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Zhao A, Xu W, Han R, Wei J, Yu Q, Wang M, Li H, Li M, Chi G. Role of histone modifications in neurogenesis and neurodegenerative disease development. Ageing Res Rev 2024; 98:102324. [PMID: 38762100 DOI: 10.1016/j.arr.2024.102324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 04/30/2024] [Accepted: 05/05/2024] [Indexed: 05/20/2024]
Abstract
Progressive neuronal dysfunction and death are key features of neurodegenerative diseases; therefore, promoting neurogenesis in neurodegenerative diseases is crucial. With advancements in proteomics and high-throughput sequencing technology, it has been demonstrated that histone post-transcriptional modifications (PTMs) are often altered during neurogenesis when the brain is affected by disease or external stimuli and that the degree of histone modification is closely associated with the development of neurodegenerative diseases. This review aimed to show the regulatory role of histone modifications in neurogenesis and neurodegenerative diseases by discussing the changing patterns and functional significance of histone modifications, including histone methylation, acetylation, ubiquitination, phosphorylation, and lactylation. Finally, we explored the control of neurogenesis and the development of neurodegenerative diseases by artificially modulating histone modifications.
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Affiliation(s)
- Anqi Zhao
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Wenhong Xu
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Rui Han
- Department of Neurovascular Surgery, First Hospital of Jilin University, Changchun, 130021, China
| | - Junyuan Wei
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Qi Yu
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Miaomiao Wang
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Haokun Li
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Meiying Li
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China.
| | - Guangfan Chi
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China.
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2
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Xu L, Fan YH, Zhang XJ, Bai L. Unraveling the relationship between histone methylation and nonalcoholic fatty liver disease. World J Hepatol 2024; 16:703-715. [PMID: 38818286 PMCID: PMC11135277 DOI: 10.4254/wjh.v16.i5.703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/09/2024] [Accepted: 04/07/2024] [Indexed: 05/22/2024] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) poses a significant health challenge in modern societies due to shifts in lifestyle and dietary habits. Its complexity stems from genetic predisposition, environmental influences, and metabolic factors. Epigenetic processes govern various cellular functions such as transcription, chromatin structure, and cell division. In NAFLD, these epigenetic tendencies, especially the process of histone methylation, are intricately intertwined with fat accumulation in the liver. Histone methylation is regulated by different enzymes like methyltransferases and demethylases and influences the expression of genes related to adipogenesis. While early-stage NAFLD is reversible, its progression to severe stages becomes almost irreversible. Therefore, early detection and intervention in NAFLD are crucial, and understanding the precise role of histone methylation in the early stages of NAFLD could be vital in halting or potentially reversing the progression of this disease.
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Affiliation(s)
- Li Xu
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases; Gannan Innovation and Translational Medicine Research Institute, Gannan Medical University, Ganzhou 341000, China
| | - Yu-Hong Fan
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases; Gannan Innovation and Translational Medicine Research Institute, Gannan Medical University, Ganzhou 341000, China
| | - Xiao-Jing Zhang
- School of Basic Medical Sciences, Wuhan University, Wuhan 430060, China; State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases, Gannan Innovation and Translational Medicine Research Institute, Gannan Medical University, Ganzhou 341000, China
| | - Lan Bai
- State Key Laboratory of New Targets Discovery and Drug Development for Major Diseases; Gannan Innovation and Translational Medicine Research Institute, Gannan Medical University, Ganzhou 341000, China.
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3
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Wu D, Zhang J, Jun Y, Liu L, Huang C, Wang W, Yang C, Xiang Z, Wu J, Huang Y, Meng D, Yang Z, Zhou X, Cheng C, Yang J. The emerging role of DOT1L in cell proliferation and differentiation: Friend or foe. Histol Histopathol 2024; 39:425-435. [PMID: 37706592 DOI: 10.14670/hh-18-658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
Cell proliferation and differentiation are the basic physiological activities of cells. Mistakes in these processes may affect cell survival, or cause cell cycle dysregulation, such as tumorigenesis, birth defects and degenerative diseases. In recent years, it has been found that histone methyltransferase DOT1L is the only H3 lysine 79 methyltransferase, which plays an important role in the process of cell fate determination through monomethylation, dimethylation and trimethylation of H3K79. DOT1L has a pro-proliferative effect in leukemia cells; however, loss of heart-specific DOT1L leads to increased proliferation of cardiac tissue. Additionally, DOT1L has carcinogenic or tumor suppressive effects in different neoplasms. At present, some DOT1L inhibitors for the treatment of MLL-driven leukemia have achieved promising results in clinical trials, but completely blocking DOT1L will also bring some side effects. Thus, this uncertainty suggests that DOT1L has a unique function in cell physiology. In this review, we summarize the primary findings of DOT1L in regulating cell proliferation and differentiation. Correlations between DOT1L and cell fate specification might suggest DOT1L as a therapeutic target for diseases.
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Affiliation(s)
- Di Wu
- Department of Cardiology, The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People's Hospital, Yichang, PR China
- Institute of Cardiovascular Diseases, China Three Gorges University, Yichang, PR China
- Hubei Clinical Research Center for Ischemic Cardiovascular Disease, Yichang, PR China
| | - Jing Zhang
- Institute of Cardiovascular Diseases, China Three Gorges University, Yichang, PR China
- Hubei Clinical Research Center for Ischemic Cardiovascular Disease, Yichang, PR China.
| | - Yang Jun
- Department of Cardiology, The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People's Hospital, Yichang, PR China
- Institute of Cardiovascular Diseases, China Three Gorges University, Yichang, PR China
- Hubei Clinical Research Center for Ischemic Cardiovascular Disease, Yichang, PR China
| | - Li Liu
- Institute of Cardiovascular Diseases, China Three Gorges University, Yichang, PR China
- Hubei Clinical Research Center for Ischemic Cardiovascular Disease, Yichang, PR China
| | - Cuiyuan Huang
- Institute of Cardiovascular Diseases, China Three Gorges University, Yichang, PR China
- Hubei Clinical Research Center for Ischemic Cardiovascular Disease, Yichang, PR China
| | - Wei Wang
- Institute of Cardiovascular Diseases, China Three Gorges University, Yichang, PR China
- Hubei Clinical Research Center for Ischemic Cardiovascular Disease, Yichang, PR China
| | - Chaojun Yang
- Institute of Cardiovascular Diseases, China Three Gorges University, Yichang, PR China
- Hubei Clinical Research Center for Ischemic Cardiovascular Disease, Yichang, PR China
| | - Zujin Xiang
- Department of Cardiology, The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People's Hospital, Yichang, PR China
- Institute of Cardiovascular Diseases, China Three Gorges University, Yichang, PR China
- Hubei Clinical Research Center for Ischemic Cardiovascular Disease, Yichang, PR China
| | - Jingyi Wu
- Department of Cardiology, The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People's Hospital, Yichang, PR China
- Institute of Cardiovascular Diseases, China Three Gorges University, Yichang, PR China
- Hubei Clinical Research Center for Ischemic Cardiovascular Disease, Yichang, PR China
| | - Yifan Huang
- Department of Cardiology, The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People's Hospital, Yichang, PR China
- Institute of Cardiovascular Diseases, China Three Gorges University, Yichang, PR China
- Hubei Clinical Research Center for Ischemic Cardiovascular Disease, Yichang, PR China
| | - Di Meng
- Department of Cardiology, The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People's Hospital, Yichang, PR China
- Institute of Cardiovascular Diseases, China Three Gorges University, Yichang, PR China
- Hubei Clinical Research Center for Ischemic Cardiovascular Disease, Yichang, PR China
| | - Zishu Yang
- Institute of Cardiovascular Diseases, China Three Gorges University, Yichang, PR China
- Hubei Clinical Research Center for Ischemic Cardiovascular Disease, Yichang, PR China
| | - Xiaoyan Zhou
- Institute of Cardiovascular Diseases, China Three Gorges University, Yichang, PR China
- Hubei Clinical Research Center for Ischemic Cardiovascular Disease, Yichang, PR China
| | - Chen Cheng
- Department of Cardiology, The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People's Hospital, Yichang, PR China
- Institute of Cardiovascular Diseases, China Three Gorges University, Yichang, PR China
- Hubei Clinical Research Center for Ischemic Cardiovascular Disease, Yichang, PR China
| | - Jian Yang
- Department of Cardiology, The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People's Hospital, Yichang, PR China
- Institute of Cardiovascular Diseases, China Three Gorges University, Yichang, PR China
- Hubei Clinical Research Center for Ischemic Cardiovascular Disease, Yichang, PR China.
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Li X, Pei P, Shen J, Yu J, Wang F, Wang L, Liu C, Wang S. Folate deficiency reduced aberrant level of DOT1L-mediated histone H3K79 methylation causes disruptive SHH gene expression involved in neural tube defects. Epigenetics Chromatin 2023; 16:50. [PMID: 38093377 PMCID: PMC10720071 DOI: 10.1186/s13072-023-00517-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/16/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Neural tube defects (NTDs) are one of the most severe congenital abnormalities characterized by failures of the neural tube to close during early embryogenesis. Maternal folate deficiency could impact the occurrence of NTDs, however, the mechanisms involved in the cause of NTDs are poorly defined. RESULTS Here, we report that histone H3 methyltransferase disruptor of telomeric silencing 1-like (DOT1L) expression was significantly downregulated, and low levels of H3K79me2 were found in the corresponding NTDs samples with their maternal serum folate under low levels. Using ChIP-seq assays, we found that a decrease of H3K79me2 downregulates the expression of Shh and Sufu in mouse embryonic stem cells (mESC) under folate deficiency. Interestingly, folate antagonist methotrexate treatment led to attenuation of H3K79me2 due to Dot1l, affecting Shh and Sufu genes regulation. Upon further analysis, we find that the genes Shh and Sufu are both downregulated in the brain tissues of mice and humans with NTDs. There was a positive correlation between the transcription levels of Shh, Sufu and the protein levels of DOT1L by Pearson correlation analysis. CONCLUSION Our results indicate that abnormal Shh and Sufu genes expression reduced by aberrant Dot1l-mediated H3K79me2 levels could be the cause of NTDs occurrence.
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Affiliation(s)
- Xue Li
- Weifang People's Hospital, Weifang, 261041, Shandong, China
- School of Clinical Medical, Weifang Medical University, Weifang, 261053, Shandong, China
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Pei Pei
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Jinying Shen
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Juan Yu
- Department of Basic Medical Sciences, Changzhi Medical College, Changzhi, 046000, China
| | - Fang Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Lei Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Changyun Liu
- School of Clinical Medical, Weifang Medical University, Weifang, 261053, Shandong, China.
| | - Shan Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China.
- Institute of Basic Medical Sciences, Chinese Academy of Medical Science, Beijing, 100730, China.
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5
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Cheffer A, Garcia-Miralles M, Maier E, Akol I, Franz H, Srinivasan VSV, Vogel T. DOT1L deletion impairs the development of cortical parvalbumin-expressing interneurons. Cereb Cortex 2023; 33:10272-10285. [PMID: 37566909 PMCID: PMC10545437 DOI: 10.1093/cercor/bhad281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 08/13/2023] Open
Abstract
The cortical plate (CP) is composed of excitatory and inhibitory neurons, the latter of which originate in the ganglionic eminences. From their origin in the ventral telencephalon, maturing postmitotic interneurons migrate during embryonic development over some distance to reach their final destination in the CP. The histone methyltransferase Disruptor of Telomeric Silencing 1-like (DOT1L) is necessary for proper CP development and layer distribution of glutamatergic neurons. However, its specific role on cortical interneuron development has not yet been explored. Here, we demonstrate that DOT1L affects interneuron development in a cell autonomous manner. Deletion of Dot1l in Nkx2.1-expressing interneuron precursor cells results in an overall reduction and altered distribution of GABAergic interneurons in the CP from postnatal day 0 onwards. We observed an altered proportion of GABAergic interneurons in the cortex, with a significant decrease in parvalbumin-expressing interneurons. Moreover, a decreased number of mitotic cells at the embryonic day E14.5 was observed upon Dot1l deletion. Altogether, our results indicate that reduced numbers of cortical interneurons upon DOT1L deletion result from premature cell cycle exit, but effects on postmitotic differentiation, maturation, and migration are likely at play as well.
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Affiliation(s)
- Arquimedes Cheffer
- Department of Molecular Embryology, Medical Faculty, Institute of Anatomy and Cell Biology, Albert-Ludwigs-University Freiburg, Freiburg 79104, Germany
| | - Marta Garcia-Miralles
- Department of Molecular Embryology, Medical Faculty, Institute of Anatomy and Cell Biology, Albert-Ludwigs-University Freiburg, Freiburg 79104, Germany
| | - Esther Maier
- Department of Molecular Embryology, Medical Faculty, Institute of Anatomy and Cell Biology, Albert-Ludwigs-University Freiburg, Freiburg 79104, Germany
| | - Ipek Akol
- Department of Molecular Embryology, Medical Faculty, Institute of Anatomy and Cell Biology, Albert-Ludwigs-University Freiburg, Freiburg 79104, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg 79104, Germany
| | - Henriette Franz
- Department of Molecular Embryology, Medical Faculty, Institute of Anatomy and Cell Biology, Albert-Ludwigs-University Freiburg, Freiburg 79104, Germany
| | - Vandana Shree Vedartham Srinivasan
- Department of Molecular Embryology, Medical Faculty, Institute of Anatomy and Cell Biology, Albert-Ludwigs-University Freiburg, Freiburg 79104, Germany
| | - Tanja Vogel
- Department of Molecular Embryology, Medical Faculty, Institute of Anatomy and Cell Biology, Albert-Ludwigs-University Freiburg, Freiburg 79104, Germany
- Center for Basics in NeuroModulation (NeuroModul Basics), Medical Faculty, Albert-Ludwigs-University Freiburg, Freiburg 79104, Germany
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6
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Willemsen L, Prange KH, Neele AE, van Roomen CP, Gijbels M, Griffith GR, Toom MD, Beckers L, Siebeler R, Spann NJ, Chen HJ, Bosmans LA, Gorbatenko A, van Wouw S, Zelcer N, Jacobs H, van Leeuwen F, de Winther MP. DOT1L regulates lipid biosynthesis and inflammatory responses in macrophages and promotes atherosclerotic plaque stability. Cell Rep 2022; 41:111703. [DOI: 10.1016/j.celrep.2022.111703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 08/29/2022] [Accepted: 11/01/2022] [Indexed: 11/23/2022] Open
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7
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Cerebellar Abiotrophy in Australian Working Kelpies Is Associated with Two Major Risk Loci. Genes (Basel) 2022; 13:genes13101709. [PMID: 36292596 PMCID: PMC9602046 DOI: 10.3390/genes13101709] [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: 09/01/2022] [Revised: 09/20/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
An autosomal recessive form of inherited cerebellar abiotrophy (CA) that is characterized by a degeneration of Purkinje and granule cells in the cerebellar cortex occurs in the Australian working kelpie dog breed. The clinical signs of CA include ataxia, head tremor, motor in-coordination, wide-based stance, and high-stepping gait. Investigation of clinical and pathological features indicated two closely related diseases with differences in age of onset. A genome-wide association study on 45 CA affected and 290 normal healthy Kelpies identified two significantly associated loci, one on CFA9 and a second on CFA20. Dogs homozygous for the risk haplotype on CFA20 (23 dogs) show clinical signs before ten weeks of age. Missense variants in the sixth exon of disruptor of telomeric silencing 1-like (DOT1Lp.R200Q) and in the only exon of Leucine Rich Repeat And Ig Domain Containing 3 (LINGO3p.R359C), both on CFA20, segregate with the associated risk marker which has incomplete penetrance (42%). Affected dogs homozygous for the risk haplotype on CFA9 have later onset ataxia. A missense variant in exon 5 of Vacuole Membrane Protein 1 (VMP1 p.P160Q) on CFA9 segregates as a fully penetrant Mendelian recessive with later-onset CA. Across mammals, the variety of causative loci so far identified as influencing cerebellar disorders reinforces the complexity of the pathways that contribute to cerebellar development and function, and to the pathophysiological mechanisms that may lead to cerebellar ataxia.
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Wille CK, Sridharan R. Connecting the DOTs on Cell Identity. Front Cell Dev Biol 2022; 10:906713. [PMID: 35733849 PMCID: PMC9207516 DOI: 10.3389/fcell.2022.906713] [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: 03/28/2022] [Accepted: 05/18/2022] [Indexed: 01/04/2023] Open
Abstract
DOT1-Like (DOT1L) is the sole methyltransferase of histone H3K79, a modification enriched mainly on the bodies of actively transcribing genes. DOT1L has been extensively studied in leukemia were some of the most frequent onco-fusion proteins contain portions of DOT1L associated factors that mislocalize H3K79 methylation and drive oncogenesis. However, the role of DOT1L in non-transformed, developmental contexts is less clear. Here we assess the known functional roles of DOT1L both in vitro cell culture and in vivo models of mammalian development. DOT1L is evicted during the 2-cell stage when cells are totipotent and massive epigenetic and transcriptional alterations occur. Embryonic stem cell lines that are derived from the blastocyst tolerate the loss of DOT1L, while the reduction of DOT1L protein levels or its catalytic activity greatly enhances somatic cell reprogramming to induced pluripotent stem cells. DOT1L knockout mice are embryonically lethal when organogenesis commences. We catalog the rapidly increasing studies of total and lineage specific knockout model systems that show that DOT1L is broadly required for differentiation. Reduced DOT1L activity is concomitant with increased developmental potential. Contrary to what would be expected of a modification that is associated with active transcription, loss of DOT1L activity results in more upregulated than downregulated genes. DOT1L also participates in various epigenetic networks that are both cell type and developmental stage specific. Taken together, the functions of DOT1L during development are pleiotropic and involve gene regulation at the locus specific and global levels.
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Affiliation(s)
- Coral K. Wille
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, United States
- *Correspondence: Coral K. Wille, , Rupa Sridharan,
| | - Rupa Sridharan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, United States
- *Correspondence: Coral K. Wille, , Rupa Sridharan,
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Sutter PA, Karki S, Crawley I, Singh V, Bernt KM, Rowe DW, Crocker SJ, Bayarsaihan D, Guzzo RM. Mesenchyme-specific loss of Dot1L histone methyltransferase leads to skeletal dysplasia phenotype in mice. Bone 2021; 142:115677. [PMID: 33022452 PMCID: PMC7744341 DOI: 10.1016/j.bone.2020.115677] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/20/2020] [Accepted: 10/01/2020] [Indexed: 12/17/2022]
Abstract
Chromatin modifying enzymes play essential roles in skeletal development and bone maintenance, and deregulation of epigenetic mechanisms can lead to skeletal growth and malformation disorders. Here, we report a novel skeletal dysplasia phenotype in mice with conditional loss of Disruptor of telomeric silencing 1-like (Dot1L) histone methyltransferase in limb mesenchymal progenitors and downstream descendants. Phenotypic characterizations of mice with Dot1L inactivation by Prrx1-Cre (Dot1L-cKOPrrx1) revealed limb shortening, abnormal bone morphologies, and forelimb dislocations. Our in vivo and in vitro data support a crucial role for Dot1L in regulating growth plate chondrocyte proliferation and differentiation, extracellular matrix production, and secondary ossification center formation. Micro-computed tomography analysis of femurs revealed that partial loss of Dot1L expression is sufficient to impair trabecular bone formation and microarchitecture in young mice. Moreover, RNAseq analysis of Dot1L deficient chondrocytes implicated Dot1L in the regulation of key genes and pathways necessary to promote cell cycle regulation and skeletal growth. Collectively, our data show that early expression of Dot1L in limb mesenchyme provides essential regulatory control of endochondral bone morphology, growth, and stability.
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Affiliation(s)
- Pearl A Sutter
- Department of Neuroscience, School of Medicine, University of Connecticut Health, Farmington, CT, United States of America
| | - Sangita Karki
- Department of Neuroscience, School of Medicine, University of Connecticut Health, Farmington, CT, United States of America
| | - Ilan Crawley
- Department of Neuroscience, School of Medicine, University of Connecticut Health, Farmington, CT, United States of America
| | - Vijender Singh
- Bioinformatics, University of Connecticut, Storrs, CT, United States of America
| | - Kathrin M Bernt
- Division of Pediatric Oncology, Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania and Abramson Cancer Center, Philadelphia, PA, United States of America
| | - David W Rowe
- Department of Reconstructive Sciences, School of Dental Medicine, University of Connecticut Health, Farmington, CT, United States of America; Center for Regenerative Medicine and Skeletal Development, Farmington, CT, United States of America
| | - Stephen J Crocker
- Department of Neuroscience, School of Medicine, University of Connecticut Health, Farmington, CT, United States of America
| | - Dashzeveg Bayarsaihan
- Department of Reconstructive Sciences, School of Dental Medicine, University of Connecticut Health, Farmington, CT, United States of America; Center for Regenerative Medicine and Skeletal Development, Farmington, CT, United States of America
| | - Rosa M Guzzo
- Department of Neuroscience, School of Medicine, University of Connecticut Health, Farmington, CT, United States of America.
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10
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Stricker SH, Götz M. Epigenetic regulation of neural lineage elaboration: Implications for therapeutic reprogramming. Neurobiol Dis 2020; 148:105174. [PMID: 33171228 DOI: 10.1016/j.nbd.2020.105174] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 10/19/2020] [Accepted: 11/06/2020] [Indexed: 01/14/2023] Open
Abstract
The vulnerability of the mammalian brain is mainly due to its limited ability to generate new neurons once fully matured. Direct conversion of non-neuronal cells to neurons opens up a new avenue for therapeutic intervention and has made great strides also for in vivo applications in the injured brain. These great achievements raise the issue of adequate identity and chromatin hallmarks of the induced neurons. This may be particularly important, as aberrant epigenetic settings may reveal their adverse effects only in certain brain activity states. Therefore, we review here the knowledge about epigenetic memory and partially resetting of chromatin hallmarks from other reprogramming fields, before moving to the knowledge in direct neuronal reprogramming, which is still limited. Most importantly, novel tools are available now to manipulate specific epigenetic marks at specific sites of the genome. Applying these will eventually allow erasing aberrant epigenetic memory and paving the way towards new therapeutic approaches for brain repair.
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Affiliation(s)
- Stefan H Stricker
- Institute for Stem Cell Research, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, 82152 Planegg, Germany; Physiological Genomics, Biomedical Center (BMC), Ludwig-Maximilians Universitaet Muenchen, 82152 Planegg, Munich, Germany; MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian-Universität, BioMedical Center, Grosshaderner Strasse 9, Planegg-Martinsried 82152, Germany.
| | - Magdalena Götz
- Institute for Stem Cell Research, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, 82152 Planegg, Germany; Physiological Genomics, Biomedical Center (BMC), Ludwig-Maximilians Universitaet Muenchen, 82152 Planegg, Munich, Germany; SYNERGY, Excellence Cluster of Systems Neurology, BioMedical Center (BMC), Ludwig-Maximilians-Universitaet Muenchen, 82152 Planegg, Munich, Germany.
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11
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Ferrari F, Arrigoni L, Franz H, Izzo A, Butenko L, Trompouki E, Vogel T, Manke T. DOT1L-mediated murine neuronal differentiation associates with H3K79me2 accumulation and preserves SOX2-enhancer accessibility. Nat Commun 2020; 11:5200. [PMID: 33060580 PMCID: PMC7562744 DOI: 10.1038/s41467-020-19001-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 09/21/2020] [Indexed: 01/27/2023] Open
Abstract
During neuronal differentiation, the transcriptional profile and the epigenetic context of neural committed cells is subject to significant rearrangements, but a systematic quantification of global histone modification changes is still missing. Here, we show that H3K79me2 increases and H3K27ac decreases globally during in-vitro neuronal differentiation of murine embryonic stem cells. DOT1L mediates all three degrees of methylation of H3K79 and its enzymatic activity is critical to modulate cellular differentiation and reprogramming. In this context, we find that inhibition of DOT1L in neural progenitor cells biases the transcriptional state towards neuronal differentiation, resulting in transcriptional upregulation of genes marked with H3K27me3 on the promoter region. We further show that DOT1L inhibition affects accessibility of SOX2-bound enhancers and impairs SOX2 binding in neural progenitors. Our work provides evidence that DOT1L activity gates differentiation of progenitors by allowing SOX2-dependent transcription of stemness programs.
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Affiliation(s)
- Francesco Ferrari
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Laura Arrigoni
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Henriette Franz
- Institute of Anatomy and Cell Biology, Department of Molecular Embryology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Annalisa Izzo
- Institute of Anatomy and Cell Biology, Department of Molecular Embryology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ludmila Butenko
- Institute of Anatomy and Cell Biology, Department of Molecular Embryology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Eirini Trompouki
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Tanja Vogel
- Institute of Anatomy and Cell Biology, Department of Molecular Embryology, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
- Center for Basics in NeuroModulation (NeuroModul Basics), Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Esse R, Grishok A. Caenorhabditis elegans Deficient in DOT-1.1 Exhibit Increases in H3K9me2 at Enhancer and Certain RNAi-Regulated Regions. Cells 2020; 9:cells9081846. [PMID: 32781660 PMCID: PMC7464606 DOI: 10.3390/cells9081846] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/29/2020] [Accepted: 07/29/2020] [Indexed: 01/06/2023] Open
Abstract
The methylation of histone H3 at lysine 79 is a feature of open chromatin. It is deposited by the conserved histone methyltransferase DOT1. Recently, DOT1 localization and H3K79 methylation (H3K79me) have been correlated with enhancers in C. elegans and mammalian cells. Since earlier research implicated H3K79me in preventing heterochromatin formation both in yeast and leukemic cells, we sought to inquire whether a H3K79me deficiency would lead to higher levels of heterochromatic histone modifications, specifically H3K9me2, at developmental enhancers in C. elegans. Therefore, we used H3K9me2 ChIP-seq to compare its abundance in control and dot-1.1 loss-of-function mutant worms, as well as in rde-4; dot-1.1 and rde-1; dot-1.1 double mutants. The rde-1 and rde-4 genes are components of the RNAi pathway in C. elegans, and RNAi is known to initiate H3K9 methylation in many organisms, including C. elegans. We have previously shown that dot-1.1(-) lethality is rescued by rde-1 and rde-4 loss-of-function. Here we found that H3K9me2 was elevated in enhancer, but not promoter, regions bound by the DOT-1.1/ZFP-1 complex in dot-1.1(-) worms. We also found increased H3K9me2 at genes targeted by the ALG-3/4-dependent small RNAs and repeat regions. Our results suggest that ectopic H3K9me2 in dot-1.1(-) could, in some cases, be induced by small RNAs.
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Gray de Cristoforis A, Ferrari F, Clotman F, Vogel T. Differentiation and localization of interneurons in the developing spinal cord depends on DOT1L expression. Mol Brain 2020; 13:85. [PMID: 32471461 PMCID: PMC7260853 DOI: 10.1186/s13041-020-00623-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/18/2020] [Indexed: 11/12/2022] Open
Abstract
Genetic and epigenetic factors contribute to the development of the spinal cord. Failure in correct exertion of the developmental programs, including neurulation, neural tube closure and neurogenesis of the diverse spinal cord neuronal subtypes results in defects of variable severity. We here report on the histone methyltransferase Disruptor of Telomeric 1 Like (DOT1L), which mediates histone H3 lysine 79 (H3K79) methylation. Conditional inactivation of DOT1L using Wnt1-cre as driver (Dot1l-cKO) showed that DOT1L expression is essential for spinal cord neurogenesis and localization of diverse neuronal subtypes, similar to its function in the development of the cerebral cortex and cerebellum. Transcriptome analysis revealed that DOT1L deficiency favored differentiation over progenitor proliferation. Dot1l-cKO mainly decreased the numbers of dI1 interneurons expressing Lhx2. In contrast, Lhx9 expressing dI1 interneurons did not change in numbers but localized differently upon Dot1l-cKO. Similarly, loss of DOT1L affected localization but not generation of dI2, dI3, dI5, V0 and V1 interneurons. The resulting derailed interneuron patterns might be responsible for increased cell death, occurrence of which was restricted to the late developmental stage E18.5. Together our data indicate that DOT1L is essential for subtype-specific neurogenesis, migration and localization of dorsal and ventral interneurons in the developing spinal cord, in part by regulating transcriptional activation of Lhx2.
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Affiliation(s)
- Angelica Gray de Cristoforis
- Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
| | - Francesco Ferrari
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Frédéric Clotman
- Laboratory of Neural Differentiation, Institute of Neuroscience, Université catholique de Louvain, Brussels, Belgium
| | - Tanja Vogel
- Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany.
- Spemann Graduate School of Biology and Medicine (SGBM), Albert-Ludwigs-University Freiburg, 79104, Freiburg, Germany.
- Centre for Basics in Neuromodulation (Neuromodul Basics), Freiburg, Germany.
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Esse R, Gushchanskaia ES, Lord A, Grishok A. DOT1L complex suppresses transcription from enhancer elements and ectopic RNAi in Caenorhabditis elegans. RNA (NEW YORK, N.Y.) 2019; 25:1259-1273. [PMID: 31300558 PMCID: PMC6800474 DOI: 10.1261/rna.070292.119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 07/10/2019] [Indexed: 05/14/2023]
Abstract
Methylation of histone H3 on lysine 79 (H3K79) by DOT1L is associated with actively transcribed genes. Earlier, we described that DOT-1.1, the Caenorhabditis elegans homolog of mammalian DOT1L, cooperates with the chromatin-binding protein ZFP-1 (AF10 homolog) to negatively modulate transcription of highly and widely expressed target genes. Also, the reduction of ZFP-1 levels has consistently been associated with lower efficiency of RNA interference (RNAi) triggered by exogenous double-stranded RNA (dsRNA), but the reason for this is not clear. Here, we demonstrate that the DOT1L complex suppresses transcription originating from enhancer elements and antisense transcription, thus potentiating the expression of enhancer-regulated genes. We also show that worms lacking H3K79 methylation do not survive, and this lethality is suppressed by a loss of caspase-3 or Dicer complex components that initiate gene silencing response to exogenous dsRNA. Our results suggest that ectopic elevation of endogenous dsRNA directly or indirectly resulting from global misregulation of transcription in DOT1L complex mutants may engage the Dicer complex and, therefore, limit the efficiency of exogenous RNAi.
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Affiliation(s)
- Ruben Esse
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | | | - Avery Lord
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Alla Grishok
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
- Genome Science Institute, Boston University School of Medicine, Boston, Massachusetts 02118, USA
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