterize the catalytic and non-catalytic mechanisms SUV420H1 uses to modify chromatin, we determined cryo- EM structures of SUV420H1 complexes with nucleosomes containing histone H2A or its variant H2A.Z. Our structural, biochemical, biophysical, and cellular analyses reveal how both SUV420H1 recognizes its substrate and H2A.Z stimulates its activity, and show that SUV420H1 binding to nucleosomes causes a dramatic detachment of nucleosomal DNA from histone octamer. We hypothesize that this detachment increases DNA accessibility to large macromolecular complexes, a prerequisite for DNA replication and repair. We also show that SUV420H1 can promote chromatin condensates, another non-catalytic role that we speculate is needed for its heterochromatin functions. Together, our studies uncover and characterize the catalytic and non-catalytic mechanisms of SUV420H1, a key histone methyltransferase that plays an essential role in genomic stability.
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Affiliation(s)
- Stephen Abini-Agbomson
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Kristjan Gretarsson
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Rochelle M. Shih
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
| | - Laura Hsieh
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Tracy Lou
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Pablo De Ioannes
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Nikita Vasilyev
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Rachel Lee
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Miao Wang
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Matthew Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jean-Paul Armache
- Department of Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Geeta Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Karim-Jean Armache
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Lead contact
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37
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Teefy BB, Benayoun BA. Putting aging on ICE. Cell Metab 2023; 35:383-385. [PMID: 36889279 PMCID: PMC10592682 DOI: 10.1016/j.cmet.2023.02.012] [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] [Indexed: 03/09/2023]
Abstract
A recent report by Yang et al. in Cell demonstrates that faithful DNA double-strand breaks and repair cycles phenocopy many aspects of aging in mice. Whether this progeroid phenotype is caused by a loss of epigenetic information remains to be conclusively determined.
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Affiliation(s)
- Bryan B Teefy
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA; Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA 90089, USA; USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA; USC Stem Cell Initiative, Los Angeles, CA 90089, USA.
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38
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Frigerio C, Di Nisio E, Galli M, Colombo CV, Negri R, Clerici M. The Chromatin Landscape around DNA Double-Strand Breaks in Yeast and Its Influence on DNA Repair Pathway Choice. Int J Mol Sci 2023; 24:ijms24043248. [PMID: 36834658 PMCID: PMC9967470 DOI: 10.3390/ijms24043248] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/21/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
DNA double-strand breaks (DSBs) are harmful DNA lesions, which elicit catastrophic consequences for genome stability if not properly repaired. DSBs can be repaired by either non-homologous end joining (NHEJ) or homologous recombination (HR). The choice between these two pathways depends on which proteins bind to the DSB ends and how their action is regulated. NHEJ initiates with the binding of the Ku complex to the DNA ends, while HR is initiated by the nucleolytic degradation of the 5'-ended DNA strands, which requires several DNA nucleases/helicases and generates single-stranded DNA overhangs. DSB repair occurs within a precisely organized chromatin environment, where the DNA is wrapped around histone octamers to form the nucleosomes. Nucleosomes impose a barrier to the DNA end processing and repair machinery. Chromatin organization around a DSB is modified to allow proper DSB repair either by the removal of entire nucleosomes, thanks to the action of chromatin remodeling factors, or by post-translational modifications of histones, thus increasing chromatin flexibility and the accessibility of repair enzymes to the DNA. Here, we review histone post-translational modifications occurring around a DSB in the yeast Saccharomyces cerevisiae and their role in DSB repair, with particular attention to DSB repair pathway choice.
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Affiliation(s)
- Chiara Frigerio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
| | - Elena Di Nisio
- Department of Biology and Biotechnologies “C. Darwin”, Sapienza University of Rome, 00185 Rome, Italy
| | - Michela Galli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
| | - Chiara Vittoria Colombo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
| | - Rodolfo Negri
- Department of Biology and Biotechnologies “C. Darwin”, Sapienza University of Rome, 00185 Rome, Italy
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR) of Italy, 00185 Rome, Italy
- Correspondence: (R.N.); (M.C.)
| | - Michela Clerici
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
- Correspondence: (R.N.); (M.C.)
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39
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Mishra LN, Thiriet C, Vasudevan D. Editorial: Chromatin structure and function. Front Genet 2023; 14:1140534. [PMID: 36824440 PMCID: PMC9941686 DOI: 10.3389/fgene.2023.1140534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 01/25/2023] [Indexed: 02/10/2023] Open
Affiliation(s)
- Laxmi Narayan Mishra
- Albert Einstein College of Medicine, Bronx, NY, United States,*Correspondence: Laxmi Narayan Mishra, ; Christophe Thiriet, , Dileep Vasudevan,
| | - Christophe Thiriet
- Université de Rennes 1, CNRS-UMR6290 Institut génétique et développement de Rennes (IGDR), Rennes, France,*Correspondence: Laxmi Narayan Mishra, ; Christophe Thiriet, , Dileep Vasudevan,
| | - Dileep Vasudevan
- DBT-Institute of Life Sciences, Bhubaneswar, India,*Correspondence: Laxmi Narayan Mishra, ; Christophe Thiriet, , Dileep Vasudevan,
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40
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Zhao Y, Simon M, Seluanov A, Gorbunova V. DNA damage and repair in age-related inflammation. Nat Rev Immunol 2023; 23:75-89. [PMID: 35831609 PMCID: PMC10106081 DOI: 10.1038/s41577-022-00751-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2022] [Indexed: 02/07/2023]
Abstract
Genomic instability is an important driver of ageing. The accumulation of DNA damage is believed to contribute to ageing by inducing cell death, senescence and tissue dysfunction. However, emerging evidence shows that inflammation is another major consequence of DNA damage. Inflammation is a hallmark of ageing and the driver of multiple age-related diseases. Here, we review the evidence linking DNA damage, inflammation and ageing, highlighting how premature ageing syndromes are associated with inflammation. We discuss the mechanisms by which DNA damage induces inflammation, such as through activation of the cGAS-STING axis and NF-κB activation by ATM. The triggers for activation of these signalling cascades are the age-related accumulation of DNA damage, activation of transposons, cellular senescence and the accumulation of persistent R-loops. We also discuss how epigenetic changes triggered by DNA damage can lead to inflammation and ageing via redistribution of heterochromatin factors. Finally, we discuss potential interventions against age-related inflammation.
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Affiliation(s)
- Yang Zhao
- Department of Biology, University of Rochester, Rochester, NY, USA.,Department of Physiology, Zhejiang University School of Medicine, Hangzhou, China.,Department of Hepatobiliary and Pancreatic Surgery of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Matthew Simon
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY, USA. .,Department of Medicine, University of Rochester, Rochester, NY, USA.
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY, USA. .,Department of Medicine, University of Rochester, Rochester, NY, USA.
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41
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Zhou L, Lin X, Zhu J, Zhang L, Chen S, Yang H, Jia L, Chen B. NEDD8-conjugating enzyme E2s: critical targets for cancer therapy. Cell Death Dis 2023; 9:23. [PMID: 36690633 PMCID: PMC9871045 DOI: 10.1038/s41420-023-01337-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/24/2023]
Abstract
NEDD8-conjugating enzymes, E2s, include the well-studied ubiquitin-conjugating enzyme E2 M (UBE2M) and the poorly characterized ubiquitin-conjugating enzyme E2 F (UBE2F). UBE2M and UBE2F have distinct and prominent roles in catalyzing the neddylation of Cullin or non-Cullin substrates. These enzymes are overexpressed in various malignancies, conferring a worse overall survival. Targeting UBE2M to influence tumor growth by either modulating several biological responses of tumor cells (such as DNA-damage response, apoptosis, or senescence) or regulating the anti-tumor immunity holds strong therapeutic potential. Multiple inhibitors that target the interaction between UBE2M and defective cullin neddylation protein 1 (DCN1), a co-E3 for neddylation, exhibit promising anti-tumor effects. By contrast, the potential benefits of targeting UBE2F are still to be explored. It is currently reported to inhibit apoptosis and then induce cell growth; hence, targeting UBE2F serves as an effective chemo-/radiosensitizing strategy by triggering apoptosis. This review highlights the most recent advances in the roles of UBE2M and UBE2F in tumor progression, indicating these E2s as two promising anti-tumor targets.
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Affiliation(s)
- Lisha Zhou
- grid.440657.40000 0004 1762 5832Taizhou Central Hospital (Taizhou University Hospital), Taizhou University, Taizhou, Zhejiang China
| | - Xiongzhi Lin
- grid.412026.30000 0004 1776 2036Graduate School of Medicine, Hebei North University, Zhangjiakou, Hebei China
| | - Jin Zhu
- grid.452533.60000 0004 1763 3891Department of Surgical Oncology, Jiangxi Cancer Hospital, Nanchang, Jiangxi China
| | - Luyi Zhang
- grid.440657.40000 0004 1762 5832Taizhou Central Hospital (Taizhou University Hospital), Taizhou University, Taizhou, Zhejiang China
| | - Siyuan Chen
- grid.440657.40000 0004 1762 5832Taizhou Central Hospital (Taizhou University Hospital), Taizhou University, Taizhou, Zhejiang China
| | - Hui Yang
- grid.8547.e0000 0001 0125 2443Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Lijun Jia
- grid.411480.80000 0004 1799 1816Cancer Institute of Traditional Chinese Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Baofu Chen
- grid.440657.40000 0004 1762 5832Taizhou Central Hospital (Taizhou University Hospital), Taizhou University, Taizhou, Zhejiang China
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42
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Nysfungin Production Improvement by UV Mutagenesis in Streptomyces noursei D-3-14. Catalysts 2023. [DOI: 10.3390/catal13020247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Streptomyces noursei D-3-14 was taken as a starting strain and treated with UV (15 W, 30 cm) mutagenesis for 40 s for three consecutive rounds. High yielding strains were screened using chemical and biological potency determination, and the components of the fermentation products were detected using HPLC. Finally, the mutant strain Streptomyces noursei 72-22-1 with a chemical potency of 8912 (U/mL) and a biological potency of 5557 (U/mL) was obtained after the genetic stability evaluation. After optimization of the fermentation conditions, the chemical potency and biological potency of Streptomyces noursei 72-22-1 reached 14,082 U/mL and 10579 U/mL, respectively, which is 1.58 and 1.91 times those before optimization. HPLC analysis indicated that the mutant strain 72-22-1 displayed a higher content of polyfungin B. When equimolar nystatin A1, A3, and polyfungin B were tested for their fungicidal activities towards Saccharomyces cerevisiae ATCC 2061, polyfungin B exhibited a better efficacy than nystatin A1 and A3.
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Tao S, Liang S, Zeng T, Yin D. Epigenetic modification-related mechanisms of hepatocellular carcinoma resistance to immune checkpoint inhibition. Front Immunol 2023; 13:1043667. [PMID: 36685594 PMCID: PMC9845774 DOI: 10.3389/fimmu.2022.1043667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/28/2022] [Indexed: 01/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) constitutes most primary liver cancers and is one of the most lethal and life-threatening malignancies globally. Unfortunately, a substantial proportion of HCC patients are identified at an advanced stage that is unavailable for curative surgery. Thus, palliative therapies represented by multi-tyrosine kinase inhibitors (TKIs) sorafenib remained the front-line treatment over the past decades. Recently, the application of immune checkpoint inhibitors (ICIs), especially targeting the PD-1/PD-L1/CTLA-4 axis, has achieved an inspiring clinical breakthrough for treating unresectable solid tumors. However, many HCC patients with poor responses lead to limited benefits in clinical applications, which has quickly drawn researchers' attention to the regulatory mechanisms of immune checkpoints in HCC immune evasion. Evasion of immune surveillance by cancer is attributed to intricate reprogramming modulation in the tumor microenvironment. Currently, more and more studies have found that epigenetic modifications, such as chromatin structure remodeling, DNA methylation, histone post-translational modifications, and non-coding RNA levels, may contribute significantly to remodeling the tumor microenvironment to avoid immune clearance, affecting the efficacy of immunotherapy for HCC. This review summarizes the rapidly emerging progress of epigenetic-related changes during HCC resistance to ICIs and discusses the mechanisms of underlying epigenetic therapies available for surmounting immune resistance. Finally, we summarize the clinical advances in combining epigenetic therapies with immunotherapy, aiming to promote the formation of immune combination therapy strategies.
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Affiliation(s)
- Shengwei Tao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Shuhang Liang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Taofei Zeng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Dalong Yin
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
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Zablon HA, VonHandorf A, Puga A. Mechanisms of chromate carcinogenesis by chromatin alterations. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2023; 96:1-23. [PMID: 36858770 DOI: 10.1016/bs.apha.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In a dynamic environment, organisms must constantly mount an adaptive response to new environmental conditions in order to survive. Novel patterns of gene expression, driven by attendant changes in chromatin architecture, aid in adaptation and survival. Critical mechanisms in the control of gene transcription govern new spatiotemporal chromatin-chromatin interactions that make regulatory DNA elements accessible to the transcription factors that control the response. Consequently, agents that disrupt chromatin structure are likely to have a direct impact on the transcriptional programs of cells and organisms and to drive alterations in fundamental physiological processes. In this regard, hexavalent chromium (Cr(VI)) is of special interest because it interacts directly with cellular proteins, DNA, and other macromolecules, and is likely to upset cell functions that may cause generalized damage to the organism. Here, we will highlight chromium-mediated mechanisms that disrupt chromatin architecture and discuss how these mechanisms are integral to its carcinogenic properties. Emerging evidence indicates that Cr(VI) targets euchromatin, particularly in genomic locations flanking the binding sites of the essential transcription factors CTCF and AP1, and, in so doing, they disrupt nucleosomal architecture. Ultimately, the ensuing changes, if occurring in critical regulatory domains, may establish a new chromatin state, either toxic or adaptive, that will be governed by the corresponding gene transcription changes in key biological processes associated with that state.
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Affiliation(s)
- Hesbon A Zablon
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Andrew VonHandorf
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Alvaro Puga
- Department of Environmental and Public Health Sciences and Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.
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Zagelbaum J, Gautier J. Double-strand break repair and mis-repair in 3D. DNA Repair (Amst) 2023; 121:103430. [PMID: 36436496 PMCID: PMC10799305 DOI: 10.1016/j.dnarep.2022.103430] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022]
Abstract
DNA double-strand breaks (DSBs) are lesions that arise frequently from exposure to damaging agents as well as from ongoing physiological DNA transactions. Mis-repair of DSBs leads to rearrangements and structural variations in chromosomes, including insertions, deletions, and translocations implicated in disease. The DNA damage response (DDR) limits pathologic mutations and large-scale chromosome rearrangements. DSB repair initiates in 2D at DNA lesions with the stepwise recruitment of repair proteins and local chromatin remodeling which facilitates break accessibility. More complex structures are then formed via protein assembly into nanodomains and via genome folding into chromatin loops. Subsequently, 3D reorganization of DSBs is guided by clustering forces which drive the assembly of repair domains harboring multiple lesions. These domains are further stabilized and insulated into condensates via liquid-liquid phase-separation. Here, we discuss the benefits and risks associated with this 3D reorganization of the broken genome.
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Affiliation(s)
- Jennifer Zagelbaum
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jean Gautier
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Genetics and Development, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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Zheng Y, Li H, Bo X, Chen H. Ionizing radiation damage and repair from 3D-genomic perspective. Trends Genet 2023; 39:1-4. [PMID: 35934594 DOI: 10.1016/j.tig.2022.07.004] [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: 03/30/2022] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 10/16/2022]
Abstract
Ionizing radiation (IR)-induced DNA damage and repair are complex and occur at hierarchical chromatin structures; radiobiology needs to be studied from a 3D-genomic perspective. Differences in IR damage and repair throughout the 3D genome may help to explain differences in radiosensitivity.
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Affiliation(s)
- Yang Zheng
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China; State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
| | - Hao Li
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Xiaochen Bo
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China.
| | - Hebing Chen
- Institute of Health Service and Transfusion Medicine, Beijing 100850, China.
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Oxidative-Stress-Associated Proteostasis Disturbances and Increased DNA Damage in the Hippocampal Granule Cells of the Ts65Dn Model of Down Syndrome. Antioxidants (Basel) 2022; 11:antiox11122438. [PMID: 36552646 PMCID: PMC9774833 DOI: 10.3390/antiox11122438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022] Open
Abstract
Oxidative stress (OS) is one of the neuropathological mechanisms responsible for the deficits in cognition and neuronal function in Down syndrome (DS). The Ts65Dn (TS) mouse replicates multiple DS phenotypes including hippocampal-dependent learning and memory deficits and similar brain oxidative status. To better understand the hippocampal oxidative profile in the adult TS mouse, we analyzed cellular OS-associated alterations in hippocampal granule cells (GCs), a neuronal population that plays an important role in memory formation and that is particularly affected in DS. For this purpose, we used biochemical, molecular, immunohistochemical, and electron microscopy techniques. Our results indicate that TS GCs show important OS-associated alterations in the systems essential for neuronal homeostasis: DNA damage response and proteostasis, particularly of the proteasome and lysosomal system. Specifically, TS GCs showed: (i) increased DNA damage, (ii) reorganization of nuclear proteolytic factories accompanied by a decline in proteasome activity and cytoplasmic aggregation of ubiquitinated proteins, (iii) formation of lysosomal-related structures containing lipid droplets of cytotoxic peroxidation products, and (iv) mitochondrial ultrastructural defects. These alterations could be implicated in enhanced cellular senescence, accelerated aging and neurodegeneration, and the early development of Alzheimer's disease neuropathology present in TS mice and the DS population.
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Mansisidor AR, Risca VI. Chromatin accessibility: methods, mechanisms, and biological insights. Nucleus 2022; 13:236-276. [PMID: 36404679 PMCID: PMC9683059 DOI: 10.1080/19491034.2022.2143106] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/23/2022] [Accepted: 10/30/2022] [Indexed: 11/22/2022] Open
Abstract
Access to DNA is a prerequisite to the execution of essential cellular processes that include transcription, replication, chromosomal segregation, and DNA repair. How the proteins that regulate these processes function in the context of chromatin and its dynamic architectures is an intensive field of study. Over the past decade, genome-wide assays and new imaging approaches have enabled a greater understanding of how access to the genome is regulated by nucleosomes and associated proteins. Additional mechanisms that may control DNA accessibility in vivo include chromatin compaction and phase separation - processes that are beginning to be understood. Here, we review the ongoing development of accessibility measurements, we summarize the different molecular and structural mechanisms that shape the accessibility landscape, and we detail the many important biological functions that are linked to chromatin accessibility.
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Affiliation(s)
- Andrés R. Mansisidor
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY
| | - Viviana I. Risca
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY
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Predictive molecular biomarkers for determining neoadjuvant chemosensitivity in muscle invasive bladder cancer. Oncotarget 2022; 13:1188-1200. [PMID: 36322407 PMCID: PMC9629806 DOI: 10.18632/oncotarget.28302] [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] [Indexed: 11/07/2022] Open
Abstract
Introduction: Identifying neoadjuvant chemotherapy (NAC) response in patients with muscle invasive bladder cancer (MIBC) has had limited success based on clinicopathological features and molecular subtyping. Identification of chemotherapy responsive cohorts would facilitate delivery to those most likely to benefit. Objective: Develop a molecular signature that can identify MIBC NAC responders (R) and non-responders (NR) using a cohort of known NAC response phenotypes, and better understand differences in molecular pathways and subtype classifications between NAC R and NR. Materials and Methods: Presented are the messenger RNA (mRNA) and microRNA (miRNA) differential expression profiles from initial transurethral resection of bladder tumor (TURBT) specimens of a discovery cohort of MIBC patients consisting of 7 known NAC R and 11 NR, and a validation cohort consisting of 3 R and 5 NR. Pathological response at time of cystectomy after NAC was used to classify initial TURBT specimens as R (pT0) versus NR (≥pT2). RNA and miRNA from FFPE blocks were sequenced using RNAseq and qPCR, respectively. Results: The discovery cohort had 2309 genes, while the validation cohort had 602 genes and 13 miRNA differentially expressed between R and NR. Gene set enrichment analysis identified mitochondrial gene expression, DNA replication initiation, DNA unwinding in the R discovery cohort and positive regulation of vascular associated smooth muscle cell proliferation in the NR discovery cohort. Canonical correlation (CC) analysis was applied to differentiate R versus NR. 3 CCs (CC13, CC16, and CC17) had an AUC >0.65 in the discovery and validation dataset. Gene ontology enrichment showed CC13 as nucleoside triphosphate metabolic process, CC16 as cell cycle and cellular response to DNA damage, CC17 as DNA packaging complex. All patients were classified using established molecular subtypes: Baylor, UNC, CIT, Lund, MD Anderson, TCGA, and Consensus Class. The MD Anderson p53-like subtype, CIT MC4 subtype and Consensus Class stroma rich subtype had the strongest correlation with a NR phenotype, while no subtype had a strong correlation with the R phenotype. Conclusions: Our results identify molecular signatures that can be used to differentiate MIBC NAC R versus NR, salient molecular pathway differences, and highlight the utility of molecular subtyping in relation to NAC response.
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Characterizing and exploiting the many roles of aberrant H2B monoubiquitination in cancer pathogenesis. Semin Cancer Biol 2022; 86:782-798. [PMID: 34953650 DOI: 10.1016/j.semcancer.2021.12.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/08/2021] [Accepted: 12/19/2021] [Indexed: 01/27/2023]
Abstract
Monoubiquitination of histone H2B on lysine 120 (H2Bub1) is implicated in the control of multiple essential processes, including transcription, DNA damage repair and mitotic chromosome segregation. Accordingly, aberrant regulation of H2Bub1 can induce transcriptional reprogramming and genome instability that may promote oncogenesis. Remarkably, alterations of the ubiquitin ligases and deubiquitinating enzymes regulating H2Bub1 are emerging as ubiquitous features in cancer, further supporting the possibility that the misregulation of H2Bub1 is an underlying mechanism contributing to cancer pathogenesis. To date, aberrant H2Bub1 dynamics have been reported in multiple cancer types and are associated with transcriptional changes that promote oncogenesis in a cancer type-specific manner. Owing to the multi-functional nature of H2Bub1, misregulation of its writers and erasers may drive disease initiation and progression through additional synergistic processes. Accordingly, understanding the molecular determinants and pathogenic impacts associated with aberrant H2Bub1 regulation may reveal novel drug targets and therapeutic vulnerabilities that can be exploited to develop innovative precision medicine strategies that better combat cancer. In this review, we present the normal functions of H2Bub1 in the control of DNA-associated processes and describe the pathogenic implications associated with its misregulation in cancer. We further discuss the challenges coupled with the development of therapeutic strategies targeting H2Bub1 misregulation and expose the potential benefits of designing treatments that synergistically exploit the multiple functionalities of H2Bub1 to improve treatment selectivity and efficacy.
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