1
|
Nishigaya Y, Takase S, Sumiya T, Sato T, Niwa H, Sato S, Nakata A, Matsuoka S, Maemoto Y, Hashimoto N, Namie R, Honma T, Umehara T, Shirouzu M, Koyama H, Yoshida M, Ito A, Shirai F. Structure-based development of novel substrate-type G9a inhibitors as epigenetic modulators for sickle cell disease treatment. Bioorg Med Chem Lett 2024; 110:129856. [PMID: 38914346 DOI: 10.1016/j.bmcl.2024.129856] [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: 04/24/2024] [Revised: 06/14/2024] [Accepted: 06/19/2024] [Indexed: 06/26/2024]
Abstract
The discovery and development of structurally distinct lysine methyltransferase G9a inhibitors have been the subject of intense research in epigenetics. Structure-based optimization was conducted, starting with the previously reported seed compound 7a and lead to the identification of a highly potent G9a inhibitor, compound 7i (IC50 = 0.024 μM). X-ray crystallography for the ligand-protein interaction and kinetics study, along with surface plasmon resonance (SPR) analysis, revealed that compound 7i interacts with G9a in a unique binding mode. In addition, compound 7i caused attenuation of cellular H3K9me2 levels and induction of γ-globin mRNA expression in HUDEP-2 cells in a dose-dependent manner.
Collapse
Affiliation(s)
- Yosuke Nishigaya
- Watarase Research Center, Discovery Research Headquarters, Kyorin Pharmaceutical Co. Ltd., 1848 Nogi, Shimotsuga-gun, Tochigi 329-0114, Japan.
| | - Shohei Takase
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Tatsunobu Sumiya
- Watarase Research Center, Discovery Research Headquarters, Kyorin Pharmaceutical Co. Ltd., 1848 Nogi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Tomohiro Sato
- Drug Discovery Computational Chemistry Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hideaki Niwa
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Shin Sato
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Akiko Nakata
- Drug Discovery Seed Compounds Exploratory Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Seiji Matsuoka
- Drug Discovery Seed Compounds Exploratory Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yuki Maemoto
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Noriaki Hashimoto
- Watarase Research Center, Discovery Research Headquarters, Kyorin Pharmaceutical Co. Ltd., 1848 Nogi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Ryosuke Namie
- Watarase Research Center, Discovery Research Headquarters, Kyorin Pharmaceutical Co. Ltd., 1848 Nogi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Teruki Honma
- Drug Discovery Computational Chemistry Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Takashi Umehara
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Mikako Shirouzu
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroo Koyama
- Drug Discovery Chemistry Platform Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Minoru Yoshida
- Drug Discovery Seed Compounds Exploratory Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Office of University Professor, the University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Akihiro Ito
- Drug Discovery Seed Compounds Exploratory Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Fumiyuki Shirai
- Drug Discovery Chemistry Platform Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| |
Collapse
|
2
|
Gomez-Pinilla F, Thapak P. Exercise epigenetics is fueled by cell bioenergetics: Supporting role on brain plasticity and cognition. Free Radic Biol Med 2024; 220:43-55. [PMID: 38677488 PMCID: PMC11144461 DOI: 10.1016/j.freeradbiomed.2024.04.237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/04/2024] [Accepted: 04/24/2024] [Indexed: 04/29/2024]
Abstract
Exercise has the unique aptitude to benefit overall health of body and brain. Evidence indicates that the effects of exercise can be saved in the epigenome for considerable time to elevate the threshold for various diseases. The action of exercise on epigenetic regulation seems central to building an "epigenetic memory" to influence long-term brain function and behavior. As an intrinsic bioenergetic process, exercise engages the function of the mitochondria and redox pathways to impinge upon molecular mechanisms that regulate synaptic plasticity and learning and memory. We discuss how the action of exercise uses mechanisms of bioenergetics to support a "epigenetic memory" with long-term implications for neural and behavioral plasticity. This information is crucial for directing the power of exercise to reduce the burden of neurological and psychiatric disorders.
Collapse
Affiliation(s)
- Fernando Gomez-Pinilla
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA; Department of Neurosurgery, UCLA Brain Injury Research Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
| | - Pavan Thapak
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| |
Collapse
|
3
|
Temgire P, Arthur R, Kumar P. Neuroinflammation and the role of epigenetic-based therapies for Huntington's disease management: the new paradigm. Inflammopharmacology 2024; 32:1791-1804. [PMID: 38653938 DOI: 10.1007/s10787-024-01477-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 04/09/2024] [Indexed: 04/25/2024]
Abstract
Huntington's disease (HD) is an inherited, autosomal, neurodegenerative ailment that affects the striatum of the brain. Despite its debilitating effect on its patients, there is no proven cure for HD management as of yet. Neuroinflammation, excitotoxicity, and environmental factors have been reported to influence the regulation of gene expression by modifying epigenetic mechanisms. Aside focusing on the etiology, changes in epigenetic mechanisms have become a crucial factor influencing the interaction between HTT protein and epigenetically transcribed genes involved in neuroinflammation and HD. This review presents relevant literature on epigenetics with special emphasis on neuroinflammation and HD. It summarizes pertinent research on the role of neuroinflammation and post-translational modifications of chromatin, including DNA methylation, histone modification, and miRNAs. To achieve this about 1500 articles were reviewed via databases like PubMed, ScienceDirect, Google Scholar, and Web of Science. They were reduced to 534 using MeSH words like 'epigenetics, neuroinflammation, and HD' coupled with Boolean operators. Results indicated that major contributing factors to the development of HD such as mitochondrial dysfunction, excitotoxicity, neuroinflammation, and apoptosis are affected by epigenetic alterations. However, the association between neuroinflammation-altered epigenetics and the reported transcriptional changes in HD is unknown. Also, the link between epigenetically dysregulated genomic regions and specific DNA sequences suggests the likelihood that transcription factors, chromatin-remodeling proteins, and enzymes that affect gene expression are all disrupted simultaneously. Hence, therapies that target pathogenic pathways in HD, including neuroinflammation, transcriptional dysregulation, triplet instability, vesicle trafficking dysfunction, and protein degradation, need to be developed.
Collapse
Affiliation(s)
- Pooja Temgire
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, 151401, Punjab, India
| | - Richmond Arthur
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, 151401, Punjab, India
| | - Puneet Kumar
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, 151401, Punjab, India.
| |
Collapse
|
4
|
Chen YZ, Zhu XM, Lv P, Hou XK, Pan Y, Li A, Du Z, Xuan JF, Guo X, Xing JX, Liu K, Yao J. Association of histone modification with the development of schizophrenia. Biomed Pharmacother 2024; 175:116747. [PMID: 38744217 DOI: 10.1016/j.biopha.2024.116747] [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: 02/29/2024] [Revised: 05/06/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024] Open
Abstract
Schizophrenia, influenced by genetic and environmental factors, may involve epigenetic alterations, notably histone modifications, in its pathogenesis. This review summarizes various histone modifications including acetylation, methylation, phosphorylation, ubiquitination, serotonylation, lactylation, palmitoylation, and dopaminylation, and their implications in schizophrenia. Current research predominantly focuses on histone acetylation and methylation, though other modifications also play significant roles. These modifications are crucial in regulating transcription through chromatin remodeling, which is vital for understanding schizophrenia's development. For instance, histone acetylation enhances transcriptional efficiency by loosening chromatin, while increased histone methyltransferase activity on H3K9 and altered histone phosphorylation, which reduces DNA affinity and destabilizes chromatin structure, are significant markers of schizophrenia.
Collapse
Affiliation(s)
- Yun-Zhou Chen
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China
| | - Xiu-Mei Zhu
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China
| | - Peng Lv
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China
| | - Xi-Kai Hou
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China
| | - Ying Pan
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China
| | - Ang Li
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China
| | - Zhe Du
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China
| | - Jin-Feng Xuan
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China
| | - Xiaochong Guo
- Laboratory Animal Center, China Medical University, PR China
| | - Jia-Xin Xing
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China.
| | - Kun Liu
- Key Laboratory of Health Ministry in Congenital Malformation, Shengjing Hospital of China Medical University, PR China.
| | - Jun Yao
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China.
| |
Collapse
|
5
|
Li Y, Li S, Li C, Zhang C, Yan L, Li J, He Y, Guo Y, Xia L. Fusion of a rice endogenous N-methylpurine DNA glycosylase to a plant adenine base transition editor ABE8e enables A-to-K base editing in rice plants. ABIOTECH 2024; 5:127-139. [PMID: 38974865 PMCID: PMC11224198 DOI: 10.1007/s42994-024-00138-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 01/11/2024] [Indexed: 07/09/2024]
Abstract
Engineering of a new type of plant base editor for simultaneous adenine transition and transversion within the editing window will greatly expand the scope and potential of base editing in directed evolution and crop improvement. Here, we isolated a rice endogenous hypoxanthine excision protein, N-methylpurine DNA glycosylase (OsMPG), and engineered two plant A-to-K (K = G or T) base editors, rAKBE01 and rAKBE02, for simultaneous adenine transition and transversion base editing in rice by fusing OsMPG or its mutant mOsMPG to a plant adenine transition base editor, ABE8e. We further coupled either OsMPG or mOsMPG with a transactivation factor VP64 to generate rAKBE03 and rAKBE04, respectively. Testing these four rAKBEs, at five endogenous loci in rice protoplasts, indicated that rAKBE03 and rAKBE04 enabled higher levels of A-to-G base transitions when compared to ABE8e and ABE8e-VP64. Furthermore, whereas rAKBE01 only enabled A-to-C/T editing at one endogenous locus, in comparison with rAKBE02 and rAKBE03, rAKBE04 could significantly improve the A-to-C/T base transversion efficiencies by up to 6.57- and 1.75-fold in the rice protoplasts, respectively. Moreover, although no stable lines with A-to-C transversion were induced by rAKBE01 and rAKBE04, rAKBE04 could enable simultaneous A-to-G and A-to-T transition and transversion base editing, at all the five target loci, with the efficiencies of A-to-G transition and A-to-T transversion editing ranging from 70.97 to 92.31% and 1.67 to 4.84% in rice stable lines, respectively. Together, these rAKBEs enable different portfolios of editing products and, thus, now expands the potential of base editing in diverse application scenario for crop improvement. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-024-00138-8.
Collapse
Affiliation(s)
- Yucai Li
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081 China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193 China
- Hainan Yazhou Bay Seed Laboratory/National Nanfan Research Institute (Sanya), CAAS, Sanya, 572024 China
| | - Shaoya Li
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081 China
- Hainan Yazhou Bay Seed Laboratory/National Nanfan Research Institute (Sanya), CAAS, Sanya, 572024 China
| | - Chenfei Li
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081 China
| | - Chen Zhang
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081 China
| | - Lei Yan
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081 China
| | - Jingying Li
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081 China
- Hainan Yazhou Bay Seed Laboratory/National Nanfan Research Institute (Sanya), CAAS, Sanya, 572024 China
| | - Yubing He
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081 China
- Hainan Yazhou Bay Seed Laboratory/National Nanfan Research Institute (Sanya), CAAS, Sanya, 572024 China
| | - Yan Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193 China
| | - Lanqin Xia
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081 China
- Hainan Yazhou Bay Seed Laboratory/National Nanfan Research Institute (Sanya), CAAS, Sanya, 572024 China
| |
Collapse
|
6
|
Dasgupta A, Nandi S, Gupta S, Roy S, Das C. To Ub or not to Ub: The epic dilemma of histones that regulate gene expression and epigenetic cross-talk. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195033. [PMID: 38750882 DOI: 10.1016/j.bbagrm.2024.195033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 01/04/2024] [Accepted: 05/06/2024] [Indexed: 05/23/2024]
Abstract
A dynamic array of histone post-translational modifications (PTMs) regulate diverse cellular processes in the eukaryotic chromatin. Among them, histone ubiquitination is particularly complex as it alters nucleosome surface area fostering intricate cross-talk with other chromatin modifications. Ubiquitin signaling profoundly impacts DNA replication, repair, and transcription. Histones can undergo varied extent of ubiquitination such as mono, multi-mono, and polyubiquitination, which brings about distinct cellular fates. Mechanistic studies of the ubiquitin landscape in chromatin have unveiled a fascinating tapestry of events that orchestrate gene regulation. In this review, we summarize the key contributors involved in mediating different histone ubiquitination and deubiquitination events, and discuss their mechanism which impacts cell transcriptional identity and DNA damage response. We also focus on the proteins bearing epigenetic reader modules critical in discerning site-specific histone ubiquitination, pivotal for establishing complex epigenetic crosstalk. Moreover, we highlight the role of histone ubiquitination in different human diseases including neurodevelopmental disorders and cancer. Overall the review elucidates the intricate orchestration of histone ubiquitination impacting diverse cellular functions and disease pathogenesis, and provides insights into the current challenges of targeting them for therapeutic interventions.
Collapse
Affiliation(s)
- Anirban Dasgupta
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology, Kolkata, India; Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Sandhik Nandi
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Sayan Gupta
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology, Kolkata, India
| | - Siddhartha Roy
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology, Kolkata, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India.
| |
Collapse
|
7
|
Zhao X, Du M, Wu S, Du Z, Liu S, Yang L, Ma H, Zhang L, Song L, Bai C, Su G, Li G. High histone crotonylation modification in bovine fibroblasts promotes cell proliferation and the developmental efficiency of preimplantation nuclear transfer embryos. Sci Rep 2024; 14:10295. [PMID: 38704415 PMCID: PMC11069573 DOI: 10.1038/s41598-024-61148-6] [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: 01/17/2024] [Accepted: 05/02/2024] [Indexed: 05/06/2024] Open
Abstract
Lysine crotonylation (Kcr) is a recently discovered histone acylation modification that is closely associated with gene expression, cell proliferation, and the maintenance of stem cell pluripotency and indicates the transcriptional activity of genes and the regulation of various biological processes. During cell culture, the introduction of exogenous croconic acid disodium salt (Nacr) has been shown to modulate intracellular Kcr levels. Although research on Kcr has increased, its role in cell growth and proliferation and its potential regulatory mechanisms remain unclear compared to those of histone methylation and acetylation. Our investigation demonstrated that the addition of 5 mM Nacr to cultured bovine fibroblasts increased the expression of genes associated with Kcr modification, ultimately promoting cell growth and stimulating cell proliferation. Somatic cell nuclear transfer of donor cells cultured in 5 mM Nacr resulted in 38.1% blastocyst development, which was significantly greater than that in the control group (25.2%). This research is important for elucidating the crotonylation modification mechanism in fibroblast proliferation to promote the efficacy of somatic cell nuclear transfer.
Collapse
Affiliation(s)
- Xiaoyu Zhao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot, 010070, China
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot, 010070, China
| | - Mengxin Du
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot, 010070, China
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot, 010070, China
| | - Shanshan Wu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot, 010070, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Zhiwen Du
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot, 010070, China
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot, 010070, China
| | - Shuqin Liu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot, 010070, China
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot, 010070, China
| | - Lei Yang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot, 010070, China
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot, 010070, China
| | - Haoran Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Liguo Zhang
- Ulanqab Agriculture and Animal Husbandry Bureau, Ulanqab Animal Husbandry Workstation, Ulanqab, 012000, Inner Mongolia, China
| | - Lishuang Song
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot, 010070, China
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot, 010070, China
| | - Chunling Bai
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot, 010070, China
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot, 010070, China
| | - Guanghua Su
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot, 010070, China.
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot, 010070, China.
| | - Guangpeng Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), Inner Mongolia University, 24 Zhaojun Rd., Hohhot, 010070, China.
- College of Life Sciences, Inner Mongolia University, 24 Zhaojun Rd., Hohhot, 010070, China.
| |
Collapse
|
8
|
Samota MK, Awana M, Krishnan V, Kumar S, Tyagi A, Pandey R, Mithra SVA, Singh A. A novel micronutrients and methyl jasmonate cocktail of elicitors via seed priming improves drought tolerance by mitigating oxidative stress in rice (Oryza sativa L.). PROTOPLASMA 2024; 261:553-570. [PMID: 38159129 DOI: 10.1007/s00709-023-01914-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 12/09/2023] [Indexed: 01/03/2024]
Abstract
Drought is a major limiting factor for rice (Oryza sativa L.) production globally, and a cost-effective seed priming technique using bio-elicitors has been found to have stress mitigating effects. Till date, mostly phytohormones have been preferred as bio-elicitors, but the present study is a novel attempt to demonstrate the favorable role of micronutrients-phytohormone cocktail, i.e., iron (Fe), zinc (Zn), and methyl jasmonate (MJ) via seed priming method in mitigating the deleterious impacts of drought stress through physio-biochemical and molecular manifestations. The effect of cocktail/priming was studied on the relative water content, chlorophyll a/b and carotenoid contents, proline content, abscisic acid (ABA) content, and on the activities of ascorbate peroxidase (APX), superoxide dismutase (SOD), NADPH oxidase (Nox), and catalase (CAT). The expressions of drought-responsive genes OsZn-SOD, OsFe-SOD, and Nox1 were found to be modulated under drought stress in contrasting rice genotypes -N-22 (Nagina-22, drought-tolerant) and PS-5 (Pusa Sugandh-5, drought-sensitive). A progressive rise in carotenoids (10-19%), ABA (18-50%), proline (60-80%), activities of SOD (27-62%), APX (46-61%), CAT (50-80%), Nox (16-30%), and upregulated (0.9-1.6-fold) expressions of OsZn-SOD, OsFe-SOD, and Nox1 genes were found in the primed plants under drought condition. This cocktail would serve as a potential supplement in modern agricultural practices utilizing seed priming technique to mitigate drought stress-induced oxidative burst in food crops.
Collapse
Affiliation(s)
- Mahesh Kumar Samota
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi-110012, India
- HCP-Division, ICAR-CIPHET, Abohar, Punjab-152116, India
| | - Monika Awana
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi-110012, India
| | - Veda Krishnan
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi-110012, India
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi-110012, India
| | - Aruna Tyagi
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi-110012, India
| | - Rakesh Pandey
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi-110012, India
| | - S V Amitha Mithra
- ICAR-National Institute for Plant Biotechnology, New Delhi-110012, India
| | - Archana Singh
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi-110012, India.
| |
Collapse
|
9
|
Kim TS, Moutsopoulos NM. Neutrophils and neutrophil extracellular traps in oral health and disease. Exp Mol Med 2024; 56:1055-1065. [PMID: 38689085 PMCID: PMC11148164 DOI: 10.1038/s12276-024-01219-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 05/02/2024] Open
Abstract
Neutrophils perform essential functions in antimicrobial defense and tissue maintenance at mucosal barriers. However, a dysregulated neutrophil response and, in particular, the excessive release of neutrophil extracellular traps (NETs) are implicated in the pathology of various diseases. In this review, we provide an overview of the basic concepts related to neutrophil functions, including NET formation, and discuss the mechanisms associated with NET activation and function in the context of the prevalent oral disease periodontitis.
Collapse
Affiliation(s)
- Tae Sung Kim
- Oral Immunity and Infection Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Niki M Moutsopoulos
- Oral Immunity and Infection Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA
| |
Collapse
|
10
|
Yang C, Ge L, Yu X, Lazarovici P, Zheng W. Artemisinin Confers Cytoprotection toward Hydrogen Peroxide-Induced Cell Apoptosis in Retinal Pigment Epithelial Cells in Correlation with the Increased Acetylation of Histone H4 at Lysine 8. Molecules 2024; 29:1789. [PMID: 38675608 PMCID: PMC11051841 DOI: 10.3390/molecules29081789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/28/2024] [Accepted: 03/31/2024] [Indexed: 04/28/2024] Open
Abstract
Increased oxidative stress is one of the critical pathologies inducing age-related macular degeneration (AMD), characterized by retinal pigment epithelial (RPE) cell damage and death. The unbalanced acetylation and deacetylation of histones have been implicated in AMD pathogenesis or hydrogen peroxide (H2O2)-induced cell damage. Therefore, strategies aimed at controlling the balance between acetylation and deacetylation may effectively protect RPE cells from oxidative damage. Artemisinin is an antimalarial lactone drug derived from Artemisia annua, with antioxidant activity known to modulate histone acetylation in the brain, but its effect on the retina is unknown. In this study, we aimed to investigate whether Artemisinin exerts a cytoprotective effect on oxidative stress-induced apoptosis in RPE cells by regulating histone acetylation. We hypothesized that Artemisinin confers cytoprotection toward H2O2-induced apoptosis in RPE cells through this mechanism. In the present study, we found that Artemisinin at a sub-clinic dosage of 20 μM inhibited the H2O2-induced cell viability decrease and B-cell lymphoma 2 (Bcl-2) protein level decrease and attenuated the H2O2-induced decrease in the histone H4 lysine (Lys) 8 acetylation [Acetyl-H4 (Lys 8)] level in the retinal RPE cell line D407. As expected, histone deacetylase inhibitor Trichostatin A at the concentration of 250 nM increased the Acetyl-H4 (Lys 8) level in D407 cells and attenuated the H2O2-induced cell viability decrease and apoptosis. Similar findings were obtained using adult RPE (ARPE)19 cells, another human RPE cell line, and primary human RPE cell cultures. In conclusion, these results confirmed our hypothesis and indicated that Artemisinin attenuated H2O2-induced apoptosis in apparent correlation with the increase in the Acetyl-H4 (Lys 8) level, which is associated with gene transcription and cell survival. By modulating histone acetylation, Artemisinin may restore the balance between acetylation and deacetylation and enhance the resistance and survival of RPE cells under oxidative stress. Our study provides novel mechanistic insights into the effect of Artemisinin on histone acetylation and apoptosis in RPE cells and supports the potential application of Artemisinin in the prevention and/or treatment of AMD.
Collapse
Affiliation(s)
- Chao Yang
- Department of Pharmaceutical Science, Faculty of Health Sciences, University of Macau, Taipa 999078, Macau, China; (C.Y.); (L.G.)
| | - Lijun Ge
- Department of Pharmaceutical Science, Faculty of Health Sciences, University of Macau, Taipa 999078, Macau, China; (C.Y.); (L.G.)
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Xiyong Yu
- School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou 511436, China;
| | - Philip Lazarovici
- School of Pharmacy Institute for Drug Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112002, Israel;
| | - Wenhua Zheng
- Department of Pharmaceutical Science, Faculty of Health Sciences, University of Macau, Taipa 999078, Macau, China; (C.Y.); (L.G.)
- Zhuhai UM Science & Technology Research Institute, Zhuhai 519000, China
| |
Collapse
|
11
|
Zhang LL, Liu JX. 3D chromatin reorganization during stress responses in plants. Sci Bull (Beijing) 2024; 69:847-849. [PMID: 38278707 DOI: 10.1016/j.scib.2024.01.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Affiliation(s)
- Lin-Lin Zhang
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Jian-Xiang Liu
- State Key Laboratory of Plant Environmental Resilience, College of Life Sciences, Zhejiang University, Hangzhou 310027, China.
| |
Collapse
|
12
|
Baptista Pereira P, Torrejón E, Ferreira I, Carvalho AS, Teshima A, Sousa-Lima I, Beck HC, Costa-Silva B, Matthiesen R, Macedo MP, de Oliveira RM. Proteomic Profiling of Plasma- and Gut-Derived Extracellular Vesicles in Obesity. Nutrients 2024; 16:736. [PMID: 38474865 DOI: 10.3390/nu16050736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Obesity entails metabolic alterations across multiple organs, highlighting the role of inter-organ communication in its pathogenesis. Extracellular vesicles (EVs) are communication agents in physiological and pathological conditions, and although they have been associated with obesity comorbidities, their protein cargo in this context remains largely unknown. To decipher the messages encapsulated in EVs, we isolated plasma-derived EVs from a diet-induced obese murine model. Obese plasma EVs exhibited a decline in protein diversity while control EVs revealed significant enrichment in protein-folding functions, highlighting the importance of proper folding in maintaining metabolic homeostasis. Previously, we revealed that gut-derived EVs' proteome holds particular significance in obesity. Here, we compared plasma and gut EVs and identified four proteins exclusively present in the control state of both EVs, revealing the potential for a non-invasive assessment of gut health by analyzing blood-derived EVs. Given the relevance of post-translational modifications (PTMs), we observed a shift in chromatin-related proteins from glycation to acetylation in obese gut EVs, suggesting a regulatory mechanism targeting DNA transcription during obesity. This study provides valuable insights into novel roles of EVs and protein PTMs in the intricate mechanisms underlying obesity, shedding light on potential biomarkers and pathways for future research.
Collapse
Affiliation(s)
- Pedro Baptista Pereira
- Metabolic Diseases Research Group, iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal
| | - Estefania Torrejón
- Metabolic Diseases Research Group, iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal
| | - Inês Ferreira
- Metabolic Diseases Research Group, iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal
| | - Ana Sofia Carvalho
- Computational and Experimental Biology Group, iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal
| | - Akiko Teshima
- Metabolic Diseases Research Group, iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal
| | - Inês Sousa-Lima
- Metabolic Diseases Research Group, iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal
| | - Hans Christian Beck
- Centre for Clinical Proteomics, Department of Clinical Biochemistry, Odense University Hospital, DK-5000 Odense, Denmark
| | - Bruno Costa-Silva
- Champalimaud Physiology and Cancer Programme, Champalimaud Foundation, 1400-038 Lisboa, Portugal
| | - Rune Matthiesen
- Computational and Experimental Biology Group, iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal
| | - Maria Paula Macedo
- Metabolic Diseases Research Group, iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal
| | - Rita Machado de Oliveira
- Metabolic Diseases Research Group, iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal
| |
Collapse
|
13
|
Travis CR, Kean KM, Albanese KI, Henriksen HC, Treacy JW, Chao EY, Houk KN, Waters ML. Trimethyllysine Reader Proteins Exhibit Widespread Charge-Agnostic Binding via Different Mechanisms to Cationic and Neutral Ligands. J Am Chem Soc 2024; 146:3086-3093. [PMID: 38266163 PMCID: PMC11140585 DOI: 10.1021/jacs.3c10031] [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] [Indexed: 01/26/2024]
Abstract
In the last 40 years, cation-π interactions have become part of the lexicon of noncovalent forces that drive protein binding. Indeed, tetraalkylammoniums are universally bound by aromatic cages in proteins, suggesting that cation-π interactions are a privileged mechanism for binding these ligands. A prominent example is the recognition of histone trimethyllysine (Kme3) by the conserved aromatic cage of reader proteins, dictating gene expression. However, two proteins have recently been suggested as possible exceptions to the conventional understanding of tetraalkylammonium recognition. To broadly interrogate the role of cation-π interactions in protein binding interactions, we report the first large-scale comparative evaluation of reader proteins for a neutral Kme3 isostere, experimental and computational mechanistic studies, and structural analysis. We find unexpected widespread binding of readers to a neutral isostere with the first examples of readers that bind the neutral isostere more tightly than Kme3. We find that no single factor dictates the charge selectivity, demonstrating the challenge of predicting such interactions. Further, readers that bind both cationic and neutral ligands differ in mechanism: binding Kme3 via cation-π interactions and the neutral isostere through the hydrophobic effect in the same aromatic cage. This discovery explains apparently contradictory results in previous studies, challenges traditional understanding of molecular recognition of tetraalkylammoniums by aromatic cages in myriad protein-ligand interactions, and establishes a new framework for selective inhibitor design by exploiting differences in charge dependence.
Collapse
Affiliation(s)
- Christopher R. Travis
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kelsey M. Kean
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Katherine I. Albanese
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Hanne C. Henriksen
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Joseph W. Treacy
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Elaine Y. Chao
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095-1569, USA
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Marcey L. Waters
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| |
Collapse
|
14
|
Scadden AW, Graybill AS, Hull-Crew C, Lundberg TJ, Lande NM, Klocko AD. Histone deacetylation and cytosine methylation compartmentalize heterochromatic regions in the genome organization of Neurospora crassa. Proc Natl Acad Sci U S A 2023; 120:e2311249120. [PMID: 37963248 PMCID: PMC10666030 DOI: 10.1073/pnas.2311249120] [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: 07/20/2023] [Accepted: 10/11/2023] [Indexed: 11/16/2023] Open
Abstract
Chromosomes must correctly fold in eukaryotic nuclei for proper genome function. Eukaryotic organisms hierarchically organize their genomes, including in the fungus Neurospora crassa, where chromatin fiber loops compact into Topologically Associated Domain-like structures formed by heterochromatic region aggregation. However, insufficient data exist on how histone posttranslational modifications (PTMs), including acetylation, affect genome organization. In Neurospora, the HCHC complex [composed of the proteins HDA-1, CDP-2 (Chromodomain Protein-2), Heterochromatin Protein-1, and CHAP (CDP-2 and HDA-1 Associated Protein)] deacetylates heterochromatic nucleosomes, as loss of individual HCHC members increases centromeric acetylation, and alters the methylation of cytosines in DNA. Here, we assess whether the HCHC complex affects genome organization by performing Hi-C in strains deleted of the cdp-2 or chap genes. CDP-2 loss increases intra- and interchromosomal heterochromatic region interactions, while loss of CHAP decreases heterochromatic region compaction. Individual HCHC mutants exhibit different patterns of histone PTMs genome-wide, as CDP-2 deletion increases heterochromatic H4K16 acetylation, yet smaller heterochromatic regions lose H3K9 trimethylation and gain interheterochromatic region interactions; CHAP loss produces minimal acetylation changes but increases heterochromatic H3K9me3 enrichment. Loss of both CDP-2 and the DIM-2 DNA methyltransferase causes extensive genome disorder as heterochromatic-euchromatic contacts increase despite additional H3K9me3 enrichment. Our results highlight how the increased cytosine methylation in HCHC mutants ensures genome compartmentalization when heterochromatic regions become hyperacetylated without HDAC activity.
Collapse
Affiliation(s)
- Ashley W. Scadden
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
| | - Alayne S. Graybill
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
| | - Clayton Hull-Crew
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
| | - Tiffany J. Lundberg
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
| | - Nickolas M. Lande
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
| | - Andrew D. Klocko
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
| |
Collapse
|
15
|
Li Y, Li S, Li C, Zhang C, Yan L, Li J, He Y, Guo Y, Lin Y, Zhang Y, Xia L. Engineering a plant A-to-K base editor with improved performance by fusion with a transactivation module. PLANT COMMUNICATIONS 2023; 4:100667. [PMID: 37528582 PMCID: PMC10721455 DOI: 10.1016/j.xplc.2023.100667] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/19/2023] [Accepted: 07/26/2023] [Indexed: 08/03/2023]
Affiliation(s)
- Yucai Li
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; Hainan Yazhou Bay Seed Laboratory/National Nanfan Research Institute (Sanya), CAAS, Sanya, Hainan Province 572024, China; State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shaoya Li
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; Hainan Yazhou Bay Seed Laboratory/National Nanfan Research Institute (Sanya), CAAS, Sanya, Hainan Province 572024, China
| | - Chenfei Li
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Chen Zhang
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Lei Yan
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Jingying Li
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; Hainan Yazhou Bay Seed Laboratory/National Nanfan Research Institute (Sanya), CAAS, Sanya, Hainan Province 572024, China
| | - Yubing He
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; Hainan Yazhou Bay Seed Laboratory/National Nanfan Research Institute (Sanya), CAAS, Sanya, Hainan Province 572024, China
| | - Yan Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yong Lin
- Beijing Dabeinong Technology Group Co., Ltd., Beijing 10080, China
| | - Yangjun Zhang
- Beijing Dabeinong Technology Group Co., Ltd., Beijing 10080, China
| | - Lanqin Xia
- Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; Hainan Yazhou Bay Seed Laboratory/National Nanfan Research Institute (Sanya), CAAS, Sanya, Hainan Province 572024, China.
| |
Collapse
|
16
|
Yoshida Y, Nishiyama A, Suameitria Dewi DNS, Yamazaki T, Yokoyama A, Kobayashi D, Kondo H, Ozeki Y, Matsumoto S. Limited proteolysis of mycobacterial DNA-binding protein 1 with an extended, lysine-rich, intrinsically disordered region to unveil posttranslational modifications. Biochem Biophys Res Commun 2023; 681:111-119. [PMID: 37774568 DOI: 10.1016/j.bbrc.2023.09.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/13/2023] [Accepted: 09/13/2023] [Indexed: 10/01/2023]
Abstract
The basic, intrinsically disordered regions of eukaryotic histones and their bacterial counterparts are presumed to act as signaling hubs to regulate the compaction of chromosomes or nucleoids and various DNA processes such as gene expression, recombination, and DNA replication. Posttranslational modifications (PTMs) on these regions are pivotal in regulating chromosomal or nucleoid compaction and DNA processes. However, the low sequence complexity and the presence of short lysine-rich repeats in the regions have hindered the accurate determination of types and locations of PTMs using conventional proteomic procedures. We described a limited proteolysis protocol using trypsin to analyze PTMs on mycobacterial DNA-binding protein 1 (MDP1), a nucleoid-associated protein in mycobacterial species that possesses an extended, lysine-rich, intrinsically disordered region in its C-terminal domain. This limited proteolysis approach successfully revealed significant methylation on many lysine residues in the C-terminal domain of MDP1 purified from Mycobacterium tuberculosis, which was lacking in the corresponding region of recombinant MDP1 expressed in Escherichia coli.
Collapse
Affiliation(s)
- Yutaka Yoshida
- Department of Bacteriology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-Ku, Niigata, 951-8510, Japan.
| | - Akihito Nishiyama
- Department of Bacteriology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-Ku, Niigata, 951-8510, Japan
| | - Desak Nyoman Surya Suameitria Dewi
- Department of Bacteriology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-Ku, Niigata, 951-8510, Japan
| | - Tomoya Yamazaki
- Department of Bacteriology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-Ku, Niigata, 951-8510, Japan
| | - Akira Yokoyama
- Department of Bacteriology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-Ku, Niigata, 951-8510, Japan
| | - Daiki Kobayashi
- Omics Unit, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-Ku, Niigata, 951-8510, Japan
| | - Hitoshi Kondo
- Department of Bacteriology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-Ku, Niigata, 951-8510, Japan
| | - Yuriko Ozeki
- Department of Bacteriology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-Ku, Niigata, 951-8510, Japan
| | - Sohkichi Matsumoto
- Department of Bacteriology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-Ku, Niigata, 951-8510, Japan
| |
Collapse
|
17
|
Ahmadpour ST, Orre C, Bertevello PS, Mirebeau-Prunier D, Dumas JF, Desquiret-Dumas V. Breast Cancer Chemoresistance: Insights into the Regulatory Role of lncRNA. Int J Mol Sci 2023; 24:15897. [PMID: 37958880 PMCID: PMC10650504 DOI: 10.3390/ijms242115897] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are a subclass of noncoding RNAs composed of more than 200 nucleotides without the ability to encode functional proteins. Given their involvement in critical cellular processes such as gene expression regulation, transcription, and translation, lncRNAs play a significant role in organism homeostasis. Breast cancer (BC) is the second most common cancer worldwide and evidence has shown a relationship between aberrant lncRNA expression and BC development. One of the main obstacles in BC control is multidrug chemoresistance, which is associated with the deregulation of multiple mechanisms such as efflux transporter activity, mitochondrial metabolism reprogramming, and epigenetic regulation as well as apoptosis and autophagy. Studies have shown the involvement of a large number of lncRNAs in the regulation of such pathways. However, the underlying mechanism is not clearly elucidated. In this review, we present the principal mechanisms associated with BC chemoresistance that can be directly or indirectly regulated by lncRNA, highlighting the importance of lncRNA in controlling BC chemoresistance. Understanding these mechanisms in deep detail may interest the clinical outcome of BC patients and could be used as therapeutic targets to overcome BC therapy resistance.
Collapse
Affiliation(s)
- Seyedeh Tayebeh Ahmadpour
- Nutrition, Croissance et Cancer, Inserm, UMR1069, Université de Tours, 37032 Tours, France; (P.S.B.); (J.-F.D.)
| | - Charlotte Orre
- Inserm U1083, UMR CNRS 6214, Angers University, 49933 Angers, France; (C.O.); (D.M.-P.)
| | - Priscila Silvana Bertevello
- Nutrition, Croissance et Cancer, Inserm, UMR1069, Université de Tours, 37032 Tours, France; (P.S.B.); (J.-F.D.)
| | | | - Jean-François Dumas
- Nutrition, Croissance et Cancer, Inserm, UMR1069, Université de Tours, 37032 Tours, France; (P.S.B.); (J.-F.D.)
| | | |
Collapse
|
18
|
Somers DJ, Kushner DB, McKinnis AR, Mehmedovic D, Flame RS, Arnold TM. Epigenetic weapons in plant-herbivore interactions: Sulforaphane disrupts histone deacetylases, gene expression, and larval development in Spodoptera exigua while the specialist feeder Trichoplusia ni is largely resistant to these effects. PLoS One 2023; 18:e0293075. [PMID: 37856454 PMCID: PMC10586618 DOI: 10.1371/journal.pone.0293075] [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: 07/19/2023] [Accepted: 10/03/2023] [Indexed: 10/21/2023] Open
Abstract
Cruciferous plants produce sulforaphane (SFN), an inhibitor of nuclear histone deacetylases (HDACs). In humans and other mammals, the consumption of SFN alters enzyme activities, DNA-histone binding, and gene expression within minutes. However, the ability of SFN to act as an HDAC inhibitor in nature, disrupting the epigenetic machinery of insects feeding on these plants, has not been explored. Here, we demonstrate that SFN consumed in the diet inhibits the activity of HDAC enzymes and slows the development of the generalist grazer Spodoptera exigua, in a dose-dependent fashion. After consuming SFN for seven days, the activities of HDAC enzymes in S. exigua were reduced by 50%. Similarly, larval mass was reduced by 50% and pupation was delayed by 2-5 days, with no additional mortality. Similar results were obtained when SFN was applied topically to eggs. RNA-seq analyses confirm that SFN altered the expression of thousands of genes in S. exigua. Genes associated with energy conversion pathways were significantly downregulated while those encoding for ribosomal proteins were dramatically upregulated in response to the consumption of SFN. In contrast, the co-evolved specialist feeder Trichoplusia ni was not negatively impacted by SFN, whether it was consumed in their diet at natural concentrations or applied topically to eggs. The activities of HDAC enzymes were not inhibited and development was not disrupted. In fact, SFN exposure sometimes accelerated T. ni development. RNA-seq analyses revealed that the consumption of SFN alters gene expression in T. ni in similar ways, but to a lesser degree, compared to S. exigua. This apparent resistance of T. ni can be overwhelmed by unnaturally high levels of SFN or by exposure to more powerful pharmaceutical HDAC inhibitors. These results demonstrate that dietary SFN interferes with the epigenetic machinery of insects, supporting the hypothesis that plant-derived HDAC inhibitors serve as "epigenetic weapons" against herbivores.
Collapse
Affiliation(s)
- Dana J. Somers
- Department of Biology, Program in Biochemistry and Molecular Biology, Dickinson College, Carlisle, PA United States of America
| | - David B. Kushner
- Department of Biology, Program in Biochemistry and Molecular Biology, Dickinson College, Carlisle, PA United States of America
| | - Alexandria R. McKinnis
- Department of Biology, Program in Biochemistry and Molecular Biology, Dickinson College, Carlisle, PA United States of America
| | - Dzejlana Mehmedovic
- Department of Biology, Program in Biochemistry and Molecular Biology, Dickinson College, Carlisle, PA United States of America
| | - Rachel S. Flame
- Department of Biology, Program in Biochemistry and Molecular Biology, Dickinson College, Carlisle, PA United States of America
| | - Thomas M. Arnold
- Department of Biology, Program in Biochemistry and Molecular Biology, Dickinson College, Carlisle, PA United States of America
| |
Collapse
|
19
|
Kleene V, Corvaglia V, Chacin E, Forne I, Konrad DB, Khosravani P, Douat C, Kurat CF, Huc I, Imhof A. DNA mimic foldamers affect chromatin composition and disturb cell cycle progression. Nucleic Acids Res 2023; 51:9629-9642. [PMID: 37650653 PMCID: PMC10570015 DOI: 10.1093/nar/gkad681] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 08/02/2023] [Accepted: 08/10/2023] [Indexed: 09/01/2023] Open
Abstract
The use of synthetic chemicals to selectively interfere with chromatin and the chromatin-bound proteome represents a great opportunity for pharmacological intervention. Recently, synthetic foldamers that mimic the charge surface of double-stranded DNA have been shown to interfere with selected protein-DNA interactions. However, to better understand their pharmacological potential and to improve their specificity and selectivity, the effect of these molecules on complex chromatin needs to be investigated. We therefore systematically studied the influence of the DNA mimic foldamers on the chromatin-bound proteome using an in vitro chromatin assembly extract. Our studies show that the foldamer efficiently interferes with the chromatin-association of the origin recognition complex in vitro and in vivo, which leads to a disturbance of cell cycle in cells treated with foldamers. This effect is mediated by a strong direct interaction between the foldamers and the origin recognition complex and results in a failure of the complex to organise chromatin around replication origins. Foldamers that mimic double-stranded nucleic acids thus emerge as a powerful tool with designable features to alter chromatin assembly and selectively interfere with biological mechanisms.
Collapse
Affiliation(s)
- Vera Kleene
- Department of Molecular Biology, Biomedical Center Munich, Faculty of Medicine, Ludwig-Maximilians University, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Valentina Corvaglia
- Department of Pharmacy, Institute of Chemical Epigenetics, Ludwig-Maximilians University, Butenandtstraße 5-13, 81377 München, Germany
| | - Erika Chacin
- Department of Molecular Biology, Biomedical Center Munich, Faculty of Medicine, Ludwig-Maximilians University, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Ignasi Forne
- Protein Analysis Unit, Biomedical Center Munich, Faculty of Medicine, Ludwig-Maximilians University, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - David B Konrad
- Department of Pharmacy, Institute of Chemical Epigenetics, Ludwig-Maximilians University, Butenandtstraße 5-13, 81377 München, Germany
| | - Pardis Khosravani
- Core Facility Flow Cytometry, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Céline Douat
- Department of Pharmacy, Institute of Chemical Epigenetics, Ludwig-Maximilians University, Butenandtstraße 5-13, 81377 München, Germany
| | - Christoph F Kurat
- Department of Molecular Biology, Biomedical Center Munich, Faculty of Medicine, Ludwig-Maximilians University, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| | - Ivan Huc
- Department of Pharmacy, Institute of Chemical Epigenetics, Ludwig-Maximilians University, Butenandtstraße 5-13, 81377 München, Germany
| | - Axel Imhof
- Department of Molecular Biology, Biomedical Center Munich, Faculty of Medicine, Ludwig-Maximilians University, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
- Protein Analysis Unit, Biomedical Center Munich, Faculty of Medicine, Ludwig-Maximilians University, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany
| |
Collapse
|
20
|
Batel A, Polović M, Glumac M, Gelemanović A, Šprung M, Marinović Terzić I. Direct and cost-effective method for histone isolation from cultured mammalian cells. Prep Biochem Biotechnol 2023; 53:1067-1080. [PMID: 36645251 DOI: 10.1080/10826068.2023.2166958] [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] [Indexed: 01/17/2023]
Abstract
Histones are an essential part of nucleosomes that regulate chromatin structure and function. Histone exchanges and modifications represent a scaffold for DNA transcription, repair, and replication. Studying histones and histone code is an important and fast-developing branch of epigenetic science. Here we propose a fast, efficient, and versatile assay for nucleosomal histone isolation from mammalian cells, without the use of acids or high salt solutions which are common for other histone isolation techniques. All components used in the protocol are common and inexpensive laboratory chemicals. The protocol has been evaluated on six commonly used cell lines and two animal tissue samples. The mild extraction conditions preserve delicate histone epigenetic changes, allowing its downstream analyses. We have demonstrated the assays' successful application during changes in the transcriptional activity of histone genes, cell cycle transitions, and DNA-damaging conditions. Histone fractions, obtained by the protocol, can be used for further applications, such as electrophoresis, immunoblot, and mass spectrometry. Therefore, the new proposed nucleosomal histone isolation method is sensitive, specific, and suitable for downstream applications of various kinds.
Collapse
Affiliation(s)
- Anja Batel
- Laboratory for Cancer Research, University of Split School of Medicine, Split, Croatia
| | - Mirjana Polović
- Laboratory for Cancer Research, University of Split School of Medicine, Split, Croatia
| | - Mateo Glumac
- Laboratory for Cancer Research, University of Split School of Medicine, Split, Croatia
| | | | - Matilda Šprung
- Department of Biology, University of Split Faculty of Science, Split, Croatia
| | | |
Collapse
|
21
|
Scadden AW, Graybill AS, Hull-Crew C, Lundberg TJ, Lande NM, Klocko AD. Histone deacetylation and cytosine methylation compartmentalize heterochromatic regions in the genome organization of Neurospora crassa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.03.547530. [PMID: 37461718 PMCID: PMC10349943 DOI: 10.1101/2023.07.03.547530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Chromosomes must correctly fold in eukaryotic nuclei for proper genome function. Eukaryotic organisms hierarchically organize their genomes, including in the fungus Neurospora crassa, where chromatin fiber loops compact into Topologically Associated Domain (TAD)-like structures formed by heterochromatic region aggregation. However, insufficient data exists on how histone post-translational modifications, including acetylation, affect genome organization. In Neurospora, the HCHC complex (comprised of the proteins HDA-1, CDP-2, HP1, and CHAP) deacetylates heterochromatic nucleosomes, as loss of individual HCHC members increases centromeric acetylation and alters the methylation of cytosines in DNA. Here, we assess if the HCHC complex affects genome organization by performing Hi-C in strains deleted of the cdp-2 or chap genes. CDP-2 loss increases intra- and inter-chromosomal heterochromatic region interactions, while loss of CHAP decreases heterochromatic region compaction. Individual HCHC mutants exhibit different patterns of histone post-translational modifications genome-wide: without CDP-2, heterochromatic H4K16 acetylation is increased, yet smaller heterochromatic regions lose H3K9 trimethylation and gain inter-heterochromatic region interactions; CHAP loss produces minimal acetylation changes but increases heterochromatic H3K9me3 enrichment. Loss of both CDP-2 and the DIM-2 DNA methyltransferase causes extensive genome disorder, as heterochromatic-euchromatic contacts increase despite additional H3K9me3 enrichment. Our results highlight how the increased cytosine methylation in HCHC mutants ensures genome compartmentalization when heterochromatic regions become hyperacetylated without HDAC activity.
Collapse
Affiliation(s)
- Ashley W. Scadden
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
| | - Alayne S. Graybill
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
| | - Clayton Hull-Crew
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
| | - Tiffany J. Lundberg
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
| | - Nickolas M. Lande
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
| | - Andrew D. Klocko
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
| |
Collapse
|
22
|
Lei X, Tian X, Wang H, Xu X, Li G, Liu W, Wang D, Xiao Z, Zhang M, Li MJ, Zhang Z, Ma Z, Liu Z. Noncoding SNP at rs1663689 represses ADGRG6 via interchromosomal interaction and reduces lung cancer progression. EMBO Rep 2023; 24:e56212. [PMID: 37154297 PMCID: PMC10328068 DOI: 10.15252/embr.202256212] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 04/05/2023] [Accepted: 04/18/2023] [Indexed: 05/10/2023] Open
Abstract
A previous genome-wide association study (GWAS) revealed an association of the noncoding SNP rs1663689 with susceptibility to lung cancer in the Chinese population. However, the underlying mechanism is unknown. In this study, using allele-specific 4C-seq in heterozygous lung cancer cells combined with epigenetic information from CRISPR/Cas9-edited cell lines, we show that the rs1663689 C/C variant represses the expression of ADGRG6, a gene located on a separate chromosome, through an interchromosomal interaction of the rs1663689 bearing region with the ADGRG6 promoter. This reduces downstream cAMP-PKA signaling and subsequently tumor growth both in vitro and in xenograft models. Using patient-derived organoids, we show that rs1663689 T/T-but not C/C-bearing lung tumors are sensitive to the PKA inhibitor H89, potentially informing therapeutic strategies. Our study identifies a genetic variant-mediated interchromosomal interaction underlying ADGRG6 regulation and suggests that targeting the cAMP-PKA signaling pathway may be beneficial in lung cancer patients bearing the homozygous risk genotype at rs1663689.
Collapse
Affiliation(s)
- Xinyue Lei
- Department of Lung Cancer CenterTianjin Medical University Cancer Institute and HospitalHaihe Laboratory of Cell EcosystemState Key Laboratory of Experimental HematologyDepartment of UrologyThe Second Hospital of Tianjin Medical UniversityKey Laboratory of Immune Microenvironment and Disease of the Ministry of EducationDepartment of ImmunologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Xiaoling Tian
- Department of Lung Cancer CenterTianjin Medical University Cancer Institute and HospitalHaihe Laboratory of Cell EcosystemState Key Laboratory of Experimental HematologyDepartment of UrologyThe Second Hospital of Tianjin Medical UniversityKey Laboratory of Immune Microenvironment and Disease of the Ministry of EducationDepartment of ImmunologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Hao Wang
- Department of Lung Cancer CenterTianjin Medical University Cancer Institute and HospitalHaihe Laboratory of Cell EcosystemState Key Laboratory of Experimental HematologyDepartment of UrologyThe Second Hospital of Tianjin Medical UniversityKey Laboratory of Immune Microenvironment and Disease of the Ministry of EducationDepartment of ImmunologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Xinran Xu
- Department of Pharmacology, School of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Guoli Li
- Department of Lung Cancer CenterTianjin Medical University Cancer Institute and HospitalHaihe Laboratory of Cell EcosystemState Key Laboratory of Experimental HematologyDepartment of UrologyThe Second Hospital of Tianjin Medical UniversityKey Laboratory of Immune Microenvironment and Disease of the Ministry of EducationDepartment of ImmunologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Wenxu Liu
- Department of Lung Cancer CenterTianjin Medical University Cancer Institute and HospitalHaihe Laboratory of Cell EcosystemState Key Laboratory of Experimental HematologyDepartment of UrologyThe Second Hospital of Tianjin Medical UniversityKey Laboratory of Immune Microenvironment and Disease of the Ministry of EducationDepartment of ImmunologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Dan Wang
- Department of Lung Cancer CenterTianjin Medical University Cancer Institute and HospitalHaihe Laboratory of Cell EcosystemState Key Laboratory of Experimental HematologyDepartment of UrologyThe Second Hospital of Tianjin Medical UniversityKey Laboratory of Immune Microenvironment and Disease of the Ministry of EducationDepartment of ImmunologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Zengtuan Xiao
- Department of Lung Cancer CenterTianjin Medical University Cancer Institute and HospitalHaihe Laboratory of Cell EcosystemState Key Laboratory of Experimental HematologyDepartment of UrologyThe Second Hospital of Tianjin Medical UniversityKey Laboratory of Immune Microenvironment and Disease of the Ministry of EducationDepartment of ImmunologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Mengzhe Zhang
- Department of Lung Cancer CenterTianjin Medical University Cancer Institute and HospitalHaihe Laboratory of Cell EcosystemState Key Laboratory of Experimental HematologyDepartment of UrologyThe Second Hospital of Tianjin Medical UniversityKey Laboratory of Immune Microenvironment and Disease of the Ministry of EducationDepartment of ImmunologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Mulin Jun Li
- Department of Pharmacology, School of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Zhenfa Zhang
- Department of Lung Cancer CenterTianjin Medical University Cancer Institute and HospitalHaihe Laboratory of Cell EcosystemState Key Laboratory of Experimental HematologyDepartment of UrologyThe Second Hospital of Tianjin Medical UniversityKey Laboratory of Immune Microenvironment and Disease of the Ministry of EducationDepartment of ImmunologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Zhenyi Ma
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Department of Cell Biology, School of Basic Medical SciencesHangzhou Normal UniversityHangzhouChina
| | - Zhe Liu
- Department of Lung Cancer CenterTianjin Medical University Cancer Institute and HospitalHaihe Laboratory of Cell EcosystemState Key Laboratory of Experimental HematologyDepartment of UrologyThe Second Hospital of Tianjin Medical UniversityKey Laboratory of Immune Microenvironment and Disease of the Ministry of EducationDepartment of ImmunologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
- Department of Pharmacology, School of Basic Medical SciencesTianjin Medical UniversityTianjinChina
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Department of Cell Biology, School of Basic Medical SciencesHangzhou Normal UniversityHangzhouChina
- Collaborative Innovation Center for Cancer Personalized MedicineNanjing Medical UniversityNanjingChina
| |
Collapse
|
23
|
Song H, Chen J, Huang J, Sun P, Liu Y, Xu L, Wei C, Mu X, Lu X, Wang W, Zhang N, Shang M, Mo M, Zhang W, Zhao H, Han F. Epigenetic modification in Parkinson's disease. Front Cell Dev Biol 2023; 11:1123621. [PMID: 37351278 PMCID: PMC10283008 DOI: 10.3389/fcell.2023.1123621] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/18/2023] [Indexed: 06/24/2023] Open
Abstract
Parkinson's disease (PD) is a common neurodegenerative disorder caused by genetic, epigenetic, and environmental factors. Recent advance in genomics and epigenetics have revealed epigenetic mechanisms in PD. These epigenetic modifications include DNA methylation, post-translational histone modifications, chromatin remodeling, and RNA-based mechanisms, which regulate cellular functions in almost all cells. Epigenetic alterations are involved in multiple aspects of neuronal development and neurodegeneration in PD. In this review, we discuss current understanding of the epigenetic mechanisms that regulate gene expression and neural degeneration and then highlight emerging epigenetic targets and diagnostic and therapeutic biomarkers for treating or preventing PD.
Collapse
Affiliation(s)
- Hao Song
- The Innovation Institute for Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
- The Institute for Tissue Engineering and Regenerative Medicine, Liaocheng University/The Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Juanli Chen
- The Institute for Tissue Engineering and Regenerative Medicine, Liaocheng University/The Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Jin Huang
- Laboratory of Basic Medical Research, PLA Strategic Support Force Characteristic Medical Centre, Beijing, China
| | - Peng Sun
- The Innovation Institute for Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Yanming Liu
- The Institute for Tissue Engineering and Regenerative Medicine, Liaocheng University/The Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Li Xu
- The Institute for Tissue Engineering and Regenerative Medicine, Liaocheng University/The Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Chuanfei Wei
- The Institute for Tissue Engineering and Regenerative Medicine, Liaocheng University/The Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Xin Mu
- The Institute for Tissue Engineering and Regenerative Medicine, Liaocheng University/The Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Xianjie Lu
- The Institute for Tissue Engineering and Regenerative Medicine, Liaocheng University/The Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Wei Wang
- The Institute for Tissue Engineering and Regenerative Medicine, Liaocheng University/The Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Nan Zhang
- The Institute for Tissue Engineering and Regenerative Medicine, Liaocheng University/The Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Miwei Shang
- The Innovation Institute for Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Mei Mo
- The Innovation Institute for Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Wei Zhang
- Affiliated Yidu Central Hospital, Weifang Medical University, Weifang, China
| | - Hui Zhao
- Zhengzhou Revogene Scientific Co., LTD., Zhengzhou, Henan, China
| | - Fabin Han
- The Institute for Tissue Engineering and Regenerative Medicine, Liaocheng University/The Liaocheng People’s Hospital, Liaocheng, Shandong, China
- Zhengzhou Revogene Scientific Co., LTD., Zhengzhou, Henan, China
| |
Collapse
|
24
|
Bogush D, Schramm J, Ding Y, He B, Singh C, Sharma A, Tukaramrao DB, Iyer S, Desai D, Nalesnik G, Hengst J, Bhalodia R, Gowda C, Dovat S. Signaling pathways and regulation of gene expression in hematopoietic cells. Adv Biol Regul 2023; 88:100942. [PMID: 36621151 DOI: 10.1016/j.jbior.2022.100942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/06/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Cellular functions are regulated by signal transduction pathway networks consisting of protein-modifying enzymes that control the activity of many downstream proteins. Protein kinases and phosphatases regulate gene expression by reversible phosphorylation of transcriptional factors, which are their direct substrates. Casein kinase II (CK2) is a serine/threonine kinase that phosphorylates a large number of proteins that have critical roles in cellular proliferation, metabolism and survival. Altered function of CK2 has been associated with malignant transformation, immunological disorders and other types of diseases. Protein phosphatase 1 (PP1) is a serine/threonine phosphatase, which regulates the phosphorylation status of many proteins that are essential for cellular functions. IKAROS is a DNA-binding protein, which functions as a regulator of gene transcription in hematopoietic cells. CK2 directly phosphorylates IKAROS at multiple phosphosites which determines IKAROS activity as a regulator of gene expression. PP1 binds to IKAROS via the PP1-consensus recognition site and dephosphorylates serine/threonine residues that are phosphorylated by CK2. Thus, the interplay between CK2 and PP1 signaling pathways have opposing effects on the phosphorylation status of their mutual substrate - IKAROS. This review summarizes the effects of CK2 and PP1 on IKAROS role in regulation of gene expression and its function as a tumor suppressor in leukemia.
Collapse
Affiliation(s)
- Daniel Bogush
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Joseph Schramm
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Yali Ding
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Bing He
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Chingakham Singh
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Arati Sharma
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | | | - Soumya Iyer
- University of Chicago, Chicago, IL, 60637, USA
| | - Dhimant Desai
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Gregory Nalesnik
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Jeremy Hengst
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Riya Bhalodia
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA
| | - Chandrika Gowda
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA.
| | - Sinisa Dovat
- Pennsylvania State University College of Medicine, Hershey, PA, 1703, USA.
| |
Collapse
|
25
|
Nishigaya Y, Takase S, Sumiya T, Kikuzato K, Sato T, Niwa H, Sato S, Nakata A, Sonoda T, Hashimoto N, Namie R, Honma T, Umehara T, Shirouzu M, Koyama H, Yoshida M, Ito A, Shirai F. Discovery of Novel Substrate-Competitive Lysine Methyltransferase G9a Inhibitors as Anticancer Agents. J Med Chem 2023; 66:4059-4085. [PMID: 36882960 DOI: 10.1021/acs.jmedchem.2c02059] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Identification of structurally novel inhibitors of lysine methyltransferase G9a has been a subject of intense research in cancer epigenetics. Starting with the high-throughput screening (HTS) hit rac-10a obtained from the chemical library of the University of Tokyo Drug Discovery Initiative, the structure-activity relationship of the unique substrate-competitive inhibitors was established with the help of X-ray crystallography and fragment molecular orbital (FMO) calculations for the ligand-protein interaction. Further optimization of the in vitro characteristics and drug metabolism and pharmacokinetics (DMPK) properties led to the identification of 26j (RK-701), which is a structurally distinct potent inhibitor of G9a/GLP (IC50 = 27/53 nM). Compound 26j exhibited remarkable selectivity against other related methyltransferases, dose-dependent attenuation of cellular H3K9me2 levels, and tumor growth inhibition in MOLT-4 cells in vitro. Moreover, compound 26j showed inhibition of tumor initiation and growth in a carcinogen-induced hepatocellular carcinoma (HCC) in vivo mouse model without overt acute toxicity.
Collapse
Affiliation(s)
- Yosuke Nishigaya
- Watarase Research Center, Discovery Research Headquarters, Kyorin Pharmaceutical Co. Ltd., 1848 Nogi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Shohei Takase
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Tatsunobu Sumiya
- Watarase Research Center, Discovery Research Headquarters, Kyorin Pharmaceutical Co. Ltd., 1848 Nogi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | | | | | | | | | | | | | - Noriaki Hashimoto
- Watarase Research Center, Discovery Research Headquarters, Kyorin Pharmaceutical Co. Ltd., 1848 Nogi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Ryosuke Namie
- Watarase Research Center, Discovery Research Headquarters, Kyorin Pharmaceutical Co. Ltd., 1848 Nogi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | | | | | | | | | - Minoru Yoshida
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Akihiro Ito
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | | |
Collapse
|
26
|
Saurabh S, Nadendla K, Purohit SS, Sivakumar PM, Cetinel S. Fuzzy Drug Targets: Disordered Proteins in the Drug-Discovery Realm. ACS OMEGA 2023; 8:9729-9747. [PMID: 36969402 PMCID: PMC10034788 DOI: 10.1021/acsomega.2c07708] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Intrinsically disordered proteins (IDPs) and regions (IDRs) form a large part of the eukaryotic proteome. Contrary to the structure-function paradigm, the disordered proteins perform a myriad of functions in vivo. Consequently, they are involved in various disease pathways and are plausible drug targets. Unlike folded proteins, that have a defined structure and well carved out drug-binding pockets that can guide lead molecule selection, the disordered proteins require alternative drug-development methodologies that are based on an acceptable picture of their conformational ensemble. In this review, we discuss various experimental and computational techniques that contribute toward understanding IDP "structure" and describe representative pursuances toward IDP-targeting drug development. We also discuss ideas on developing rational drug design protocols targeting IDPs.
Collapse
Affiliation(s)
- Suman Saurabh
- Molecular
Sciences Research Hub, Department of Chemistry, Imperial College London, London W12 0BZ, U.K.
| | - Karthik Nadendla
- Center
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, Lensfield
Road, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Shubh Sanket Purohit
- Department
of Clinical Haematology, Sahyadri Superspeciality
Hospital, Pune, Maharashtra 411038, India
| | - Ponnurengam Malliappan Sivakumar
- Institute
of Research and Development, Duy Tan University, Da Nang 550000, Vietnam
- School
of Medicine and Pharmacy, Duy Tan University, Da Nang 550000, Vietnam
- Nanotechnology
Research and Application Center (SUNUM), Sabanci University, Istanbul 34956, Turkey
| | - Sibel Cetinel
- Nanotechnology
Research and Application Center (SUNUM), Sabanci University, Istanbul 34956, Turkey
- Faculty of
Engineering and Natural Sciences, Molecular Biology, Genetics and
Bioengineering Program, Sabanci University, Istanbul 34956, Turkey
| |
Collapse
|
27
|
Application of Nicotinamide to Culture Medium Improves the Efficiency of Genome Editing in Hexaploid Wheat. Int J Mol Sci 2023; 24:ijms24054416. [PMID: 36901844 PMCID: PMC10002385 DOI: 10.3390/ijms24054416] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 02/25/2023] Open
Abstract
Histone acetylation is the earliest and most well-characterized of post-translation modifications. It is mediated by histone acetyltransferases (HAT) and histone deacetylases (HDAC). Histone acetylation could change the chromatin structure and status and further regulate gene transcription. In this study, nicotinamide, a histone deacetylase inhibitor (HDACi), was used to enhance the efficiency of gene editing in wheat. Transgenic immature and mature wheat embryos harboring a non-mutated GUS gene, the Cas9 and a GUS-targeting sgRNA were treated with nicotinamide in two concentrations (2.5 and 5 mM) for 2, 7, and 14 days in comparison with a no-treatment control. The nicotinamide treatment resulted in GUS mutations in up to 36% of regenerated plants, whereas no mutants were obtained from the non-treated embryos. The highest efficiency was achieved when treated with 2.5 mM nicotinamide for 14 days. To further validate the impact of nicotinamide treatment on the effectiveness of genome editing, the endogenous TaWaxy gene, which is responsible for amylose synthesis, was tested. Utilizing the aforementioned nicotinamide concentration to treat embryos containing the molecular components for editing the TaWaxy gene, the editing efficiency could be increased to 30.3% and 13.3%, respectively, for immature and mature embryos in comparison to the 0% efficiency observed in the control group. In addition, nicotinamide treatment during transformation progress could also improve the efficiency of genome editing approximately threefold in a base editing experiment. Nicotinamide, as a novel approach, may be employed to improve the editing efficacy of low-efficiency genome editing tools such as base editing and prime editing (PE) systems in wheat.
Collapse
|
28
|
Xie SS, Zhang YZ, Peng L, Yu DT, Zhu G, Zhao Q, Wang CH, Xie Q, Duan CG. JMJ28 guides sequence-specific targeting of ATX1/2-containing COMPASS-like complex in Arabidopsis. Cell Rep 2023; 42:112163. [PMID: 36827182 DOI: 10.1016/j.celrep.2023.112163] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 09/21/2022] [Accepted: 02/09/2023] [Indexed: 02/25/2023] Open
Abstract
Despite extensive investigations in mammals and yeasts, the importance and specificity of COMPASS-like complex, which catalyzes histone 3 lysine 4 methylation (H3K4me), are not fully understood in plants. Here, we report that JMJ28, a Jumonji C domain-containing protein in Arabidopsis, recognizes specific DNA motifs through a plant-specific WRC domain and acts as an interacting factor to guide the chromatin targeting of ATX1/2-containing COMPASS-like complex. JMJ28 associates with COMPASS-like complex in vivo via direct interaction with RBL. The DNA-binding activity of JMJ28 is essential for both the targeting specificity of ATX1/2-COMPASS and the deposition of H3K4me at specific loci but exhibit functional redundancy with alternative COMPASS-like complexes at other loci. Finally, we demonstrate that JMJ28 is a negative regulator of plant immunity. In summary, our findings reveal a plant-specific recruitment mechanism of COMPASS-like complex. These findings help to gain deeper insights into the regulatory mechanism of COMPASS-like complex in plants.
Collapse
Affiliation(s)
- Si-Si Xie
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi-Zhe Zhang
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Peng
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ding-Tian Yu
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guohui Zhu
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Qingzhen Zhao
- School of Life Sciences, Liaocheng University, Liaocheng 252000, China
| | - Chun-Han Wang
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qi Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Cheng-Guo Duan
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
29
|
Rapps K, Kisliouk T, Marco A, Weller A, Meiri N. Dieting reverses histone methylation and hypothalamic AgRP regulation in obese rats. Front Endocrinol (Lausanne) 2023; 14:1121829. [PMID: 36817590 PMCID: PMC9930686 DOI: 10.3389/fendo.2023.1121829] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/17/2023] [Indexed: 02/04/2023] Open
Abstract
INTRODUCTION Although dieting is a key factor in improving physiological functions associated with obesity, the role by which histone methylation modulates satiety/hunger regulation of the hypothalamus through weight loss remains largely elusive. Canonically, H3K9me2 is a transcriptional repressive post-translational epigenetic modification that is involved in obesity, however, its role in the hypothalamic arcuate nucleus (ARC) has not been thoroughly explored. Here we explore the role that KDM4D, a specific demethylase of residue H3K9, plays in energy balance by directly modulating the expression of AgRP, a key neuropeptide that regulates hunger response. METHODS We used a rodent model of diet-induced obesity (DIO) to assess whether histone methylation malprogramming impairs energy balance control and how caloric restriction may reverse this phenotype. Using ChIP-qPCR, we assessed the repressive modification of H3K9me2 at the site of AgRP. To elucidate the functional role of KDM4D in reversing obesity via dieting, a pharmacological agent, JIB-04 was used to inhibit the action of KDM4D in vivo. RESULTS In DIO, downregulation of Kdm4d mRNA results in both enrichment of H3K9me2 on the AgRP promoter and transcriptional repression of AgRP. Because epigenetic modifications are dynamic, it is possible for some of these modifications to be reversed when external cues are altered. The reversal phenomenon was observed in calorically restricted rats, in which upregulation of Kdm4d mRNA resulted in demethylation of H3K9 on the AgRP promoter and transcriptional increase of AgRP. In order to verify that KDM4D is necessary to reverse obesity by dieting, we demonstrated that in vivo inhibition of KDM4D activity by pharmacological agent JIB-04 in naïve rats resulted in transcriptional repression of AgRP, decreasing orexigenic signaling, thus inhibiting hunger. DISCUSSION We propose that the action of KDM4D through the demethylation of H3K9 is critical in maintaining a stable epigenetic landscape of the AgRP promoter, and may offer a target to develop new treatments for obesity.
Collapse
Affiliation(s)
- Kayla Rapps
- Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel
- Institute of Animal Science, Agricultural Research Organization, The Volcani Center, Rishon LeZiyyon, Israel
- Gonda Multidisciplinary Brain Research Center, Bar Ilan University, Ramat-Gan, Israel
| | - Tatiana Kisliouk
- Institute of Animal Science, Agricultural Research Organization, The Volcani Center, Rishon LeZiyyon, Israel
| | - Asaf Marco
- Neuro-Epigenetics Laboratory, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Aron Weller
- Gonda Multidisciplinary Brain Research Center, Bar Ilan University, Ramat-Gan, Israel
- Department of Psychology, Bar Ilan University, Ramat-Gan, Israel
| | - Noam Meiri
- Institute of Animal Science, Agricultural Research Organization, The Volcani Center, Rishon LeZiyyon, Israel
| |
Collapse
|
30
|
Zhang SM, Cao J, Yan Q. KDM5 Lysine Demethylases in Pathogenesis, from Basic Science Discovery to the Clinic. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1433:113-137. [PMID: 37751138 DOI: 10.1007/978-3-031-38176-8_6] [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] [Indexed: 09/27/2023]
Abstract
The histone lysine demethylase 5 (KDM5) family proteins are Fe2+ and α-ketoglutarate-dependent dioxygenases, with jumonji C (JmjC) domain as their catalytic core and several plant homeodomains (PHDs) to bind different histone methylation marks. These enzymes are capable of demethylating tri-, di- and mono-methylated lysine 4 in histone H3 (H3K4me3/2/1), the key epigenetic marks for active chromatin. Thus, this H3K4 demethylase family plays critical roles in cell fate determination during development as well as malignant transformation. KDM5 demethylases have both oncogenic and tumor suppressive functions in a cancer type-dependent manner. In solid tumors, KDM5A/B are generally oncogenic, whereas KDM5C/D have tumor suppressive roles. Their involvement in de-differentiation, cancer metastasis, drug resistance, and tumor immunoevasion indicated that KDM5 family proteins are promising drug targets for cancer therapy. Significant efforts from both academia and industry have led to the development of potent and selective KDM5 inhibitors for preclinical experiments and phase I clinical trials. However, a better understanding of the roles of KDM5 demethylases in different physiological and pathological conditions is critical for further developing KDM5 modulators for clinical applications.
Collapse
Affiliation(s)
- Shang-Min Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Jian Cao
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, 08901, USA.
- Department of Medicine, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA.
| | - Qin Yan
- Department of Pathology, Yale Cancer Center, Yale Stem Cell Center, Yale Center for Immuno-Oncology, Yale Center for Research on Aging, Yale School of Medicine, P.O. Box 208023, New Haven, CT, 06520-8023, USA.
| |
Collapse
|
31
|
Nunez-Vazquez R, Desvoyes B, Gutierrez C. Histone variants and modifications during abiotic stress response. FRONTIERS IN PLANT SCIENCE 2022; 13:984702. [PMID: 36589114 PMCID: PMC9797984 DOI: 10.3389/fpls.2022.984702] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 09/28/2022] [Indexed: 06/17/2023]
Abstract
Plants have developed multiple mechanisms as an adaptive response to abiotic stresses, such as salinity, drought, heat, cold, and oxidative stress. Understanding these regulatory networks is critical for coping with the negative impact of abiotic stress on crop productivity worldwide and, eventually, for the rational design of strategies to improve plant performance. Plant alterations upon stress are driven by changes in transcriptional regulation, which rely on locus-specific changes in chromatin accessibility. This process encompasses post-translational modifications of histone proteins that alter the DNA-histones binding, the exchange of canonical histones by variants that modify chromatin conformation, and DNA methylation, which has an implication in the silencing and activation of hypervariable genes. Here, we review the current understanding of the role of the major epigenetic modifications during the abiotic stress response and discuss the intricate relationship among them.
Collapse
|
32
|
Zhang Z, Yang W, Chu Y, Yin X, Liang Y, Wang Q, Wang L, Han Z. AtHD2D, a plant-specific histone deacetylase involved in abscisic acid response and lateral root development. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7380-7400. [PMID: 36125085 DOI: 10.1093/jxb/erac381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 09/18/2022] [Indexed: 06/15/2023]
Abstract
In eukaryotes, histone acetylation levels directly regulate downstream gene expression. As a plant-specific histone deacetylase (HDAC), HD2D is involved in plant development and abiotic stress. However, the response of HD2D to drought stress and its interacting proteins, is still unclear. In this study, we analysed HD2D gene expression patterns in Arabidopsis, revealing that HD2D gene was highly expressed in roots and rosette leaves, but poorly expressed in other tissues such as stems, flowers, and young siliques. The HD2D gene expression was induced by d-mannitol. We investigated the responses to drought stress in the wild-type plant, HD2D overexpression lines, and hd2d mutants. HD2D-overexpressing lines showed abscisic acid (ABA) hypersensitivity and drought tolerance, and these phenotypes were not present in hd2d mutants. RNA-seq analysis revealed the transcriptome changes caused by HD2D under drought stress, and showed that HD2D responded to drought stress via the ABA signalling pathway. In addition, we demonstrated that CASEIN KINASE II (CKA4) directly interacted with HD2D. The phosphorylation of Ser residues on HD2D by CKA4 enhanced HD2D enzymatic activity. Furthermore, the phosphorylation of HD2D was shown to contribute to lateral root development and ABA sensing in Arabidopsis, but, these phenotypes could not be reproduced by the overexpression of Ser-phospho-null HD2D lines. Collectively, this study suggests that HD2D responded to drought stress by regulating the ABA signalling pathway, and the expression of drought stress-related genes. The regulatory mechanism of HD2D mediated by CKII phosphorylation provides new insights into the ABA response and lateral root development in Arabidopsis.
Collapse
Affiliation(s)
- Zhaochen Zhang
- College of Life Science, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Weixia Yang
- College of Chemistry & Pharmacy, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Yueyang Chu
- College of Life Science, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Xiaotong Yin
- College of Life Science, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Yueqi Liang
- College of Innovation and Experiment, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Qiuping Wang
- College of Life Science, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Lei Wang
- College of Life Science, Northwest A & F University, Yangling, Shanxi 712100, China
| | - Zhaofen Han
- College of Life Science, Northwest A & F University, Yangling, Shanxi 712100, China
| |
Collapse
|
33
|
Serra-Bardenys G, Peiró S. Enzymatic lysine oxidation as a posttranslational modification. FEBS J 2022; 289:8020-8031. [PMID: 34535954 PMCID: PMC10078733 DOI: 10.1111/febs.16205] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 09/09/2021] [Accepted: 09/16/2021] [Indexed: 01/14/2023]
Abstract
Oxidoreductases catalyze oxidation-reduction reactions and comprise a very large and diverse group of enzymes, which can be subclassified depending on the catalytic mechanisms of the enzymes. One of the most prominent oxidative modifications in proteins is carbonylation, which involves the formation of aldehyde and keto groups in the side chain of lysines. This modification can alter the local macromolecular structure of proteins, thereby regulating their function, stability, and/or localization, as well as the nature of any protein-protein and/or protein-nucleic acid interactions. In this review, we focus on copper-dependent amine oxidases, which catalyze oxidative deamination of amines to aldehydes. In particular, we discuss oxidation reactions that involve lysine residues and that are regulated by members of the lysyl oxidase (LOX) family of proteins. We summarize what is known about the newly identified substrates and how this posttranslational modification regulates protein function in different contexts.
Collapse
Affiliation(s)
| | - Sandra Peiró
- Vall d´Hebron Institute of Oncology (VHIO), Barcelona, Spain
| |
Collapse
|
34
|
Cerutti E, D'Amico M, Cainero I, Pelicci PG, Faretta M, Dellino GI, Diaspro A, Lanzanò L. Alterations induced by the PML-RARα oncogene revealed by image cross correlation spectroscopy. Biophys J 2022; 121:4358-4367. [PMID: 36196056 PMCID: PMC9703036 DOI: 10.1016/j.bpj.2022.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/30/2022] [Accepted: 10/03/2022] [Indexed: 12/14/2022] Open
Abstract
The molecular mechanisms that underlie oncogene-induced genomic damage are still poorly understood. To understand how oncogenes affect chromatin architecture, it is important to visualize fundamental processes such as DNA replication and transcription in intact nuclei and quantify the alterations of their spatiotemporal organization induced by oncogenes. Here, we apply superresolution microscopy in combination with image cross correlation spectroscopy to the U937-PR9 cell line, an in vitro model of acute promyelocytic leukemia that allows us to activate the expression of the PML-RARα oncogene and analyze its effects on the spatiotemporal organization of functional nuclear processes. More specifically, we perform Tau-stimulated emission depletion imaging, a superresolution technique based on the concept of separation of photons by lifetime tuning. Tau-stimulated emission depletion imaging is combined with a robust image analysis protocol that quickly produces a value of colocalization fraction on several hundreds of single cells and allows observation of cell-to-cell variability. Upon activation of the oncogene, we detect a significant increase in the fraction of transcription sites colocalized with PML/PML-RARα. This increase of colocalization can be ascribed to oncogene-induced disruption of physiological PML bodies and the abnormal occurrence of a relatively large number of PML-RARα microspeckles. We also detect a significant cell-to-cell variability of this increase of colocalization, which can be ascribed, at least in part, to a heterogeneous response of the cells to the activation of the oncogene. These results prove that our method efficiently reveals oncogene-induced alterations in the spatial organization of nuclear processes and suggest that the abnormal localization of PML-RARα could interfere with the transcription machinery, potentially leading to DNA damage and genomic instability.
Collapse
Affiliation(s)
- Elena Cerutti
- Department of Physics and Astronomy "Ettore Majorana", University of Catania, Catania, Italy; Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Morgana D'Amico
- Department of Physics and Astronomy "Ettore Majorana", University of Catania, Catania, Italy
| | - Isotta Cainero
- Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Mario Faretta
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Gaetano Ivan Dellino
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.
| | - Alberto Diaspro
- Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Genoa, Italy; DIFILAB, Department of Physics, University of Genoa, Genoa, Italy
| | - Luca Lanzanò
- Department of Physics and Astronomy "Ettore Majorana", University of Catania, Catania, Italy; Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Genoa, Italy.
| |
Collapse
|
35
|
Phylogenomic and Evolutionary Analyses Reveal Diversifications of SET-Domain Proteins in Fungi. J Fungi (Basel) 2022; 8:jof8111159. [DOI: 10.3390/jof8111159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/28/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
In recent years, many publications have established histone lysine methylation as a central epigenetic modification in the regulation of chromatin and transcription. The histone lysine methyltransferases contain a conserved SET domain and are widely distributed in various organisms. However, a comprehensive study on the origin and diversification of the SET-domain-containing genes in fungi has not been conducted. In this study, a total of 3816 SET-domain-containing genes, which were identified and characterized using HmmSearch from 229 whole genomes sequenced fungal species, were used to ascertain their evolution and diversification in fungi. Using the CLANS program, all the SET-domain-containing genes were grouped into three main clusters, and each cluster contains several groups. Domain organization analysis showed that genes belonging to the same group have similar sequence structures. In contrast, different groups process domain organizations or locations differently, suggesting the SET-domain-containing genes belonging to different groups may have obtained distinctive regulatory mechanisms during their evolution. These genes that conduct the histone methylations (such as H3K4me, H3K9me, H3K27me, H4K20me, H3K36me) are mainly grouped into Cluster 1 while the other genes grouped into Clusters 2 and 3 are still functionally undetermined. Our results also showed that numerous gene duplication and loss events have happened during the evolution of those fungal SET-domain-containing proteins. Our results provide novel insights into the roles of SET-domain genes in fungal evolution and pave a fundamental path to further understanding the epigenetic basis of gene regulation in fungi.
Collapse
|
36
|
Korenfeld HT, Avram-Shperling A, Zukerman Y, Iluz A, Boocholez H, Ben-Shimon L, Ben-Aroya S. Reversal of histone H2B mono-ubiquitination is required for replication stress recovery. DNA Repair (Amst) 2022; 119:103387. [DOI: 10.1016/j.dnarep.2022.103387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 07/11/2022] [Accepted: 08/09/2022] [Indexed: 11/15/2022]
|
37
|
Caetano MAF, Castelucci P. Role of short chain fatty acids in gut health and possible therapeutic approaches in inflammatory bowel diseases. World J Clin Cases 2022; 10:9985-10003. [PMID: 36246826 PMCID: PMC9561599 DOI: 10.12998/wjcc.v10.i28.9985] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/02/2022] [Accepted: 08/25/2022] [Indexed: 02/05/2023] Open
Abstract
Inflammatory bowel diseases (IBDs) are characterized by inflammation in the gastrointestinal tract and include Ulcerative Colitis and Crohn’s Disease. These diseases are costly to health services, substantially reduce patients’ quality of life, and can lead to complications such as cancer and even death. Symptoms include abdominal pain, stool bleeding, diarrhea, and weight loss. The treatment of these diseases is symptomatic, seeking disease remission. The intestine is colonized by several microorganisms, such as fungi, viruses, and bacteria, which constitute the intestinal microbiota (IM). IM bacteria promotes dietary fibers fermentation and produces short-chain fatty acids (SCFAs) that exert several beneficial effects on intestinal health. SCFAs can bind to G protein-coupled receptors, such as GPR41 and GPR43, promoting improvements in the intestinal barrier, anti-inflammatory, and antioxidant effects. Thus, SCFAs could be a therapeutic tool for IBDs. However, the mechanisms involved in these beneficial effects of SCFAs remain poorly understood. Therefore, this paper aims to provide a review addressing the main aspects of IBDs, and a more detailed sight of SCFAs, focusing on the main effects on different aspects of the intestine with an emphasis on IBDs.
Collapse
Affiliation(s)
| | - Patricia Castelucci
- Department of Anatomy, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508900, SP, Brazil
| |
Collapse
|
38
|
A critical review of datasets and computational suites for improving cancer theranostics and biomarker discovery. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:206. [PMID: 36175717 DOI: 10.1007/s12032-022-01815-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/29/2022] [Indexed: 10/14/2022]
Abstract
Cancer has been constantly evolving and so is the research pertaining to cancer diagnosis and therapeutic regimens. Early detection and specific therapeutics are the key features of modern cancer therapy. These requirements can only be fulfilled with the integration of diverse high-throughput technologies. Integration of advanced omics methodology involving genomics, epigenomics, proteomics, and transcriptomics provide a clear understanding of multi-faceted cancer. In the past few years, tremendous high-throughput data have been generated from cancer genomics and epigenomic analyses, which on further methodological analyses can yield better biological insights. The major epigenetic alterations reported in cancer are DNA methylation levels, histone post-translational modifications, and epi-miRNA regulating the oncogenes and tumor suppressor genes. While the genomic analyses like gene expression profiling, cancer gene prediction, and genome annotation divulge the genetic alterations in oncogenes or tumor suppressor genes. Also, systems biology approach using biological networks is being extensively used to identify novel cancer biomarkers. Therefore, integration of these multi-dimensional approaches will help to identify potential diagnostic and therapeutic biomarkers. Here, we reviewed the critical databases and tools dedicated to various epigenomic and genomic alterations in cancer. The review further focuses on the multi-omics resources available for further validating the identified cancer biomarkers. We also highlighted the tools for cancer biomarker discovery using a systems biology approach utilizing genomic and epigenomic data. Biomarkers predicted using such integrative approaches are shown to be more clinically relevant.
Collapse
|
39
|
Tanaka Y, Yamanaka N, Koyano I, Hasunuma I, Kobayashi T, Kikuyama S, Iwamuro S. Dual Roles of Extracellular Histone H3 in Host Defense: Its Differential Regions Responsible for Antimicrobial and Cytotoxic Properties and Their Modes of Action. Antibiotics (Basel) 2022; 11:antibiotics11091240. [PMID: 36140018 PMCID: PMC9495139 DOI: 10.3390/antibiotics11091240] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/05/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
Extracellular histones play a dual role—antimicrobial and cytotoxic—in host defense. In this study, we evaluated the antimicrobial and cytotoxic activities of histone H3 and identified the responsible molecular regions for these properties. Broth microdilution assays indicated that histone H3 exhibits growth inhibitory activity against not only Gram-negative and -positive bacteria but also fungi. Observations under scanning electron microscopy (SEM) revealed that histone H3 induced morphological abnormalities on the cell surface of a wide range of reference pathogens. MTT assays and SEM observations indicated that histone H3 has strong cytotoxic and cell lytic effects on mammalian normal, immortal, and tumor cell lines. Assays using synthetic peptides corresponding to fragments 1–34 (H3DP1), 35–68 (H3DP2), 69–102 (H3DP3), and 103–135 (H3DP4) of histone H3 molecule demonstrated that its antimicrobial activity and cytotoxicity are elicited by the H3DP2 and H3DP3 protein regions, respectively. Enzyme-linked endotoxin binding assays indicated that histones H3 and H3DP1, H3DP2, and H3DP4, but not H3DP3, exhibited high affinities toward lipopolysaccharide and lipoteichoic acid. Our findings are expected to contribute to the development of new histone H3-based peptide antibiotics that are not cytotoxic.
Collapse
Affiliation(s)
- Yuri Tanaka
- Department of Biology, Faculty of Science, Toho University, Chiba 274-8510, Japan
| | - Nanako Yamanaka
- Department of Biology, Faculty of Science, Toho University, Chiba 274-8510, Japan
| | - Izumi Koyano
- Department of Biology, Faculty of Science, Toho University, Chiba 274-8510, Japan
| | - Itaru Hasunuma
- Department of Biology, Faculty of Science, Toho University, Chiba 274-8510, Japan
| | - Tetsuya Kobayashi
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Sakae Kikuyama
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Center for Advanced Biomedical Sciences, Waseda University, Tokyo 162-8480, Japan
| | - Shawichi Iwamuro
- Department of Biology, Faculty of Science, Toho University, Chiba 274-8510, Japan
- Correspondence: ; Tel.: +81-47-472-5206
| |
Collapse
|
40
|
Zhou X, Jin S, Pan J, Lin Q, Yang S, Ambe PC, Basharat Z, Zimmer V, Wang W, Hong W. Damage associated molecular patterns and neutrophil extracellular traps in acute pancreatitis. Front Cell Infect Microbiol 2022; 12:927193. [PMID: 36034701 PMCID: PMC9411527 DOI: 10.3389/fcimb.2022.927193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 07/21/2022] [Indexed: 11/15/2022] Open
Abstract
Previous researches have emphasized a trypsin-centered theory of acute pancreatitis (AP) for more than a century. With additional studies into the pathogenesis of AP, new mechanisms have been explored. Among them, the role of immune response bears great importance. Pro-inflammatory substances, especially damage-associated molecular patterns (DAMPs), play an essential role in activating, signaling, and steering inflammation. Meanwhile, activated neutrophils attach great importance to the immune defense by forming neutrophil extracellular traps (NETs), which cause ductal obstruction, premature trypsinogen activation, and modulate inflammation. In this review, we discuss the latest advances in understanding the pathological role of DAMPs and NETs in AP and shed light on the flexible crosstalk between these vital inflammatory mediators. We, then highlight the potentially promising treatment for AP targeting DAMPs and NETs, with a focus on novel insights into the mechanism, diagnosis, and management of AP.
Collapse
Affiliation(s)
- Xiaoying Zhou
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- School of the First Clinical Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Shengchun Jin
- School of the First Clinical Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jingyi Pan
- School of the First Clinical Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qingyi Lin
- School of the First Clinical Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Shaopeng Yang
- School of the First Clinical Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Peter C. Ambe
- Department of General Surgery, Visceral Surgery and Coloproctology, Vinzenz-Pallotti-Hospital Bensberg, Bensberg, Germany
| | - Zarrin Basharat
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Centre for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Vincent Zimmer
- Department of Medicine, Marienhausklinik St. Josef Kohlhof, Neunkirchen, Germany
- Department of Medicine II, Saarland University Medical Center, Saarland University, Homburg, Germany
| | - Wei Wang
- School of Mental Health, Wenzhou Medical University, Wenzhou, China
- Zhejiang Provincial Clinical Research Center for Mental Disorders, The Affiliated Wenzhou Kangning Hospital, Wenzhou Medical University, Wenzhou, China
- *Correspondence: Wandong Hong, ; Wei Wang,
| | - Wandong Hong
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- *Correspondence: Wandong Hong, ; Wei Wang,
| |
Collapse
|
41
|
Nofi CP, Wang P, Aziz M. Chromatin-Associated Molecular Patterns (CAMPs) in sepsis. Cell Death Dis 2022; 13:700. [PMID: 35961978 PMCID: PMC9372964 DOI: 10.1038/s41419-022-05155-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 01/21/2023]
Abstract
Several molecular patterns have been identified that recognize pattern recognition receptors. Pathogen-associated molecular patterns (PAMPs) and damage-associated molecular patterns (DAMPs) are commonly used terminologies to classify molecules originating from pathogen and endogenous molecules, respectively, to heighten the immune response in sepsis. Herein, we focus on a subgroup of endogenous molecules that may be detected as foreign and similarly trigger immune signaling pathways. These chromatin-associated molecules, i.e., chromatin containing nuclear DNA and histones, extracellular RNA, mitochondrial DNA, telomeric repeat-containing RNA, DNA- or RNA-binding proteins, and extracellular traps, may be newly classified as chromatin-associated molecular patterns (CAMPs). Herein, we review the release of CAMPs from cells, their mechanism of action and downstream immune signaling pathways, and targeted therapeutic approaches to mitigate inflammation and tissue injury in inflammation and sepsis.
Collapse
Affiliation(s)
- Colleen P. Nofi
- grid.250903.d0000 0000 9566 0634Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, Manhasset, NY USA ,Elmezi Graduate School of Molecular Medicine, Manhasset, NY USA ,grid.512756.20000 0004 0370 4759Department of Surgery, Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY USA
| | - Ping Wang
- grid.250903.d0000 0000 9566 0634Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, Manhasset, NY USA ,Elmezi Graduate School of Molecular Medicine, Manhasset, NY USA ,grid.512756.20000 0004 0370 4759Department of Surgery, Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY USA ,grid.512756.20000 0004 0370 4759Department of Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY USA
| | - Monowar Aziz
- grid.250903.d0000 0000 9566 0634Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, Manhasset, NY USA ,Elmezi Graduate School of Molecular Medicine, Manhasset, NY USA ,grid.512756.20000 0004 0370 4759Department of Surgery, Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY USA ,grid.512756.20000 0004 0370 4759Department of Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY USA
| |
Collapse
|
42
|
Liu Q, Liu P, Ji T, Zheng L, Shen C, Ran S, Liu J, Zhao Y, Niu Y, Wang T, Dong J. The histone methyltransferase SUVR2 promotes DSB repair via chromatin remodeling and liquid-liquid phase separation. MOLECULAR PLANT 2022; 15:1157-1175. [PMID: 35610973 DOI: 10.1016/j.molp.2022.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/15/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Maintaining genomic integrity and stability is particularly important for stem cells, which are at the top of the cell lineage origin. Here, we discovered that the plant-specific histone methyltransferase SUVR2 maintains the genome integrity of the root tip stem cells through chromatin remodeling and liquid-liquid phase separation (LLPS) when facing DNA double-strand breaks (DSBs). The histone methyltransferase SUVR2 (MtSUVR2) has histone methyltransferase activity and catalyzes the conversion of histone H3 lysine 9 monomethylation (H3K9me1) to H3K9me2/3 in vitro and in Medicago truncatula. Under DNA damage, the proportion of heterochromatin decreased and the level of DSB damage marker γ-H2AX increased in suvr2 mutants, indicating that MtSUVR2 promotes the compaction of the chromatin structure through H3K9 methylation modification to protect DNA from damage. Interestingly, MtSUVR2 was induced by DSBs to phase separate and form droplets to localize at the damage sites, and this was confirmed by immunofluorescence and fluorescence recovery after photobleaching experiments. The IDR1 and low-complexity domain regions of MtSUVR2 determined its phase separation in the nucleus, whereas the IDR2 region determined the interaction with the homologous recombinase MtRAD51. Furthermore, we found that MtSUVR2 drove the phase separation of MtRAD51 to form "DNA repair bodies," which could enhance the stability of MtRAD51 proteins to facilitate error-free homologous recombination repair of stem cells. Taken together, our study reveals that chromatin remodeling-associated proteins participate in DNA repair through LLPS.
Collapse
Affiliation(s)
- Qianwen Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Peng Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Tuo Ji
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Lihua Zheng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Chen Shen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shasha Ran
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jinling Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yafei Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yiding Niu
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Tao Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Jiangli Dong
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| |
Collapse
|
43
|
Grau-Bové X, Navarrete C, Chiva C, Pribasnig T, Antó M, Torruella G, Galindo LJ, Lang BF, Moreira D, López-Garcia P, Ruiz-Trillo I, Schleper C, Sabidó E, Sebé-Pedrós A. A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution. Nat Ecol Evol 2022; 6:1007-1023. [PMID: 35680998 PMCID: PMC7613034 DOI: 10.1038/s41559-022-01771-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 04/21/2022] [Indexed: 02/06/2023]
Abstract
Histones and associated chromatin proteins have essential functions in eukaryotic genome organization and regulation. Despite this fundamental role in eukaryotic cell biology, we lack a phylogenetically-comprehensive understanding of chromatin evolution. Here, we combine comparative proteomics and genomics analysis of chromatin in eukaryotes and archaea. Proteomics uncovers the existence of histone post-translational modifications in Archaea. However, archaeal histone modifications are scarce, in contrast with the highly conserved and abundant marks we identify across eukaryotes. Phylogenetic analysis reveals that chromatin-associated catalytic functions (e.g., methyltransferases) have pre-eukaryotic origins, whereas histone mark readers and chaperones are eukaryotic innovations. We show that further chromatin evolution is characterized by expansion of readers, including capture by transposable elements and viruses. Overall, our study infers detailed evolutionary history of eukaryotic chromatin: from its archaeal roots, through the emergence of nucleosome-based regulation in the eukaryotic ancestor, to the diversification of chromatin regulators and their hijacking by genomic parasites.
Collapse
Affiliation(s)
- Xavier Grau-Bové
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Cristina Navarrete
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | | | - Thomas Pribasnig
- Department of Functional and Evolutionary Ecology, Archaea Biology Unit, University of Vienna, Vienna, Austria
| | - Meritxell Antó
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Guifré Torruella
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Luis Javier Galindo
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Bernd Franz Lang
- Robert Cedergren Centre in Bioinformatics and Genomics, Department of Biochemistry, Université de Montréal, Montréal, Quebec, Canada
| | - David Moreira
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Purificación López-Garcia
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Christa Schleper
- Department of Functional and Evolutionary Ecology, Archaea Biology Unit, University of Vienna, Vienna, Austria
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Arnau Sebé-Pedrós
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| |
Collapse
|
44
|
The Intricate Epigenetic and Transcriptional Alterations in Pediatric High-Grade Gliomas: Targeting the Crosstalk as the Oncogenic Achilles’ Heel. Biomedicines 2022; 10:biomedicines10061311. [PMID: 35740334 PMCID: PMC9219798 DOI: 10.3390/biomedicines10061311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/27/2022] [Accepted: 05/28/2022] [Indexed: 02/01/2023] Open
Abstract
Pediatric high-grade gliomas (pHGGs) are a deadly and heterogenous subgroup of gliomas for which the development of innovative treatments is urgent. Advances in high-throughput molecular techniques have shed light on key epigenetic components of these diseases, such as K27M and G34R/V mutations on histone 3. However, modification of DNA compaction is not sufficient by itself to drive those tumors. Here, we review molecular specificities of pHGGs subcategories in the context of epigenomic rewiring caused by H3 mutations and the subsequent oncogenic interplay with transcriptional signaling pathways co-opted from developmental programs that ultimately leads to gliomagenesis. Understanding how transcriptional and epigenetic alterations synergize in each cellular context in these tumors could allow the identification of new Achilles’ heels, thereby highlighting new levers to improve their therapeutic management.
Collapse
|
45
|
Ferreira WAS, Vitiello GAF, da Silva Medina T, de Oliveira EHC. Comprehensive analysis of epigenetics regulation, prognostic and the correlation with immune infiltrates of GPX7 in adult gliomas. Sci Rep 2022; 12:6442. [PMID: 35440701 PMCID: PMC9018725 DOI: 10.1038/s41598-022-10114-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 03/24/2022] [Indexed: 12/15/2022] Open
Abstract
Gliomas are the most commonly occurring malignant brain tumor characterized by an immunosuppressive microenvironment accompanied by profound epigenetic changes, thus influencing the prognosis. Glutathione peroxidase 7 (GPX7) is essential for regulating reactive oxygen species homeostasis under oxidative stress. However, little is known about the function of GPX7 in gliomas. In this study, we hypothesized that GPX7 methylation status could influence biological functions and local immune responses that ultimately impact prognosis in adult gliomas. We conducted an integrated bioinformatics analysis mining GPX7 DNA methylation status, transcriptional and survival data of glioma patients. We discovered that GPX7 was remarkably increased in glioma tissues and cell lines, and was associated with poor prognosis. This upregulation was significantly linked to clinicopathological and molecular features, besides being expressed in a cell cycle-dependent manner. Our results consistently demonstrated that upregulation of GPX7 is tightly modulated by epigenetic processes, which also impacted the overall survival of patients with low-grade gliomas (LGG). Based on the analysis of biological functions, we found that GPX7 might be involved in immune mechanisms involving both innate and adaptive immunity, type I interferon production and regulation of synaptic transmission in LGG, whereas in GBM, it is mainly related to metabolic regulation of mitochondrial dynamics. We also found that GPX7 strongly correlates with immune cell infiltration and diverse immune cell markers, suggesting its role in tumor-specific immune response and in regulating the migration of immune cell types to the tumor microenvironment. Combining these multiple data, we provided the first evidence regarding the epigenetic-mediated regulatory mechanisms underlying GPX7 activation in gliomas. Furthermore, our study brings key insights into the significant effect of GPX7 in modulating both immune molecules and in immune cell infiltration in the microenvironment of gliomas, which might impact the patient outcome, opening up future opportunities to regulate the local immune response.
Collapse
Affiliation(s)
- Wallax Augusto Silva Ferreira
- Laboratory of Cytogenomics and Environmental Mutagenesis, Environment Section (SAMAM), Evandro Chagas Institute (IEC), Ananindeua, Brazil.
| | | | - Tiago da Silva Medina
- Translational Immuno-Oncology Group, International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil.,National Institute of Science and Technology in Oncogenomics and Therapeutic Innovation, São Paulo, Brazil
| | - Edivaldo Herculano Correa de Oliveira
- Laboratory of Cytogenomics and Environmental Mutagenesis, Environment Section (SAMAM), Evandro Chagas Institute (IEC), Ananindeua, Brazil.,Institute of Exact and Natural Sciences, Faculty of Natural Sciences, Federal University of Pará (UFPA), Belém, Brazil
| |
Collapse
|
46
|
Fang H, Luo Z, Lin C. Epigenetic reorganization during early embryonic lineage specification. Genes Genomics 2022; 44:379-387. [PMID: 35133623 DOI: 10.1007/s13258-021-01213-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 12/28/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Dynamic chromatin reorganization occurs during two waves of cell lineage specification process, blastocyst formation and gastrulation, to generate distinct cell types. Epigenetic defects have been associated with severe developmental defects and diseases. How epigenetic remodeling coordinates the two lineage specification waves is becoming uncovered, benefiting from the development and application of new technologies including low-input or single-cell epigenome analysis approached in the past few years. OBJECTIVE In this review, we aim to highlight the most recent findings on epigenetic remodeling in cell lineage specification during blastocyst formation and gastrulation. METHODS First, we introduce how DNA methylation dynamically changes in blastocyst formation and gastrulation and its function in transcriptional regulation lineage-specific genes. Then, we discuss widespread remodeling of histone modification at promoters and enhancers in orchestrating the trajectory of cell lineage specification. Finally, we review dynamics of chromatin accessibility and 3D structure regulating developmental gene expression and associating with specific transcription factor binding events at stage specific manner. We also highlight the key questions that remain to be answered to fully understand chromatin regulation and reorganization in lineage specification. CONCLUSION Here, we summarize the recent advances and discoveries on epigenetic reorganization and its roles in blastocyst formation and gastrulation, and how it cooperates with the lineage specification, painting from global sequencing data from mouse in vivo tissues.
Collapse
Affiliation(s)
- Haitong Fang
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, 210096, China.
| | - Zhuojuan Luo
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, 210096, China.,Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Chengqi Lin
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, 210096, China. .,Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China.
| |
Collapse
|
47
|
Liu X, Quan W, Bartels D. Stress memory responses and seed priming correlate with drought tolerance in plants: an overview. PLANTA 2022; 255:45. [PMID: 35066685 PMCID: PMC8784359 DOI: 10.1007/s00425-022-03828-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 01/08/2022] [Indexed: 05/08/2023]
Abstract
Environmental-friendly techniques based on plant stress memory, cross-stress tolerance, and seed priming help sustainable agriculture by mitigating negative effects of dehydration stress. The frequently uneven rainfall distribution caused by global warming will lead to more irregular and multiple abiotic stresses, such as heat stress, dehydration stress, cold stress or the combination of these stresses. Dehydration stress is one of the major environmental factors affecting the survival rate and productivity of plants. Hence, there is an urgent need to develop improved resilient varieties. Presently, technologies based on plant stress memory, cross-stress tolerance and priming of seeds represent fruitful and promising areas of future research and applied agricultural science. In this review, we will provide an overview of plant drought stress memory from physiological, biochemical, molecular and epigenetic perspectives. Drought priming-induced cross-stress tolerance to cold and heat stress will be discussed and the application of seed priming will be illustrated for different species.
Collapse
Affiliation(s)
- Xun Liu
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, 53115, Bonn, Germany
- College of Bioengineering, Sichuan University of Science & Engineering, Zigong, 643000, China
| | - Wenli Quan
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, 53115, Bonn, Germany
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000, Hubei, China
| | - Dorothea Bartels
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, 53115, Bonn, Germany.
| |
Collapse
|
48
|
Hawkins C, Lubanszky E. The diverse landscape of histone-mutant pediatric high-grade gliomas: A narrative review. GLIOMA 2022. [DOI: 10.4103/glioma.glioma_1_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
|
49
|
Min S, Lee HS, Ji JH, Heo Y, Kim Y, Chae S, Choi YW, Kang HC, Nakanishi M, Cho H. The chromatin remodeler RSF1 coordinates epigenetic marks for transcriptional repression and DSB repair. Nucleic Acids Res 2021; 49:12268-12283. [PMID: 34850117 PMCID: PMC8643642 DOI: 10.1093/nar/gkab1093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 02/06/2023] Open
Abstract
DNA lesions impact on local transcription and the damage-induced transcriptional repression facilitates efficient DNA repair. However, how chromatin dynamics cooperates with these two events remained largely unknown. We here show that histone H2A acetylation at K118 is enriched in transcriptionally active regions. Under DNA damage, the RSF1 chromatin remodeling factor recruits HDAC1 to DSB sites. The RSF1-HDAC1 complex induces the deacetylation of H2A(X)-K118 and its deacetylation is indispensable for the ubiquitination of histone H2A at K119. Accordingly, the acetylation mimetic H2A-K118Q suppressed the H2A-K119ub level, perturbing the transcriptional repression at DNA lesions. Intriguingly, deacetylation of H2AX at K118 also licenses the propagation of γH2AX and recruitment of MDC1. Consequently, the H2AX-K118Q limits DNA repair. Together, the RSF1-HDAC1 complex controls the traffic of the DNA damage response and transcription simultaneously in transcriptionally active chromatins. The interplay between chromatin remodelers and histone modifiers highlights the importance of chromatin versatility in the maintenance of genome integrity.
Collapse
Affiliation(s)
- Sunwoo Min
- Department of Biochemistry, Ajou University School of Medicine, Suwon 16499, Korea.,Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499, Korea
| | - Ho-Soo Lee
- Department of Biochemistry, Ajou University School of Medicine, Suwon 16499, Korea.,Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499, Korea
| | - Jae-Hoon Ji
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499, Korea.,Department of Biochemistry and Structural Biology, The University of Texas Health San Antonio, TX 78229-3000, USA
| | - Yungyeong Heo
- Department of Biomedical Sciences, the Graduate School of Ajou University, Suwon, Korea
| | - Yonghyeon Kim
- Department of Biomedical Sciences, the Graduate School of Ajou University, Suwon, Korea
| | - Sunyoung Chae
- Institute of Medical Science, Ajou University School of Medicine, Suwon 16499, Korea
| | - Yong Won Choi
- Department of Hematology-Oncology, Ajou University School of Medicine, Suwon, Korea
| | - Ho-Chul Kang
- Department of Physiology, Ajou University School of Medicine, Suwon, Korea
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The University of Tokyo, Tokyo 108-8639, Japan
| | - Hyeseong Cho
- Department of Biochemistry, Ajou University School of Medicine, Suwon 16499, Korea.,Genomic Instability Research Center, Ajou University School of Medicine, Suwon 16499, Korea
| |
Collapse
|
50
|
Zhang J, Lu X, MoghaddamKohi S, Shi L, Xu X, Zhu WG. Histone lysine modifying enzymes and their critical roles in DNA double-strand break repair. DNA Repair (Amst) 2021; 107:103206. [PMID: 34411909 DOI: 10.1016/j.dnarep.2021.103206] [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: 03/29/2021] [Revised: 07/24/2021] [Accepted: 08/05/2021] [Indexed: 10/20/2022]
Abstract
Cells protect the integrity of the genome against DNA double-strand breaks through several well-characterized mechanisms including nonhomologous end-joining repair, homologous recombination repair, microhomology-mediated end-joining and single-strand annealing. However, aberrant DNA damage responses (DDRs) lead to genome instability and tumorigenesis. Clarification of the mechanisms underlying the DDR following lethal damage will facilitate the identification of therapeutic targets for cancer. Histones are small proteins that play a major role in condensing DNA into chromatin and regulating gene function. Histone modifications commonly occur in several residues including lysine, arginine, serine, threonine and tyrosine, which can be acetylated, methylated, ubiquitinated and phosphorylated. Of these, lysine modifications have been extensively explored during DDRs. Here, we focus on discussing the roles of lysine modifying enzymes involved in acetylation, methylation, and ubiquitination during the DDR. We provide a comprehensive understanding of the basis of potential epigenetic therapies driven by histone lysine modifications.
Collapse
Affiliation(s)
- Jun Zhang
- Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, 518055, China
| | - Xiaopeng Lu
- Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, 518055, China
| | - Sara MoghaddamKohi
- Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, 518055, China
| | - Lei Shi
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.
| | - Xingzhi Xu
- Department of Cell Biology and Medical Genetics, School of Medicine, Shenzhen University, Shenzhen, 518055, China.
| | - Wei-Guo Zhu
- Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, 518055, China.
| |
Collapse
|