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Yokotsuka-Ishida S, Nakamura M, Tomiyasu Y, Nagai M, Kato Y, Tomiyasu A, Umehara H, Hayashi T, Sasaki N, Ueno SI, Sano A. Positional cloning and comprehensive mutation analysis identified a novel KDM2B mutation in a Japanese family with minor malformations, intellectual disability, and schizophrenia. J Hum Genet 2021; 66:597-606. [PMID: 33402700 DOI: 10.1038/s10038-020-00889-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/25/2020] [Accepted: 11/29/2020] [Indexed: 11/09/2022]
Abstract
The importance of epigenetic control in the development of the central nervous system has recently been attracting attention. Methylation patterns of lysine 4 and lysine 36 in histone H3 (H3K4 and H3K36) in the central nervous system are highly conserved among species. Numerous complications of body malformations and neuropsychiatric disorders are due to abnormal histone H3 methylation modifiers. In this study, we analyzed a Japanese family with a dominant inheritance of symptoms including Marfan syndrome-like minor physical anomalies (MPAs), intellectual disability, and schizophrenia (SCZ). We performed positional cloning for this family using a single nucleotide polymorphism (SNP) array and whole-exome sequencing, which revealed a missense coding strand mutation (rs1555289644, NM_032590.4: c.2173G>A, p.A725T) in exon 15 on the plant homeodomain of the KDM2B gene as a possible cause of the disease in the family. The exome sequencing revealed that within the coding region, only a point mutation in KDM2B was present in the region with the highest logarithm of odds score of 2.41 resulting from whole genome linkage analysis. Haplotype analysis revealed co-segregation with four affected family members (IV-9, III-4, IV-5, and IV-8). Lymphoblastoid cell lines from the proband with this mutation showed approximately halved KDM2B expression in comparison with healthy controls. KDM2B acts as an H3K4 and H3K36 histone demethylase. Our findings suggest that haploinsufficiency of KDM2B in the process of development, like other H3K4 and H3K36 methylation modifiers, may have caused MPAs, intellectual disability, and SCZ in this Japanese family.
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Affiliation(s)
- Saeko Yokotsuka-Ishida
- Department of Psychiatry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Masayuki Nakamura
- Department of Psychiatry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.
| | - Yoko Tomiyasu
- Department of Psychiatry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Mio Nagai
- Division of Psychiatry, Matsuyama Red Cross Hospital, Matsuyama, Japan
| | - Yuko Kato
- Division of Psychiatry, Jiundo Hospital, Tokyo, Japan
| | - Akiyuki Tomiyasu
- Department of Psychiatry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Hiromi Umehara
- Department of Psychiatry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Takehiro Hayashi
- Department of Social Welfare, The International University of Kagoshima, Kagoshima, Japan
| | - Natsuki Sasaki
- Department of Psychiatry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Shu-Ichi Ueno
- Department of Neuropsychiatry, Ehime University Graduate School of Medicine Toon, Kagoshima, Japan
| | - Akira Sano
- Department of Psychiatry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
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Abstract
The 5-methylcytosine (5mC) oxidation pathway mediated by TET proteins involves step-wise oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC and 5caC can be removed from DNA by base excision repair and the completion of this pathway results in "demethylation" of 5mC by converting the modified base back into cytosine. In vitro studies with TET proteins aimed at analyzing their DNA substrate specificities and their activity within defined chromatin templates are relatively limited. Here we describe purification methods for mammalian TET proteins based on expression in insect cells or in 293T cells. We also briefly summarize a method that can be used to monitor 5-methylcytosine oxidase activity of the purified TET proteins in vitro.
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Affiliation(s)
- Zhijun Huang
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Jiyoung Yu
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
- Asan Medical Center, University of Ulsan, College of Medicine, Seoul, South Korea
| | - Jennifer Johnson
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Seung-Gi Jin
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Gerd P Pfeifer
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.
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Aberrant Activity of Histone-Lysine N-Methyltransferase 2 (KMT2) Complexes in Oncogenesis. Int J Mol Sci 2020; 21:ijms21249340. [PMID: 33302406 PMCID: PMC7762615 DOI: 10.3390/ijms21249340] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/04/2020] [Accepted: 12/06/2020] [Indexed: 02/06/2023] Open
Abstract
KMT2 (histone-lysine N-methyltransferase subclass 2) complexes methylate lysine 4 on the histone H3 tail at gene promoters and gene enhancers and, thus, control the process of gene transcription. These complexes not only play an essential role in normal development but have also been described as involved in the aberrant growth of tissues. KMT2 mutations resulting from the rearrangements of the KMT2A (MLL1) gene at 11q23 are associated with pediatric mixed-lineage leukemias, and recent studies demonstrate that KMT2 genes are frequently mutated in many types of human cancers. Moreover, other components of the KMT2 complexes have been reported to contribute to oncogenesis. This review summarizes the recent advances in our knowledge of the role of KMT2 complexes in cell transformation. In addition, it discusses the therapeutic targeting of different components of the KMT2 complexes.
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Astori A, Matherat G, Munoz I, Gautier EF, Surdez D, Zermati Y, Verdier F, Zaidi S, Feuillet V, Kadi A, Lauret E, Delattre O, Lefèvre C, Fontenay M, Ségal-Bendirdjian E, Dusanter-Fourt I, Bouscary D, Hermine O, Mayeux P, Pendino F. The epigenetic regulator RINF (CXXC5) maintains <i>SMAD7</i> expression in human immature erythroid cells and sustains red blood cells expansion. Haematologica 2020; 107:268-283. [PMID: 33241676 PMCID: PMC8719099 DOI: 10.3324/haematol.2020.263558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Indexed: 11/16/2022] Open
Abstract
The gene CXXC5, encoding a retinoid-inducible nuclear factor (RINF), is located within a region at 5q31.2 commonly deleted in myelodysplastic syndrome and adult acute myeloid leukemia. RINF may act as an epigenetic regulator and has been proposed as a tumor suppressor in hematopoietic malignancies. However, functional studies in normal hematopoiesis are lacking, and its mechanism of action is unknown. Here, we evaluated the consequences of RINF silencing on cytokine-induced erythroid differentiation of human primary CD34+ progenitors. We found that RINF is expressed in immature erythroid cells and that RINF-knockdown accelerated erythropoietin-driven maturation, leading to a significant reduction (~45%) in the number of red blood cells, without affecting cell viability. The phenotype induced by RINF-silencing was dependent on tumor growth factor b (TGFb) and mediated by SMAD7, a TGFb-signaling inhibitor. RINF upregulates SMAD7 expression by direct binding to its promoter and we found a close correlation between RINF and SMAD7 mRNA levels both in CD34+ cells isolated from bone marrow of healthy donors and myelodysplastic syndrome patients with del(5q). Importantly, RINF knockdown attenuated SMAD7 expression in primary cells and ectopic SMAD7 expression was sufficient to prevent the RINF knockdown-dependent erythroid phenotype. Finally, RINF silencing affects 5’-hydroxymethylation of human erythroblasts, in agreement with its recently described role as a TET2-anchoring platform in mouse. Collectively, our data bring insight into how the epigenetic factor RINF, as a transcriptional regulator of SMAD7, may fine-tune cell sensitivity to TGFb superfamily cytokines and thus play an important role in both normal and pathological erythropoiesis.
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Affiliation(s)
- Audrey Astori
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France; Laboratory of Excellence GR-ex, Paris, France; Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris
| | - Gabriel Matherat
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France; Laboratory of Excellence GR-ex, Paris, France; Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris
| | - Isabelle Munoz
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France; Laboratory of Excellence GR-ex, Paris, France; Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris
| | - Emilie-Fleur Gautier
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France; Laboratory of Excellence GR-ex, Paris, France; Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris
| | - Didier Surdez
- Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris, France; PSL Research University, Institut Curie Research Center, INSERM U830, Paris, France; SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris
| | - Yaël Zermati
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France; Laboratory of Excellence GR-ex, Paris
| | - Frédérique Verdier
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France; Laboratory of Excellence GR-ex, Paris
| | - Sakina Zaidi
- Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris, France; PSL Research University, Institut Curie Research Center, INSERM U830, Paris, France; SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris
| | - Vincent Feuillet
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris
| | - Amir Kadi
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris
| | - Evelyne Lauret
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France; Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris
| | - Olivier Delattre
- Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris, France; PSL Research University, Institut Curie Research Center, INSERM U830, Paris, France; SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris
| | - Carine Lefèvre
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France; Laboratory of Excellence GR-ex, Paris
| | - Michaela Fontenay
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France; Laboratory of Excellence GR-ex, Paris, France; Service d'Hématologie Biologique, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Centre-Université de Paris, Paris
| | | | - Isabelle Dusanter-Fourt
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France; Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris
| | - Didier Bouscary
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France; Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris
| | - Olivier Hermine
- Laboratory of Excellence GR-ex, Paris, France; Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris, France; Université de Paris, Institut Imagine, INSERM, CNRS, F-75015, Paris
| | - Patrick Mayeux
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France; Laboratory of Excellence GR-ex, Paris, France; Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris
| | - Frédéric Pendino
- Université de Paris, Institut Cochin, INSERM, CNRS, F-75014 Paris, France; Laboratory of Excellence GR-ex, Paris, France; Equipe Labellisée Ligue Nationale Contre le Cancer (LNCC), Paris.
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55
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Aljazi MB, Gao Y, Wu Y, Mias GI, He J. Cell Signaling Coordinates Global PRC2 Recruitment and Developmental Gene Expression in Murine Embryonic Stem Cells. iScience 2020; 23:101646. [PMID: 33103084 PMCID: PMC7578752 DOI: 10.1016/j.isci.2020.101646] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 08/16/2020] [Accepted: 10/01/2020] [Indexed: 01/12/2023] Open
Abstract
The recruitment of Polycomb repressive complex 2 (PRC2) to gene promoters is critical for its function in repressing gene expression in murine embryonic stem cells (mESCs). However, previous studies have demonstrated that although the expression of early lineage-specific genes is largely repressed, the genome-wide PRC2 occupancy is unexpectedly reduced in naive mESCs. In this study, we provide evidence that fibroblast growth factor/extracellular signal-regulated kinase signaling determines the global PRC2 occupancy through regulating the expression of PRC2-recruiting factor JARID2 in naive mESCs. At the transcriptional level, the de-repression of bivalent genes is predominantly determined by the presence of cell signaling-associated transcription factors but not the status of PRC2 occupancy at gene promoters. Hence, this study not only reveals a key molecular mechanism by which cell signaling regulates the PRC2 occupancy in mESCs but also elucidates the functional roles of transcription factors and Polycomb-mediated epigenetic mechanisms in transcriptional regulation. FGF/ERK signaling positively regulates Jarid2 expression in mESCs Reduced JARID2 causes global reduction of PRC2 occupancy in naive mESCs Reduced PRC2 occupancy alone is insufficient to induce transcriptional activation Cell signaling-associated transcription factors drive bivalent gene expression
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Affiliation(s)
- Mohammad B Aljazi
- Department of Biochemistry and Molecular Biology, College of Natural Science, Michigan State University, East Lansing, MI 48824, USA
| | - Yuen Gao
- Department of Biochemistry and Molecular Biology, College of Natural Science, Michigan State University, East Lansing, MI 48824, USA
| | - Yan Wu
- Department of Biochemistry and Molecular Biology, College of Natural Science, Michigan State University, East Lansing, MI 48824, USA
| | - George I Mias
- Department of Biochemistry and Molecular Biology, College of Natural Science, Michigan State University, East Lansing, MI 48824, USA.,Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Jin He
- Department of Biochemistry and Molecular Biology, College of Natural Science, Michigan State University, East Lansing, MI 48824, USA
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Iwakawa H, Takahashi H, Machida Y, Machida C. Roles of ASYMMETRIC LEAVES2 (AS2) and Nucleolar Proteins in the Adaxial-Abaxial Polarity Specification at the Perinucleolar Region in Arabidopsis. Int J Mol Sci 2020; 21:E7314. [PMID: 33022996 PMCID: PMC7582388 DOI: 10.3390/ijms21197314] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/27/2020] [Accepted: 09/29/2020] [Indexed: 12/14/2022] Open
Abstract
Leaves of Arabidopsis develop from a shoot apical meristem grow along three (proximal-distal, adaxial-abaxial, and medial-lateral) axes and form a flat symmetric architecture. ASYMMETRIC LEAVES2 (AS2), a key regulator for leaf adaxial-abaxial partitioning, encodes a plant-specific nuclear protein and directly represses the abaxial-determining gene ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3). How AS2 could act as a critical regulator, however, has yet to be demonstrated, although it might play an epigenetic role. Here, we summarize the current understandings of the genetic, molecular, and cellular functions of AS2. A characteristic genetic feature of AS2 is the presence of a number of (about 60) modifier genes, mutations of which enhance the leaf abnormalities of as2. Although genes for proteins that are involved in diverse cellular processes are known as modifiers, it has recently become clear that many modifier proteins, such as NUCLEOLIN1 (NUC1) and RNA HELICASE10 (RH10), are localized in the nucleolus. Some modifiers including ribosomal proteins are also members of the small subunit processome (SSUP). In addition, AS2 forms perinucleolar bodies partially colocalizing with chromocenters that include the condensed inactive 45S ribosomal RNA genes. AS2 participates in maintaining CpG methylation in specific exons of ETT/ARF3. NUC1 and RH10 genes are also involved in maintaining the CpG methylation levels and repressing ETT/ARF3 transcript levels. AS2 and nucleolus-localizing modifiers might cooperatively repress ETT/ARF3 to develop symmetric flat leaves. These results raise the possibility of a nucleolus-related epigenetic repression system operating for developmental genes unique to plants and predict that AS2 could be a molecule with novel functions that cannot be explained by the conventional concept of transcription factors.
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Affiliation(s)
- Hidekazu Iwakawa
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200, Matsumoto-cho, Kasugai, Aichi 487-8501, Japan;
| | - Hiro Takahashi
- Graduate School of Medical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan;
| | - Yasunori Machida
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Chiyoko Machida
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200, Matsumoto-cho, Kasugai, Aichi 487-8501, Japan;
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57
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Abstract
The Trithorax group (TrxG) of proteins is a large family of epigenetic regulators that form multiprotein complexes to counteract repressive developmental gene expression programmes established by the Polycomb group of proteins and to promote and maintain an active state of gene expression. Recent studies are providing new insights into how two crucial families of the TrxG - the COMPASS family of histone H3 lysine 4 methyltransferases and the SWI/SNF family of chromatin remodelling complexes - regulate gene expression and developmental programmes, and how misregulation of their activities through genetic abnormalities leads to pathologies such as developmental disorders and malignancies.
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58
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Boukas L, Bjornsson HT, Hansen KD. Promoter CpG Density Predicts Downstream Gene Loss-of-Function Intolerance. Am J Hum Genet 2020; 107:487-498. [PMID: 32800095 PMCID: PMC7477270 DOI: 10.1016/j.ajhg.2020.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 07/22/2020] [Indexed: 12/26/2022] Open
Abstract
The aggregation and joint analysis of large numbers of exome sequences has recently made it possible to derive estimates of intolerance to loss-of-function (LoF) variation for human genes. Here, we demonstrate strong and widespread coupling between genic LoF intolerance and promoter CpG density across the human genome. Genes downstream of the most CpG-rich promoters (top 10% CpG density) have a 67.2% probability of being highly LoF intolerant, using the LOEUF metric from gnomAD. This is in contrast to 7.4% of genes downstream of the most CpG-poor (bottom 10% CpG density) promoters. Combining promoter CpG density with exonic and promoter conservation explains 33.4% of the variation in LOEUF, and the contribution of CpG density exceeds the individual contributions of exonic and promoter conservation. We leverage this to train a simple and easily interpretable predictive model that outperforms other existing predictors and allows us to classify 1,760 genes-which are currently unascertained in gnomAD-as highly LoF intolerant or not. These predictions have the potential to aid in the interpretation of novel variants in the clinical setting. Moreover, our results reveal that high CpG density is not merely a generic feature of human promoters but is preferentially encountered at the promoters of the most selectively constrained genes, calling into question the prevailing view that CpG islands are not subject to selection.
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Affiliation(s)
- Leandros Boukas
- Human Genetics Training Program, Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD 21205, USA
| | - Hans T Bjornsson
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD 21205, USA; Department of Pediatrics, Johns Hopkins University School of Medicine, 1800 Orleans Street, Baltimore, MD 21287, USA; Faculty of Medicine, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland; Landspitali University Hospital, Hringbraut, 101 Reykjavik, Iceland.
| | - Kasper D Hansen
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD 21205, USA; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD 21205, USA.
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KDM2B in polycomb repressive complex 1.1 functions as a tumor suppressor in the initiation of T-cell leukemogenesis. Blood Adv 2020; 3:2537-2549. [PMID: 31471323 DOI: 10.1182/bloodadvances.2018028522] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 06/21/2019] [Indexed: 12/11/2022] Open
Abstract
KDM2B together with RING1B, PCGF1, and BCOR or BCORL1 comprise polycomb repressive complex 1.1 (PRC1.1), a noncanonical PRC1 that catalyzes H2AK119ub1. It binds to nonmethylated CpG islands through its zinc finger-CxxC DNA binding domain and recruits the complex to target gene loci. Recent studies identified the loss of function mutations in the PRC1.1 gene, BCOR and BCORL1 in human T-cell acute lymphoblastic leukemia (T-ALL). We previously reported that Bcor insufficiency induces T-ALL in mice, supporting a tumor suppressor role for BCOR. However, the function of BCOR responsible for tumor suppression, either its corepressor function for BCL6 or that as a component of PRC1.1, remains unclear. We herein examined mice specifically lacking the zinc finger-CxxC domain of KDM2B in hematopoietic cells. Similar to Bcor-deficient mice, Kdm2b-deficient mice developed lethal T-ALL mostly in a NOTCH1-dependent manner. A chromatin immunoprecipitation sequence analysis of thymocytes revealed the binding of KDM2B at promoter regions, at which BCOR and EZH2 colocalized. KDM2B target genes markedly overlapped with those of NOTCH1 in human T-ALL cells, suggesting that noncanonical PRC1.1 antagonizes NOTCH1-mediated gene activation. KDM2B target genes were expressed at higher levels than the others and were marked with high levels of H2AK119ub1 and H3K4me3, but low levels of H3K27me3, suggesting that KDM2B target genes are transcriptionally active or primed for activation. These results indicate that PRC1.1 plays a key role in restricting excessive transcriptional activation by active NOTCH1, thereby acting as a tumor suppressor in the initiation of T-cell leukemogenesis.
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Chen X, Wang X, Yi L, Song Y. The KN Motif and Ankyrin Repeat Domains 1/CXXC Finger Protein 5 Axis Regulates Epithelial-Mesenchymal Transformation, Metastasis and Apoptosis of Gastric Cancer via Wnt Signaling. Onco Targets Ther 2020; 13:7343-7352. [PMID: 32801759 PMCID: PMC7395690 DOI: 10.2147/ott.s240991] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 06/12/2020] [Indexed: 12/26/2022] Open
Abstract
Background Emerging research indicates that CXXC finger protein 5 (CXXC5) is involved in the development of various cancers. Besides, KN motif and ankyrin repeat domains 1 (KANK1) was proved as a tumor suppressor in multiple cancers. Our study aimed to illustrate the functional role and mechanism of CXXC5 and KANK1 in gastric cancer (GC) pathogenesis. Methods The tissues of 55 GC patients and six GC cell lines were used to investigate CXXC5 and KANK1 expression using RT-qPCR. Western blot assay was conducted to measure the protein levels of CXXC5, KANK1, epithelial-mesenchymal transformation (EMT) proteins (Vimentin, E-cadherin) and Wnt signaling proteins (β-catenin, Axin2). The correlation between KANK1 and CXXC5 was estimated by Pearson’s correlation analysis. The results of Transwell assays showed the migration and invasion abilities of GC cells, while the apoptosis rate was detected by flow cytometry. Results The expressions of CXXC5 and KANK1 were both decreased in GC tissues and cells, compared with the normal ones (P < 0.01). Overexpressing CXXC5 significantly induced apoptosis (P < 0.05) and inhibited EMT, migration (P < 0.05) and invasion (P < 0.01) in GC cells. Wnt/β-catenin/Axin2 signaling was suppressed by CXXC5 overexpression, and activating Wnt/β-catenin/Axin2 signaling reversed the effects of CXXC5. The expression of KANK1 was found to be positively correlated with CXXC5 (r2 = 0.4024). KANK1 presented similar effects with CXXC5 on GC cells; however, silencing CXXC5 or activating Wnt/β-catenin/Axin2 signaling antagonized the effects of KANK1 overexpression on EMT and apoptosis in GC (P < 0.05). Conclusion Our study suggested that CXXC5 was downregulated in GC and participated in EMT and apoptosis regulations via the Wnt/β-catenin/Axin2 pathway. Besides, the decreased expression of CXXC5 in GC was caused by KANK1 dysregulation.
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Affiliation(s)
- Xin Chen
- Gastroenteric Medicine and Digestive Endoscopy Center, The Second Hospital of Jilin University, Changchun, Jilin 13000, People's Republic of China
| | - Xiaodong Wang
- Gastroenteric Medicine and Digestive Endoscopy Center, The Second Hospital of Jilin University, Changchun, Jilin 13000, People's Republic of China
| | - Lanjuan Yi
- Department of Gastroenterology, Yantaishan Hospital of Yantai City, Yantai, Shandong 264000, People's Republic of China
| | - Ying Song
- Gastroenteric Medicine and Digestive Endoscopy Center, The Second Hospital of Jilin University, Changchun, Jilin 13000, People's Republic of China
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61
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Rezazadeh S, Yang D, Biashad SA, Firsanov D, Takasugi M, Gilbert M, Tombline G, Bhanu NV, Garcia BA, Seluanov A, Gorbunova V. SIRT6 mono-ADP ribosylates KDM2A to locally increase H3K36me2 at DNA damage sites to inhibit transcription and promote repair. Aging (Albany NY) 2020; 12:11165-11184. [PMID: 32584788 PMCID: PMC7343504 DOI: 10.18632/aging.103567] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 06/09/2020] [Indexed: 01/06/2023]
Abstract
When transcribed DNA is damaged, the transcription and DNA repair machineries must interact to ensure successful DNA repair. The mechanisms of this interaction in the context of chromatin are still being elucidated. Here we show that the SIRT6 protein enhances non-homologous end joining (NHEJ) DNA repair by transiently repressing transcription. Specifically, SIRT6 mono-ADP ribosylates the lysine demethylase JHDM1A/KDM2A leading to rapid displacement of KDM2A from chromatin, resulting in increased H3K36me2 levels. Furthermore, we found that through HP1α binding, H3K36me2 promotes subsequent H3K9 tri-methylation. This results in transient suppression of transcription initiation by RNA polymerase II and recruitment of NHEJ factors to DNA double-stranded breaks (DSBs). These data reveal a mechanism where SIRT6 mediates a crosstalk between transcription and DNA repair machineries to promote DNA repair. SIRT6 functions in multiple pathways related to aging, and its novel function coordinating DNA repair and transcription is yet another way by which SIRT6 promotes genome stability and longevity.
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Affiliation(s)
- Sarallah Rezazadeh
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - David Yang
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Seyed Ali Biashad
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Denis Firsanov
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Masaki Takasugi
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Michael Gilbert
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Gregory Tombline
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Natarajan V. Bhanu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
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62
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Taka N, Yoshida W. Quantification of global DNA methylation level using 5-methylcytosine dioxygenase. Anal Bioanal Chem 2020; 412:5299-5305. [PMID: 32504107 DOI: 10.1007/s00216-020-02745-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/22/2020] [Accepted: 05/28/2020] [Indexed: 12/19/2022]
Abstract
DNA methylation is one of the best studied epigenetic modifications. Alteration of the global DNA methylation level occurs in abnormal cells, such as those associated with cancers and Alzheimer's disease. Several assays are used to determine the global DNA methylation level, including the bisulfite-based assay, high-performance liquid chromatography (HPLC)-based assay, enzyme-linked immunosorbent assay (ELISA), and methyl acceptance assay. However, these assays require several cumbersome steps to detect methylation levels. We developed a simpler enzymatic assay for the quantification of the global DNA methylation level using the Ten-eleven translocation (TET) protein. TET proteins mediate DNA demethylation through the oxidation of 5-methylcytosine (5mC) in CpG in mammalian cells. Succinate is produced during this oxidation reaction, and the amount of succinate produced correlates to the global DNA methylation level. The catalytic domain of the TET2 was expressed in Escherichia coli (E. coli), and the purified TET2 catalytic domain was reacted with human genomic DNA. The reaction solution was used for enzymatic succinate quantification with no purification step. The results showed that the succinate produced through TET-mediated oxidation increased with increasing global DNA methylation levels in human genomic DNA, which was determined using the bisulfite method. These results show that the global DNA methylation level is quantifiable by measuring the amount of succinate produced by the TET2-mediated 5mC oxidation reaction. Graphical abstract.
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Affiliation(s)
- Natsumi Taka
- Graduate School of Bionics, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan
| | - Wataru Yoshida
- Graduate School of Bionics, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan. .,School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan.
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63
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Sensitivity of transcription factors to DNA methylation. Essays Biochem 2020; 63:727-741. [PMID: 31755929 PMCID: PMC6923324 DOI: 10.1042/ebc20190033] [Citation(s) in RCA: 158] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 12/17/2022]
Abstract
Dynamic binding of transcription factors (TFs) to regulatory elements controls transcriptional states throughout organism development. Epigenetics modifications, such as DNA methylation mostly within cytosine-guanine dinucleotides (CpGs), have the potential to modulate TF binding to DNA. Although DNA methylation has long been thought to repress TF binding, a more recent model proposes that TF binding can also inhibit DNA methylation. Here, we review the possible scenarios by which DNA methylation and TF binding affect each other. Further in vivo experiments will be required to generalize these models.
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64
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Feldmann A, Dimitrova E, Kenney A, Lastuvkova A, Klose RJ. CDK-Mediator and FBXL19 prime developmental genes for activation by promoting atypical regulatory interactions. Nucleic Acids Res 2020; 48:2942-2955. [PMID: 31996894 PMCID: PMC7102981 DOI: 10.1093/nar/gkaa064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 02/05/2023] Open
Abstract
Appropriate developmental gene regulation relies on the capacity of gene promoters to integrate inputs from distal regulatory elements, yet how this is achieved remains poorly understood. In embryonic stem cells (ESCs), a subset of silent developmental gene promoters are primed for activation by FBXL19, a CpG island binding protein, through its capacity to recruit CDK-Mediator. How mechanistically these proteins function together to prime genes for activation during differentiation is unknown. Here we discover that in mouse ESCs FBXL19 and CDK-Mediator support long-range interactions between silent gene promoters that rely on FBXL19 for their induction during differentiation and gene regulatory elements. During gene induction, these distal regulatory elements behave in an atypical manner, in that the majority do not acquire histone H3 lysine 27 acetylation and no longer interact with their target gene promoter following gene activation. Despite these atypical features, we demonstrate by targeted deletions that these distal elements are required for appropriate gene induction during differentiation. Together these discoveries demonstrate that CpG-island associated gene promoters can prime genes for activation by communicating with atypical distal gene regulatory elements to achieve appropriate gene expression.
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Affiliation(s)
- Angelika Feldmann
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Emilia Dimitrova
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Alexander Kenney
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Anna Lastuvkova
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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65
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Understanding the interplay between CpG island-associated gene promoters and H3K4 methylation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194567. [PMID: 32360393 PMCID: PMC7294231 DOI: 10.1016/j.bbagrm.2020.194567] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/24/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023]
Abstract
The precise regulation of gene transcription is required to establish and maintain cell type-specific gene expression programs during multicellular development. In addition to transcription factors, chromatin, and its chemical modification, play a central role in regulating gene expression. In vertebrates, DNA is pervasively methylated at CG dinucleotides, a modification that is repressive to transcription. However, approximately 70% of vertebrate gene promoters are associated with DNA elements called CpG islands (CGIs) that are refractory to DNA methylation. CGIs integrate the activity of a range of chromatin-regulating factors that can post-translationally modify histones and modulate gene expression. This is exemplified by the trimethylation of histone H3 at lysine 4 (H3K4me3), which is enriched at CGI-associated gene promoters and correlates with transcriptional activity. Through studying H3K4me3 at CGIs it has become clear that CGIs shape the distribution of H3K4me3 and, in turn, H3K4me3 influences the chromatin landscape at CGIs. Here we will discuss our understanding of the emerging relationship between CGIs, H3K4me3, and gene expression.
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66
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Identification of Structural Elements of the Lysine Specific Demethylase 2B CxxC Domain Associated with Replicative Senescence Bypass in Primary Mouse Cells. Protein J 2020; 39:232-239. [DOI: 10.1007/s10930-020-09895-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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67
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Ayaz G, Razizadeh N, Yaşar P, Kars G, Kahraman DC, Saatci Ö, Şahin Ö, Çetin-Atalay R, Muyan M. CXXC5 as an unmethylated CpG dinucleotide binding protein contributes to estrogen-mediated cellular proliferation. Sci Rep 2020; 10:5971. [PMID: 32249801 PMCID: PMC7136269 DOI: 10.1038/s41598-020-62912-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 03/17/2020] [Indexed: 02/07/2023] Open
Abstract
Evidence suggests that the CXXC type zinc finger (ZF-CXXC) protein 5 (CXXC5) is a critical regulator/integrator of various signaling pathways that include the estrogen (E2)-estrogen receptor α (ERα). Due to its ZF-CXXC domain, CXXC5 is considered to be a member of the ZF-CXXC family, which binds to unmethylated CpG dinucleotides of DNA and through enzymatic activities for DNA methylation and/or chromatin modifications generates a chromatin state critical for gene expressions. Structural/functional features of CXXC5 remain largely unknown. CXXC5, suggested as transcription and/or epigenetic factor, participates in cellular proliferation, differentiation, and death. To explore the role of CXXC5 in E2-ERα mediated cellular events, we verified by generating a recombinant protein that CXXC5 is indeed an unmethylated CpG binder. We uncovered that CXXC5, although lacks a transcription activation/repression function, participates in E2-driven cellular proliferation by modulating the expression of distinct and mutual genes also regulated by E2. Furthermore, we found that the overexpression of CXXC5, which correlates with mRNA and protein levels of ERα, associates with poor prognosis in ER-positive breast cancer patients. Thus, CXXC5 as an unmethylated CpG binder contributes to E2-mediated gene expressions that result in the regulation of cellular proliferation and may contribute to ER-positive breast cancer progression.
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Affiliation(s)
- Gamze Ayaz
- Department of Biological Sciences, Middle East Technical University, Ankara, 06800, Turkey.,Cancer and Stem Cell Epigenetics Section, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Negin Razizadeh
- Department of Biological Sciences, Middle East Technical University, Ankara, 06800, Turkey
| | - Pelin Yaşar
- Department of Biological Sciences, Middle East Technical University, Ankara, 06800, Turkey
| | - Gizem Kars
- Department of Biological Sciences, Middle East Technical University, Ankara, 06800, Turkey
| | - Deniz Cansen Kahraman
- Enformatics Institute, Middle East Technical University, Ankara, 06800, Turkey.,Cansyl Laboratories, Middle East Technical University, Ankara, 06800, Turkey
| | - Özge Saatci
- Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, 29208, USA
| | - Özgür Şahin
- Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, 29208, USA.,Department of Molecular Biology and Genetics, Bilkent University, Ankara, 06800, Turkey
| | - Rengül Çetin-Atalay
- Enformatics Institute, Middle East Technical University, Ankara, 06800, Turkey.,Cansyl Laboratories, Middle East Technical University, Ankara, 06800, Turkey
| | - Mesut Muyan
- Department of Biological Sciences, Middle East Technical University, Ankara, 06800, Turkey. .,Cansyl Laboratories, Middle East Technical University, Ankara, 06800, Turkey.
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68
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Luo L, Ando S, Sakamoto Y, Suzuki T, Takahashi H, Ishibashi N, Kojima S, Kurihara D, Higashiyama T, Yamamoto KT, Matsunaga S, Machida C, Sasabe M, Machida Y. The formation of perinucleolar bodies is important for normal leaf development and requires the zinc-finger DNA-binding motif in Arabidopsis ASYMMETRIC LEAVES2. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1118-1134. [PMID: 31639235 PMCID: PMC7155070 DOI: 10.1111/tpj.14579] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/30/2019] [Accepted: 10/08/2019] [Indexed: 05/27/2023]
Abstract
In Arabidopsis, the ASYMMETRIC LEAVES2 (AS2) protein plays a key role in the formation of flat symmetric leaves via direct repression of the abaxial gene ETT/ARF3. AS2 encodes a plant-specific nuclear protein that contains the AS2/LOB domain, which includes a zinc-finger (ZF) motif that is conserved in the AS2/LOB family. We have shown that AS2 binds to the coding DNA of ETT/ARF3, which requires the ZF motif. AS2 is co-localized with AS1 in perinucleolar bodies (AS2 bodies). To identify the amino acid signals in AS2 required for formation of AS2 bodies and function(s) in leaf formation, we constructed recombinant DNAs that encoded mutant AS2 proteins fused to yellow fluorescent protein. We examined the subcellular localization of these proteins in cells of cotyledons and leaf primordia of transgenic plants and cultured cells. The amino acid signals essential for formation of AS2 bodies were located within and adjacent to the ZF motif. Mutant AS2 that failed to form AS2 bodies also failed to rescue the as2-1 mutation. Our results suggest the importance of the formation of AS2 bodies and the nature of interactions of AS2 with its target DNA and nucleolar factors including NUCLEOLIN1. The partial overlap of AS2 bodies with perinucleolar chromocenters with condensed ribosomal RNA genes implies a correlation between AS2 bodies and the chromatin state. Patterns of AS2 bodies in cells during interphase and mitosis in leaf primordia were distinct from those in cultured cells, suggesting that the formation and distribution of AS2 bodies are developmentally modulated in plants.
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Affiliation(s)
- Lilan Luo
- Division of Biological ScienceGraduate School of ScienceNagoya UniversityNagoyaAichi464‐8602Japan
- Present address:
Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing100101China
| | - Sayuri Ando
- Graduate School of Bioscience and BiotechnologyChubu UniversityKasugaiAichi487‐8501Japan
| | - Yuki Sakamoto
- Department of Applied Biological ScienceFaculty of Science and TechnologyTokyo University of ScienceNodaChiba278‐8510Japan
- Department of Biological SciencesGraduate School of ScienceOsaka University1‐1 Machikaneyama‐choToyonakaOsaka560‐0043Japan
| | - Takanori Suzuki
- Division of Biological ScienceGraduate School of ScienceNagoya UniversityNagoyaAichi464‐8602Japan
- Central Research InstituteIshihara Sangyo Kaisha, Ltd.2‐3‐1 Nishi‐ShibukawaKusatsuShiga525‐0025Japan
| | - Hiro Takahashi
- Graduate School of Medical SciencesKanazawa UniversityKakuma‐machiKanazawaIshikawa920‐1192Japan
| | - Nanako Ishibashi
- Division of Biological ScienceGraduate School of ScienceNagoya UniversityNagoyaAichi464‐8602Japan
| | - Shoko Kojima
- Graduate School of Bioscience and BiotechnologyChubu UniversityKasugaiAichi487‐8501Japan
| | - Daisuke Kurihara
- JST, PRESTOFuro‐cho, Chikusa‐kuNagoyaAichi464‐8601Japan
- Institute of Transformative Bio‐Molecules (ITbM)Nagoya UniversityFuro‐cho, Chiku00sa‐kuNagoyaAichi464‐8601Japan
| | - Tetsuya Higashiyama
- Division of Biological ScienceGraduate School of ScienceNagoya UniversityNagoyaAichi464‐8602Japan
- Institute of Transformative Bio‐Molecules (ITbM)Nagoya UniversityFuro‐cho, Chiku00sa‐kuNagoyaAichi464‐8601Japan
- Department of Biological SciencesGraduate School of ScienceUniversity of Tokyo7‐3‐1 Hongo, Bukyo‐kuTokyo113‐0033Japan
| | - Kotaro T. Yamamoto
- Division of Biological SciencesFaculty of ScienceHokkaido UniversitySapporo060‐0810Japan
| | - Sachihiro Matsunaga
- Department of Applied Biological ScienceFaculty of Science and TechnologyTokyo University of ScienceNodaChiba278‐8510Japan
| | - Chiyoko Machida
- Graduate School of Bioscience and BiotechnologyChubu UniversityKasugaiAichi487‐8501Japan
| | - Michiko Sasabe
- Department of BiologyFaculty of Agriculture and Life ScienceHirosaki University3 Bunkyo‐choHirosaki036‐8561Japan
| | - Yasunori Machida
- Division of Biological ScienceGraduate School of ScienceNagoya UniversityNagoyaAichi464‐8602Japan
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69
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Joshi HR, Hill HR, Zhou Z, He X, Voelkerding KV, Kumánovics A. Frontline Science: Cxxc5 expression alters cell cycle and myeloid differentiation of mouse hematopoietic stem and progenitor cells. J Leukoc Biol 2020; 108:469-484. [PMID: 32083332 DOI: 10.1002/jlb.1hi0120-169r] [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: 05/29/2019] [Revised: 01/28/2020] [Accepted: 02/07/2020] [Indexed: 12/19/2022] Open
Abstract
CXXC5 is a member of the CXXC-type zinc finger epigenetic regulators. Various hematopoietic and nonhematopoietic roles have been assigned to CXXC5. In the present study, the role of Cxxc5 in myelopoiesis was studied using overexpression and short hairpin RNA-mediated knockdown in mouse early stem and progenitor cells defined as Lineage- Sca-1+ c-Kit+ (LSK) cells. Knockdown of Cxxc5 in mouse progenitor cells reduced monocyte and increased granulocyte development in ex vivo culture systems. In addition, ex vivo differentiation and proliferation experiments demonstrated that the expression of Cxxc5 affects the cell cycle in stem/progenitor cells and myeloid cells. Flow cytometry-based analyses revealed that down-regulation of Cxxc5 leads to an increase in the percentage of cells in the S phase, whereas overexpression results in a decrease in the percentage of cells in the S phase. Progenitor cells proliferate more after Cxxc5 knockdown, and RNA sequencing of LSK cells, and single-cell RNA sequencing of differentiating myeloid cells showed up-regulation of genes involved in the regulation of cell cycle after Cxxc5 knockdown. These results provide novel insights into the physiologic function of Cxxc5 during hematopoiesis, and demonstrate for the first time that it plays a role in monocyte development.
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Affiliation(s)
- Hemant R Joshi
- Department of Pathology, University of Utah, Salt Lake City, Utah, USA
| | - Harry R Hill
- Department of Pathology, University of Utah, Salt Lake City, Utah, USA.,Departments of Medicine and Pediatrics, University of Utah, Salt Lake City, Utah, USA.,ARUP Institute for Clinical and Experimental pathology, ARUP Laboratories, Salt Lake City, Utah, USA
| | - Zemin Zhou
- Department of Pathology, University of Utah, Salt Lake City, Utah, USA
| | - Xiao He
- Department of Pathology, University of Utah, Salt Lake City, Utah, USA
| | - Karl V Voelkerding
- Department of Pathology, University of Utah, Salt Lake City, Utah, USA.,ARUP Institute for Clinical and Experimental pathology, ARUP Laboratories, Salt Lake City, Utah, USA
| | - Attila Kumánovics
- Department of Pathology, University of Utah, Salt Lake City, Utah, USA.,ARUP Institute for Clinical and Experimental pathology, ARUP Laboratories, Salt Lake City, Utah, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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70
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Moradi Sarabi M, Mohammadrezaei Khorramabadi R, Zare Z, Eftekhar E. Polyunsaturated fatty acids and DNA methylation in colorectal cancer. World J Clin Cases 2019; 7:4172-4185. [PMID: 31911898 PMCID: PMC6940323 DOI: 10.12998/wjcc.v7.i24.4172] [Citation(s) in RCA: 10] [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: 09/18/2019] [Revised: 11/27/2019] [Accepted: 12/13/2019] [Indexed: 02/05/2023] Open
Abstract
Colorectal cancer (CRC) has been designated a major global problem, especially due to its high prevalence in developed countries. CRC mostly occurs sporadically (75%-80%), and only 20%-25% of patients have a family history. Several processes are involved in the development of CRC such as a combination of genetic and epigenetic alterations. Epigenetic changes, including DNA methylation play a vital role in the progression of CRC. Complex interactions between susceptibility genes and environmental factors, such as a diet and sedentary lifestyle, lead to the development of CRC. Clinical and experimental studies have confirmed the beneficial effects of dietary polyunsaturated fatty acids (PUFAs) in preventing CRC. From a mechanistic viewpoint, it has been suggested that PUFAs are pleiotropic agents that alter chromatin remodeling, membrane structure and downstream cell signaling. Moreover, PUFAs can alter the epigenome via modulation of DNA methylation. In this review, we summarize recent investigations linking PUFAs and DNA methylation-associated CRC risk.
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Affiliation(s)
- Mostafa Moradi Sarabi
- Department of Biochemistry and Genetics, School of Medicine, Lorestan University of Medical Sciences, Khorramabad 381251698, Iran
| | - Reza Mohammadrezaei Khorramabadi
- Department of Biochemistry and Genetics, School of Medicine, Lorestan University of Medical Sciences, Khorramabad 381251698, Iran
| | - Zohre Zare
- Department of Pharmaceutics, School of Pharmacy, Lorestan University of Medical Sciences, Khorramabad 381251698, Iran
| | - Ebrahim Eftekhar
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas 7919915519, Iran
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71
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Turberfield AH, Kondo T, Nakayama M, Koseki Y, King HW, Koseki H, Klose RJ. KDM2 proteins constrain transcription from CpG island gene promoters independently of their histone demethylase activity. Nucleic Acids Res 2019; 47:9005-9023. [PMID: 31363749 PMCID: PMC6753492 DOI: 10.1093/nar/gkz607] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 12/14/2022] Open
Abstract
CpG islands (CGIs) are associated with the majority of mammalian gene promoters and function to recruit chromatin modifying enzymes. It has therefore been proposed that CGIs regulate gene expression through chromatin-based mechanisms, however in most cases this has not been directly tested. Here, we reveal that the histone H3 lysine 36 (H3K36) demethylase activity of the CGI-binding KDM2 proteins contributes only modestly to the H3K36me2-depleted state at CGI-associated gene promoters and is dispensable for normal gene expression. Instead, we discover that KDM2 proteins play a widespread and demethylase-independent role in constraining gene expression from CGI-associated gene promoters. We further show that KDM2 proteins shape RNA Polymerase II occupancy but not chromatin accessibility at CGI-associated promoters. Together this reveals a demethylase-independent role for KDM2 proteins in transcriptional repression and uncovers a new function for CGIs in constraining gene expression.
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Affiliation(s)
| | - Takashi Kondo
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Manabu Nakayama
- Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Yoko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hamish W King
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,CREST, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
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72
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Li Z, Lv F, Dai C, Wang Q, Jiang C, Fang M, Xu Y. Activation of Galectin-3 (LGALS3) Transcription by Injurious Stimuli in the Liver Is Commonly Mediated by BRG1. Front Cell Dev Biol 2019; 7:310. [PMID: 31850346 PMCID: PMC6901944 DOI: 10.3389/fcell.2019.00310] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/13/2019] [Indexed: 01/13/2023] Open
Abstract
Galectin-3 (encoded by LGALS3) is a glycan-binding protein that regulates a diverse range of pathophysiological processes contributing to the pathogenesis of human diseases. Previous studies have found that galectin-3 levels are up-regulated in the liver by a host of different injurious stimuli. The underlying epigenetic mechanism, however, is unclear. Here we report that conditional knockout of Brahma related gene (BRG1), a chromatin remodeling protein, in hepatocytes attenuated induction of galectin-3 expression in several different animal models of liver injury. Similarly, BRG1 depletion or pharmaceutical inhibition in cultured hepatocytes suppressed the induction of galectin-3 expression by treatment with LPS plus free fatty acid (palmitate). Further analysis revealed that BRG1 interacted with AP-1 to bind to the proximal galectin-3 promoter and activate transcription. Mechanistically, DNA demethylation surrounding the galectin-3 promoter appeared to be a rate-limiting step in BRG1-mediated activation of galectin-3 transcription. BRG1 recruited the DNA 5-methylcytosine dioxygenase TET1 to the galectin-3 to promote active DNA demethylation thereby activating galectin-3 transcription. Finally, TET1 silencing abrogated induction of galectin-3 expression by LPS plus palmitate in cultured hepatocytes. In conclusion, our data unveil a novel epigenetic pathway that contributes to injury-associated activation of galectin-3 transcription in hepatocytes.
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Affiliation(s)
- Zilong Li
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Fangqiao Lv
- Department of Cell Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Congxin Dai
- Department of Neurosurgery, Peking Union Medical College Hospital, Beijing, China
| | - Qiong Wang
- Department of Surgical Oncology, the Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Traditional Chinese Medicine, Nanjing, China
| | - Chao Jiang
- Department of Surgical Oncology, the Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Traditional Chinese Medicine, Nanjing, China
| | - Mingming Fang
- Department of Clinical Medicine, Laboratory Center for Basic Medical Sciences, Jiangsu Health Vocational College, Nanjing, China.,Institute of Biomedical Research, Liaocheng University, Liaocheng, China
| | - Yong Xu
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China.,Institute of Biomedical Research, Liaocheng University, Liaocheng, China
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73
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de Mendoza A, Lister R, Bogdanovic O. Evolution of DNA Methylome Diversity in Eukaryotes. J Mol Biol 2019:S0022-2836(19)30659-X. [PMID: 31726061 DOI: 10.1016/j.jmb.2019.11.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/03/2019] [Accepted: 11/04/2019] [Indexed: 12/23/2022]
Abstract
Cytosine DNA methylation (5mC) is a widespread base modification in eukaryotic genomes with critical roles in transcriptional regulation. In recent years, our understanding of 5mC has changed because of advances in 5mC detection techniques that allow mapping of this mark on the whole genome scale. Profiling DNA methylomes from organisms across the eukaryotic tree of life has reshaped our views on the evolution of 5mC. In this review, we explore the macroevolution of 5mC in major eukaryotic groups, and then focus on recent advances made in animals. Genomic 5mC patterns as well as the mechanisms of 5mC deposition tend to be evolutionary labile across large phylogenetic distances; however, some common patterns are starting to emerge. Within the animal kingdom, 5mC diversity has proven to be much greater than anticipated. For example, a previously held common view that genome hypermethylation is a trait exclusive to vertebrates has recently been challenged. Also, data from genome-wide studies are starting to yield insights into the potential roles of 5mC in invertebrate cis regulation. Here we provide an evolutionary perspective of both the well-known and enigmatic roles of 5mC across the eukaryotic tree of life.
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Affiliation(s)
- Alex de Mendoza
- ARC CoE Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia; Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia.
| | - Ryan Lister
- ARC CoE Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia; Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Ozren Bogdanovic
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
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Squassina A, Meloni A, Chillotti C, Pisanu C. Zinc finger proteins in psychiatric disorders and response to psychotropic medications. Psychiatr Genet 2019; 29:132-141. [PMID: 31464994 DOI: 10.1097/ypg.0000000000000231] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Zinc finger proteins are a large family of abundantly expressed small motifs that play a crucial role in a wide range of physiological and pathophysiological mechanisms. Findings published so far support an involvement of zinc fingers in psychiatric disorders. Most of the evidence has been provided for the zinc finger protein 804A (ZNF804A) gene, which has been suggested to be implicated in schizophrenia and bipolar disorder. This evidence has been corroborated by a wide range of functional studies showing that ZNF804A regulates the expression of genes involved in cell adhesion and plays a crucial role in neurite formation and maintenance of dendritic spines. On the other hand, far less is known on other zinc finger proteins and their involvement in psychiatric disorders. In this review, we discussed studies exploring the role of zinc finger proteins in schizophrenia, bipolar disorder, and major depressive disorder as well as in pharmacogenetics of psychotropic drugs.
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Affiliation(s)
- Alessio Squassina
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari Unit of Clinical Pharmacology, University Hospital of Cagliari, Cagliari, Italy Department of Psychiatry, Dalhousie University, Halifax, NS, Canada Department of Neuroscience, Unit of Functional Pharmacology, Uppsala University, Uppsala, Sweden
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75
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Hahn MA, Jin SG, Li AX, Liu J, Huang Z, Wu X, Kim BW, Johnson J, Bilbao ADV, Tao S, Yim JA, Fong Y, Goebbels S, Schwab MH, Lu Q, Pfeifer GP. Reprogramming of DNA methylation at NEUROD2-bound sequences during cortical neuron differentiation. SCIENCE ADVANCES 2019; 5:eaax0080. [PMID: 31681843 PMCID: PMC6810389 DOI: 10.1126/sciadv.aax0080] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 09/13/2019] [Indexed: 05/03/2023]
Abstract
The characteristics of DNA methylation changes that occur during neurogenesis in vivo remain unknown. We used whole-genome bisulfite sequencing to quantitate DNA cytosine modifications in differentiating neurons and their progenitors isolated from mouse brain at the peak of embryonic neurogenesis. Localized DNA hypomethylation was much more common than hypermethylation and often occurred at putative enhancers within genes that were upregulated in neurons and encoded proteins crucial for neuronal differentiation. The hypomethylated regions strongly overlapped with mapped binding sites of the key neuronal transcription factor NEUROD2. The 5-methylcytosine oxidase ten-eleven translocation 2 (TET2) interacted with NEUROD2, and its reaction product 5-hydroxymethylcytosine accumulated at the demethylated regions. NEUROD2-targeted differentially methylated regions retained higher methylation levels in Neurod2 knockout mice, and inducible expression of NEUROD2 caused TET2-associated demethylation at its in vivo binding sites. The data suggest that the reorganization of DNA methylation in developing neurons involves NEUROD2 and TET2-mediated DNA demethylation.
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Affiliation(s)
- Maria A. Hahn
- Department of Surgery, City of Hope, Duarte, CA 91010, USA
| | - Seung-Gi Jin
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Arthur X. Li
- Department of Information Sciences, City of Hope, Duarte, CA 91010
| | - Jiancheng Liu
- Department of Developmental and Stem Cell Biology, City of Hope, Duarte, CA 91010, USA
| | - Zhijun Huang
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Xiwei Wu
- Department of Molecular and Cellular Biology, City of Hope, Duarte, CA 91010, USA
| | - Byung-Wook Kim
- Department of Surgery, City of Hope, Duarte, CA 91010, USA
| | - Jennifer Johnson
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | | | - Shu Tao
- Department of Molecular and Cellular Biology, City of Hope, Duarte, CA 91010, USA
| | - Jacob A. Yim
- Department of Surgery, City of Hope, Duarte, CA 91010, USA
| | - Yuman Fong
- Department of Surgery, City of Hope, Duarte, CA 91010, USA
| | - Sandra Goebbels
- Max Planck Institute of Experimental Medicine, Department of Neurogenetics, D-37075 Göttingen, Germany
| | - Markus H. Schwab
- Max Planck Institute of Experimental Medicine, Department of Neurogenetics, D-37075 Göttingen, Germany
- Cellular Neurophysiology and Center for Systems Neuroscience (ZSN), Hannover Medical School, 30625 Hannover, Germany
| | - Qiang Lu
- Department of Developmental and Stem Cell Biology, City of Hope, Duarte, CA 91010, USA
- Corresponding author. (G.P.P.); (Q.L.)
| | - Gerd P. Pfeifer
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
- Corresponding author. (G.P.P.); (Q.L.)
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76
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Vacík T, Lađinović D, Raška I. KDM2A/B lysine demethylases and their alternative isoforms in development and disease. Nucleus 2019; 9:431-441. [PMID: 30059280 PMCID: PMC7000146 DOI: 10.1080/19491034.2018.1498707] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Aberrant levels of histone modifications lead to chromatin malfunctioning and consequently to various developmental defects and human diseases. Therefore, the proteins bearing the ability to modify histones have been extensively studied and the molecular mechanisms of their action are now fairly well understood. However, little attention has been paid to naturally occurring alternative isoforms of chromatin modifying proteins and to their biological roles. In this review, we focus on mammalian KDM2A and KDM2B, the only two lysine demethylases whose genes have been described to produce also an alternative isoform lacking the N-terminal demethylase domain. These short KDM2A/B-SF isoforms arise through alternative promoter usage and seem to play important roles in development and disease. We hypothesise about the biological significance of these alternative isoforms, which might represent a more common evolutionarily conserved regulatory mechanism.
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Affiliation(s)
- Tomáš Vacík
- a Institute of Biology and Medical Genetics, First Faculty of Medicine , Charles University and General University Hospital in Prague , Praha 2 , Czech Republic
| | - Dijana Lađinović
- a Institute of Biology and Medical Genetics, First Faculty of Medicine , Charles University and General University Hospital in Prague , Praha 2 , Czech Republic
| | - Ivan Raška
- a Institute of Biology and Medical Genetics, First Faculty of Medicine , Charles University and General University Hospital in Prague , Praha 2 , Czech Republic
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77
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Zhang C, Hung YH, Rim HJ, Zhang D, Frost JM, Shin H, Jang H, Liu F, Xiao W, Iyer LM, Aravind L, Zhang XQ, Fischer RL, Huh JH, Hsieh TF. The catalytic core of DEMETER guides active DNA demethylation in Arabidopsis. Proc Natl Acad Sci U S A 2019; 116:17563-17571. [PMID: 31409710 PMCID: PMC6717269 DOI: 10.1073/pnas.1907290116] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The Arabidopsis DEMETER (DME) DNA glycosylase demethylates the maternal genome in the central cell prior to fertilization and is essential for seed viability. DME preferentially targets small transposons that flank coding genes, influencing their expression and initiating plant gene imprinting. DME also targets intergenic and heterochromatic regions, but how it is recruited to these differing chromatin landscapes is unknown. The C-terminal half of DME consists of 3 conserved regions required for catalysis in vitro. We show that this catalytic core guides active demethylation at endogenous targets, rescuing dme developmental and genomic hypermethylation phenotypes. However, without the N terminus, heterochromatin demethylation is significantly impeded, and abundant CG-methylated genic sequences are ectopically demethylated. Comparative analysis revealed that the conserved DME N-terminal domains are present only in flowering plants, whereas the domain architecture of DME-like proteins in nonvascular plants mainly resembles the catalytic core, suggesting that it might represent the ancestral form of the 5mC DNA glycosylase found in plant lineages. We propose a bipartite model for DME protein action and suggest that the DME N terminus was acquired late during land plant evolution to improve specificity and facilitate demethylation at heterochromatin targets.
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Affiliation(s)
- Changqing Zhang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695
- Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC 28081
| | - Yu-Hung Hung
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695
- Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC 28081
| | - Hyun Jung Rim
- Department of Plant Science, Seoul National University, 08826 Seoul, Republic of Korea
- Research Institute for Agriculture and Life Sciences, Seoul National University, 08826 Seoul, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, 08826 Seoul, Republic of Korea
| | - Dapeng Zhang
- Department of Biology, St. Louis University, St. Louis, MO 63103
| | - Jennifer M Frost
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Hosub Shin
- Department of Plant Science, Seoul National University, 08826 Seoul, Republic of Korea
- Research Institute for Agriculture and Life Sciences, Seoul National University, 08826 Seoul, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, 08826 Seoul, Republic of Korea
| | - Hosung Jang
- Department of Plant Science, Seoul National University, 08826 Seoul, Republic of Korea
- Research Institute for Agriculture and Life Sciences, Seoul National University, 08826 Seoul, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, 08826 Seoul, Republic of Korea
| | - Fang Liu
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695
- Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC 28081
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 530004 Nanning, China
| | - Wenyan Xiao
- Department of Biology, St. Louis University, St. Louis, MO 63103
| | - Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - Xiang-Qian Zhang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695;
- Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC 28081
- College of Forestry and Landscape Architecture, South China Agricultural University, 510642 Guangzhou, China
| | - Robert L Fischer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720;
| | - Jin Hoe Huh
- Department of Plant Science, Seoul National University, 08826 Seoul, Republic of Korea;
- Research Institute for Agriculture and Life Sciences, Seoul National University, 08826 Seoul, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, 08826 Seoul, Republic of Korea
| | - Tzung-Fu Hsieh
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695;
- Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC 28081
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78
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Pfeifer GP, Szabó PE, Song J. Protein Interactions at Oxidized 5-Methylcytosine Bases. J Mol Biol 2019:S0022-2836(19)30501-7. [PMID: 31401118 DOI: 10.1016/j.jmb.2019.07.039] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 07/31/2019] [Indexed: 12/19/2022]
Abstract
5-Methylcytosine (5mC), the major modified DNA base in mammalian cells, can be oxidized enzymatically to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) by the Ten-Eleven-Translocation (TET) family of proteins. Whereas 5fC and 5caC are recognized and removed by base excision repair proteins, the 5hmC base accumulates to substantial levels in certain cell types such as brain-derived neurons and is viewed as a relatively stable DNA base. As such, the existence of "reader" proteins that recognize 5hmC would be a logical assumption, and various searches have been undertaken to identify proteins that specifically bind to 5hmC and the other oxidized 5mC bases. However, the existence of definitive 5hmC "readers" has remained unclear and proteins interacting specifically with 5fC or 5caC are also very few. On the other hand, 5hmC is incapable of interacting with a number of proteins that recognize 5mC at CpG sequences, suggesting that 5hmC is an anti-reader modification that may serve to displace 5mC readers from DNA. In this review article, we discuss candidate proteins that may interact with oxidized 5mC bases.
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Affiliation(s)
- Gerd P Pfeifer
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
| | - Piroska E Szabó
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Jikui Song
- Department of Biochemistry, University of California Riverside, Riverside, CA 92521, USA
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79
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Crump NT, Milne TA. Why are so many MLL lysine methyltransferases required for normal mammalian development? Cell Mol Life Sci 2019; 76:2885-2898. [PMID: 31098676 PMCID: PMC6647185 DOI: 10.1007/s00018-019-03143-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 05/10/2019] [Indexed: 12/12/2022]
Abstract
The mixed lineage leukemia (MLL) family of proteins became known initially for the leukemia link of its founding member. Over the decades, the MLL family has been recognized as an important class of histone H3 lysine 4 (H3K4) methyltransferases that control key aspects of normal cell physiology and development. Here, we provide a brief history of the discovery and study of this family of proteins. We address two main questions: why are there so many H3K4 methyltransferases in mammals; and is H3K4 methylation their key function?
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Affiliation(s)
- Nicholas T Crump
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Thomas A Milne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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80
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Abstract
As the process that silences gene expression ensues during development, the stage is set for the activity of Polycomb-repressive complex 2 (PRC2) to maintain these repressed gene profiles. PRC2 catalyzes a specific histone posttranslational modification (hPTM) that fosters chromatin compaction. PRC2 also facilitates the inheritance of this hPTM through its self-contained "write and read" activities, key to preserving cellular identity during cell division. As these changes in gene expression occur without changes in DNA sequence and are inherited, the process is epigenetic in scope. Mutants of mammalian PRC2 or of its histone substrate contribute to the cancer process and other diseases, and research into these aberrant pathways is yielding viable candidates for therapeutic targeting. The effectiveness of PRC2 hinges on its being recruited to the proper chromatin sites; however, resolving the determinants to this process in the mammalian case was not straightforward and thus piqued the interest of many in the field. Here, we chronicle the latest advances toward exposing mammalian PRC2 and its high maintenance.
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Affiliation(s)
- Jia-Ray Yu
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Chul-Hwan Lee
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Ozgur Oksuz
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - James M Stafford
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Danny Reinberg
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
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81
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Antunes C, Sousa N, Pinto L, Marques CJ. TET enzymes in neurophysiology and brain function. Neurosci Biobehav Rev 2019; 102:337-344. [DOI: 10.1016/j.neubiorev.2019.05.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 05/08/2019] [Accepted: 05/08/2019] [Indexed: 02/07/2023]
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82
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Rajavelu A, Lungu C, Emperle M, Dukatz M, Bröhm A, Broche J, Hanelt I, Parsa E, Schiffers S, Karnik R, Meissner A, Carell T, Rathert P, Jurkowska RZ, Jeltsch A. Chromatin-dependent allosteric regulation of DNMT3A activity by MeCP2. Nucleic Acids Res 2019; 46:9044-9056. [PMID: 30102379 PMCID: PMC6158614 DOI: 10.1093/nar/gky715] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 07/26/2018] [Indexed: 12/22/2022] Open
Abstract
Despite their central importance in mammalian development, the mechanisms that regulate the DNA methylation machinery and thereby the generation of genomic methylation patterns are still poorly understood. Here, we identify the 5mC-binding protein MeCP2 as a direct and strong interactor of DNA methyltransferase 3 (DNMT3) proteins. We mapped the interaction interface to the transcriptional repression domain of MeCP2 and the ADD domain of DNMT3A and find that binding of MeCP2 strongly inhibits the activity of DNMT3A in vitro. This effect was reinforced by cellular studies where a global reduction of DNA methylation levels was observed after overexpression of MeCP2 in human cells. By engineering conformationally locked DNMT3A variants as novel tools to study the allosteric regulation of this enzyme, we show that MeCP2 stabilizes the closed, autoinhibitory conformation of DNMT3A. Interestingly, the interaction with MeCP2 and its resulting inhibition were relieved by the binding of K4 unmodified histone H3 N-terminal tail to the DNMT3A-ADD domain. Taken together, our data indicate that the localization and activity of DNMT3A are under the combined control of MeCP2 and H3 tail modifications where, depending on the modification status of the H3 tail at the binding sites, MeCP2 can act as either a repressor or activator of DNA methylation.
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Affiliation(s)
- Arumugam Rajavelu
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Cristiana Lungu
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Max Emperle
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Michael Dukatz
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Alexander Bröhm
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Julian Broche
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Ines Hanelt
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Edris Parsa
- Center for Integrated Protein Science (CiPSM) at the Department of Chemistry, Ludwig-Maximilians-University, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Sarah Schiffers
- Center for Integrated Protein Science (CiPSM) at the Department of Chemistry, Ludwig-Maximilians-University, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Rahul Karnik
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexander Meissner
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Thomas Carell
- Center for Integrated Protein Science (CiPSM) at the Department of Chemistry, Ludwig-Maximilians-University, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Philipp Rathert
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Renata Z Jurkowska
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
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83
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Vidal M. Polycomb Assemblies Multitask to Regulate Transcription. EPIGENOMES 2019; 3:12. [PMID: 34968234 PMCID: PMC8594731 DOI: 10.3390/epigenomes3020012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 06/14/2019] [Accepted: 06/16/2019] [Indexed: 02/06/2023] Open
Abstract
The Polycomb system is made of an evolutionary ancient group of proteins, present throughout plants and animals. Known initially from developmental studies with the fly Drosophila melanogaster, they were associated with stable sustainment of gene repression and maintenance of cell identity. Acting as multiprotein assemblies with an ability to modify chromatin, through chemical additions to histones and organization of topological domains, they have been involved subsequently in control of developmental transitions and in cell homeostasis. Recent work has unveiled an association of Polycomb components with transcriptionally active loci and the promotion of gene expression, in clear contrast with conventional recognition as repressors. Focusing on mammalian models, I review here advances concerning roles in transcriptional control. Among new findings highlighted is the regulation of their catalytic properties, recruiting to targets, and activities in chromatin organization and compartmentalization. The need for a more integrated approach to the study of the Polycomb system, given its fundamental complexity and its adaptation to cell context, is discussed.
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Affiliation(s)
- Miguel Vidal
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
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84
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Hartl D, Krebs AR, Grand RS, Baubec T, Isbel L, Wirbelauer C, Burger L, Schübeler D. CG dinucleotides enhance promoter activity independent of DNA methylation. Genome Res 2019; 29:554-563. [PMID: 30709850 PMCID: PMC6442381 DOI: 10.1101/gr.241653.118] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 01/24/2019] [Indexed: 11/24/2022]
Abstract
Most mammalian RNA polymerase II initiation events occur at CpG islands, which are rich in CpGs and devoid of DNA methylation. Despite their relevance for gene regulation, it is unknown to what extent the CpG dinucleotide itself actually contributes to promoter activity. To address this question, we determined the transcriptional activity of a large number of chromosomally integrated promoter constructs and monitored binding of transcription factors assumed to play a role in CpG island activity. This revealed that CpG density significantly improves motif-based prediction of transcription factor binding. Our experiments also show that high CpG density alone is insufficient for transcriptional activity, yet results in increased transcriptional output when combined with particular transcription factor motifs. However, this CpG contribution to promoter activity is independent of DNA methyltransferase activity. Together, this refines our understanding of mammalian promoter regulation as it shows that high CpG density within CpG islands directly contributes to an environment permissive for full transcriptional activity.
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Affiliation(s)
- Dominik Hartl
- Friedrich Miescher Institute for Biomedical Research, CH 4058 Basel, Switzerland.,Faculty of Sciences, University of Basel, CH 4003 Basel, Switzerland
| | - Arnaud R Krebs
- Friedrich Miescher Institute for Biomedical Research, CH 4058 Basel, Switzerland
| | - Ralph S Grand
- Friedrich Miescher Institute for Biomedical Research, CH 4058 Basel, Switzerland
| | - Tuncay Baubec
- Friedrich Miescher Institute for Biomedical Research, CH 4058 Basel, Switzerland
| | - Luke Isbel
- Friedrich Miescher Institute for Biomedical Research, CH 4058 Basel, Switzerland
| | | | - Lukas Burger
- Friedrich Miescher Institute for Biomedical Research, CH 4058 Basel, Switzerland.,Swiss Institute of Bioinformatics, CH 4058 Basel, Switzerland
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, CH 4058 Basel, Switzerland.,Faculty of Sciences, University of Basel, CH 4003 Basel, Switzerland
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85
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5-Methylcytosine and Its Oxidized Derivatives. Clin Epigenetics 2019. [DOI: 10.1007/978-981-13-8958-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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86
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Florean C, Kim KR, Schnekenburger M, Kim HJ, Moriou C, Debitus C, Dicato M, Al-Mourabit A, Han BW, Diederich M. Synergistic AML Cell Death Induction by Marine Cytotoxin (+)-1( R), 6( S), 1'( R), 6'( S), 11( R), 17( S)-Fistularin-3 and Bcl-2 Inhibitor Venetoclax. Mar Drugs 2018; 16:md16120518. [PMID: 30572618 PMCID: PMC6316187 DOI: 10.3390/md16120518] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/13/2018] [Accepted: 12/14/2018] [Indexed: 11/23/2022] Open
Abstract
Treatment of acute myeloid leukemia (AML) patients is still hindered by resistance and relapse, resulting in an overall poor survival rate. Recently, combining specific B-cell lymphoma (Bcl)-2 inhibitors with compounds downregulating myeloid cell leukemia (Mcl)-1 has been proposed as a new effective strategy to eradicate resistant AML cells. We show here that 1(R), 6(S), 1’(R), 6’(S), 11(R), 17(S)-fistularin-3, a bromotyrosine compound of the fistularin family, isolated from the marine sponge Suberea clavata, synergizes with Bcl-2 inhibitor ABT-199 to efficiently kill Mcl-1/Bcl-2-positive AML cell lines, associated with Mcl-1 downregulation and endoplasmic reticulum stress induction. The absolute configuration of carbons 11 and 17 of the fistularin-3 stereoisomer was fully resolved in this study for the first time, showing that the fistularin we isolated from the marine sponge Subarea clavata is in fact the (+)-11(R), 17(S)-fistularin-3 stereoisomer keeping the known configuration 1(R), 6(S), 1’(R), and 6’(S) for the verongidoic acid part. Docking studies and in vitro assays confirm the potential of this family of molecules to inhibit DNA methyltransferase 1 activity.
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MESH Headings
- Animals
- Antineoplastic Combined Chemotherapy Protocols/pharmacology
- Bridged Bicyclo Compounds, Heterocyclic/administration & dosage
- Bridged Bicyclo Compounds, Heterocyclic/pharmacology
- Cell Line, Tumor
- Cell Survival/drug effects
- Drug Screening Assays, Antitumor
- Drug Synergism
- Endoplasmic Reticulum Stress/drug effects
- HL-60 Cells
- Humans
- Isoxazoles/administration & dosage
- Isoxazoles/chemistry
- Isoxazoles/isolation & purification
- Isoxazoles/pharmacology
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Molecular Docking Simulation
- Porifera/chemistry
- Proto-Oncogene Proteins c-bcl-2/antagonists & inhibitors
- Proto-Oncogene Proteins c-bcl-2/metabolism
- Sulfonamides/administration & dosage
- Sulfonamides/pharmacology
- Tyrosine/administration & dosage
- Tyrosine/analogs & derivatives
- Tyrosine/chemistry
- Tyrosine/isolation & purification
- Tyrosine/pharmacology
- U937 Cells
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Affiliation(s)
- Cristina Florean
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540 Luxembourg, Luxembourg.
| | - Kyung Rok Kim
- Department of Pharmacy, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea.
| | - Michael Schnekenburger
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540 Luxembourg, Luxembourg.
| | - Hyun-Jung Kim
- College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Korea.
| | - Céline Moriou
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Univ. Paris-Sud, University of Paris-Saclay, 1, Avenue de la Terrasse, 91198 Gif-Sur-Yvette, France.
| | - Cécile Debitus
- LEMAR, IRD, UBO, CNRS, IFREMER, IUEM, 29280 Plouzané, France.
| | - Mario Dicato
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540 Luxembourg, Luxembourg.
| | - Ali Al-Mourabit
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Univ. Paris-Sud, University of Paris-Saclay, 1, Avenue de la Terrasse, 91198 Gif-Sur-Yvette, France.
| | - Byung Woo Han
- Department of Pharmacy, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea.
| | - Marc Diederich
- Department of Pharmacy, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea.
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87
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Isshiki Y, Iwama A. Emerging role of noncanonical polycomb repressive complexes in normal and malignant hematopoiesis. Exp Hematol 2018; 68:10-14. [DOI: 10.1016/j.exphem.2018.10.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/17/2018] [Accepted: 10/19/2018] [Indexed: 12/09/2022]
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88
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Xiong X, Tu S, Wang J, Luo S, Yan X. CXXC5: A novel regulator and coordinator of TGF-β, BMP and Wnt signaling. J Cell Mol Med 2018; 23:740-749. [PMID: 30479059 PMCID: PMC6349197 DOI: 10.1111/jcmm.14046] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 10/23/2018] [Indexed: 12/18/2022] Open
Abstract
CXXC5 is a member of the CXXC-type zinc-finger protein family. Proteins in this family play a pivotal role in epigenetic regulation by binding to unmethylated CpG islands in gene promoters through their characteristic CXXC domain. CXXC5 is a short protein (322 amino acids in length) that does not have any catalytic domain, but is able to bind to DNA and act as a transcription factor and epigenetic factor through protein-protein interactions. Intriguingly, increasing evidence indicates that expression of the CXXC5 gene is controlled by multiple signaling pathways and a variety of transcription factors, positioning CXXC5 as an important signal integrator. In addition, CXXC5 is capable of regulating various signal transduction processes, including the TGF-β, Wnt and ATM-p53 pathways, thereby acting as a novel and crucial signaling coordinator. CXXC5 plays an important role in embryonic development and adult tissue homeostasis by regulating cell proliferation, differentiation and apoptosis. In keeping with these functions, aberrant expression or altered activity of CXXC5 has been shown to be involved in several human diseases including tumourigenesis. This review summarizes the current understanding of CXXC5 as a transcription factor and signaling regulator and coordinator.
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Affiliation(s)
- Xiangyang Xiong
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Nanchang University, Nanchang, China
| | - Shuo Tu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Nanchang University, Nanchang, China
| | - Jianbin Wang
- School of Basic Medical Sciences, Nanchang University, Nanchang, China
| | - Shiwen Luo
- Center for Experimental Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiaohua Yan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Nanchang University, Nanchang, China
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89
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Jeltsch A, Broche J, Bashtrykov P. Molecular Processes Connecting DNA Methylation Patterns with DNA Methyltransferases and Histone Modifications in Mammalian Genomes. Genes (Basel) 2018; 9:genes9110566. [PMID: 30469440 PMCID: PMC6266221 DOI: 10.3390/genes9110566] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/13/2018] [Accepted: 11/16/2018] [Indexed: 12/20/2022] Open
Abstract
DNA methylation is an essential part of the epigenome chromatin modification network, which also comprises several covalent histone protein post-translational modifications. All these modifications are highly interconnected, because the writers and erasers of one mark, DNA methyltransferases (DNMTs) and ten eleven translocation enzymes (TETs) in the case of DNA methylation, are directly or indirectly targeted and regulated by other marks. Here, we have collected information about the genomic distribution and variability of DNA methylation in human and mouse DNA in different genomic elements. After summarizing the impact of DNA methylation on genome evolution including CpG depletion, we describe the connection of DNA methylation with several important histone post-translational modifications, including methylation of H3K4, H3K9, H3K27, and H3K36, but also with nucleosome remodeling. Moreover, we present the mechanistic features of mammalian DNA methyltransferases and their associated factors that mediate the crosstalk between DNA methylation and chromatin modifications. Finally, we describe recent advances regarding the methylation of non-CpG sites, methylation of adenine residues in human cells and methylation of mitochondrial DNA. At several places, we highlight controversial findings or open questions demanding future experimental work.
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Affiliation(s)
- Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany.
| | - Julian Broche
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany.
| | - Pavel Bashtrykov
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany.
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90
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Yarychkivska O, Shahabuddin Z, Comfort N, Boulard M, Bestor TH. BAH domains and a histone-like motif in DNA methyltransferase 1 (DNMT1) regulate de novo and maintenance methylation in vivo. J Biol Chem 2018; 293:19466-19475. [PMID: 30341171 DOI: 10.1074/jbc.ra118.004612] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 10/12/2018] [Indexed: 12/31/2022] Open
Abstract
DNA methyltransferase 1 (DNMT1) is a multidomain protein believed to be involved only in the passive transmission of genomic methylation patterns via maintenance methylation. The mechanisms that regulate DNMT1 activity and targeting are complex and poorly understood. We used embryonic stem (ES) cells to investigate the function of the uncharacterized bromo-adjacent homology (BAH) domains and the glycine-lysine (GK) repeats that join the regulatory and catalytic domains of DNMT1. We removed the BAH domains by means of a CRISPR/Cas9-mediated deletion within the endogenous Dnmt1 locus. The internally deleted protein failed to associate with replication foci during S phase in vivo and lost the ability to mediate maintenance methylation. The data indicate that ablation of the BAH domains causes DNMT1 to be excluded from replication foci even in the presence of the replication focus-targeting sequence (RFTS). The GK repeats resemble the N-terminal tails of histones H2A and H4 and are normally acetylated. Substitution of lysines within the GK repeats with arginines to prevent acetylation did not alter the maintenance activity of DNMT1 but unexpectedly activated de novo methylation of paternal imprinting control regions (ICRs) in mouse ES cells; maternal ICRs remained unmethylated. We propose a model under which DNMT1 deposits paternal imprints in male germ cells in an acetylation-dependent manner. These data reveal that DNMT1 responds to multiple regulatory inputs that control its localization as well as its activity and is not purely a maintenance methyltransferase but can participate in the de novo methylation of a small but essential compartment of the genome.
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Affiliation(s)
| | | | - Nicole Comfort
- Environmental Health Science, College of Physicians and Surgeons of Columbia University, New York, New York 10032, and
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91
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van de Lagemaat LN, Flenley M, Lynch MD, Garrick D, Tomlinson SR, Kranc KR, Vernimmen D. CpG binding protein (CFP1) occupies open chromatin regions of active genes, including enhancers and non-CpG islands. Epigenetics Chromatin 2018; 11:59. [PMID: 30292235 PMCID: PMC6173865 DOI: 10.1186/s13072-018-0230-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 09/28/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The mechanism by which protein complexes interact to regulate the deposition of post-translational modifications of histones remains poorly understood. This is particularly important at regulatory regions, such as CpG islands (CGIs), which are known to recruit Trithorax (TrxG) and Polycomb group proteins. The CxxC zinc finger protein 1 (CFP1, also known as CGBP) is a subunit of the TrxG SET1 protein complex, a major catalyst of trimethylation of H3K4 (H3K4me3). RESULTS Here, we used ChIP followed by high-throughput sequencing (ChIP-seq) to analyse genomic occupancy of CFP1 in two human haematopoietic cell types. We demonstrate that CFP1 occupies CGIs associated with active transcription start sites (TSSs), and is mutually exclusive with H3K27 trimethylation (H3K27me3), a marker of polycomb repressive complex 2. Strikingly, rather than being restricted to active CGI TSSs, CFP1 also occupies a substantial fraction of active non-CGI TSSs and enhancers of transcribed genes. However, relative to other TrxG subunits, CFP1 was specialised to TSSs. Finally, we found enrichment of CpG-containing DNA motifs in CFP1 peaks at CGI promoters. CONCLUSIONS We found that CFP1 is not solely recruited to CpG islands as it was originally defined, but also other regions including non-CpG island promoters and enhancers.
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Affiliation(s)
- Louie N. van de Lagemaat
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
| | - Maria Flenley
- MRC Molecular Haematology Unit, Weatherall Institute for Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS UK
| | - Magnus D. Lynch
- MRC Molecular Haematology Unit, Weatherall Institute for Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS UK
- Centre for Stem Cells and Regenerative Medicine, 28th Floor Guy’s Tower, Great Maze Pond, London, SE1 9RT UK
- st John’s institute of dermatology, Great Maze Pond, London, SE1 9RT UK
| | - David Garrick
- INSERM, UMRS-1126, Institut Universitaire d’Hématologie, Université Paris Diderot, 75010 Paris, France
| | - Simon R. Tomlinson
- MRC Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU UK
| | - Kamil R. Kranc
- MRC Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU UK
- Laboratory of Haematopoietic Stem Cell & Leukaemia Biology, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
| | - Douglas Vernimmen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
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92
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Deng X, Qiu Q, He K, Cao X. The seekers: how epigenetic modifying enzymes find their hidden genomic targets in Arabidopsis. CURRENT OPINION IN PLANT BIOLOGY 2018; 45:75-81. [PMID: 29864678 DOI: 10.1016/j.pbi.2018.05.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 05/03/2018] [Accepted: 05/12/2018] [Indexed: 05/23/2023]
Abstract
Epigenetic regulation plays fundamental roles in modulating chromatin-based processes and shaping the epigenome in multicellular eukaryotes, including plants. How epigenetic factors recognize their target loci hiding in the vast genomic DNA sequence remains a long-standing mystery. During the past several years, a growing body of work has revealed the complex, dynamic, and diverse chromatin-targeting mechanisms of these epigenetic factors. In this review, we focus on recent advances in understanding the recruitment of epigenetic factors to specific genomic regions, based on data from Arabidopsis thaliana.
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Affiliation(s)
- Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi Qiu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Kaixuan He
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China.
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93
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CFP1 coordinates histone H3 lysine-4 trimethylation and meiotic cell cycle progression in mouse oocytes. Nat Commun 2018; 9:3477. [PMID: 30154440 PMCID: PMC6113306 DOI: 10.1038/s41467-018-05930-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/27/2018] [Indexed: 12/27/2022] Open
Abstract
Trimethylation of histone H3 on lysine-4 (H3K4me3) is associated with gene-regulatory elements, but its transcription-independent function in cell division is unclear. CxxC-finger protein-1 (CFP1) is a major mediator of H3K4 trimethylation in mouse oocytes. Here we report that oocyte-specific knockout of Cxxc1, inhibition of CFP1 function, or abrogation of H3K4 methylation in oocytes each causes a delay of meiotic resumption as well as metaphase I arrest owing to defective spindle assembly and chromosome misalignment. These phenomena are partially attributed to insufficient phosphorylation of histone H3 at threonine-3. CDK1 triggers cell division–coupled degradation and inhibitory phosphorylation of CFP1. Preventing CFP1 degradation and phosphorylation causes CFP1 accumulation on chromosomes and impairs meiotic maturation and preimplantation embryo development. Therefore, CFP1-mediated H3K4 trimethylation provides 3a permission signal for the G2–M transition. Dual inhibition of CFP1 removes the SETD1–CFP1 complex from chromatin and ensures appropriate chromosome configuration changes during meiosis and mitosis. The transcription-independent function of trimethylation of histone H3 (H3K4me) in cell division is unclear. Here, Heng-Yu Fan and colleagues report that CFP1, a subunit of the H3K4 methyltransferase, is required for oocyte meiosis, being phosphorylated and degraded during cell cycle transition.
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94
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Biswas S, Rao CM. Epigenetic tools (The Writers, The Readers and The Erasers) and their implications in cancer therapy. Eur J Pharmacol 2018; 837:8-24. [PMID: 30125562 DOI: 10.1016/j.ejphar.2018.08.021] [Citation(s) in RCA: 216] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/26/2018] [Accepted: 08/15/2018] [Indexed: 02/08/2023]
Abstract
Addition of chemical tags on the DNA and modification of histone proteins impart a distinct feature on chromatin architecture. With the advancement in scientific research, the key players underlying these changes have been identified as epigenetic modifiers of the chromatin. Indeed, the plethora of enzymes catalyzing these modifications, portray the diversity of epigenetic space and the intricacy in regulating gene expression. These epigenetic players are categorized as writers: that introduce various chemical modifications on DNA and histones, readers: the specialized domain containing proteins that identify and interpret those modifications and erasers: the dedicated group of enzymes proficient in removing these chemical tags. Research over the past few decades has established that these epigenetic tools are associated with numerous disease conditions especially cancer. Besides, with the involvement of epigenetics in cancer, these enzymes and protein domains provide new targets for cancer drug development. This is certain from the volume of epigenetic research conducted in universities and R&D sector of pharmaceutical industry. Here we have highlighted the different types of epigenetic enzymes and protein domains with an emphasis on methylation and acetylation. This review also deals with the recent developments in small molecule inhibitors as potential anti-cancer drugs targeting the epigenetic space.
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Affiliation(s)
- Subhankar Biswas
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - C Mallikarjuna Rao
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
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95
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Vial-Pradel S, Keta S, Nomoto M, Luo L, Takahashi H, Suzuki M, Yokoyama Y, Sasabe M, Kojima S, Tada Y, Machida Y, Machida C. Arabidopsis Zinc-Finger-Like Protein ASYMMETRIC LEAVES2 (AS2) and Two Nucleolar Proteins Maintain Gene Body DNA Methylation in the Leaf Polarity Gene ETTIN (ARF3). PLANT & CELL PHYSIOLOGY 2018; 59:1385-1397. [PMID: 29415182 DOI: 10.1093/pcp/pcy031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/02/2018] [Indexed: 05/25/2023]
Abstract
Arabidopsis ASYMMETRIC LEAVES2 (AS2) plays a critical role in leaf adaxial-abaxial partitioning by repressing expression of the abaxial-determining gene ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3). We previously reported that six CpG dinucleotides in its exon 6 are thoroughly methylated by METHYLTRASFERASE1, that CpG methylation levels are inversely correlated with ETT/ARF3 transcript levels and that methylation levels at three out of the six CpG dinucleotides are decreased in as2-1. All these imply that AS2 is involved in epigenetic repression of ETT/ARF3 by gene body DNA methylation. The mechanism of the epigenetic repression by AS2, however, is unknown. Here, we tested mutations of NUCLEOLIN1 (NUC1) and RNA HELICASE10 (RH10) encoding nucleolus-localized proteins for the methylation in exon 6 as these mutations enhance the level of ETT/ARF3 transcripts in as2-1. Methylation levels at three specific CpGs were decreased in rh10-1, and two of those three overlapped with those in as2-1. Methylation levels at two specific CpGs were decreased in nuc1-1, and one of those three overlapped with that in as2-1. No site was affected by both rh10-1 and nuc1-1. One specific CpG was unaffected by these mutations. These results imply that the way in which RH10, NUC1 and AS2 are involved in maintaining methylation at five CpGs in exon 6 might be through at least several independent pathways, which might interact with each other. Furthermore, we found that AS2 binds specifically the sequence containing CpGs in exon 1 of ETT/ARF3, and that the binding requires the zinc-finger-like motif in AS2 that is structurally similar to the zinc finger-CxxC domain in vertebrate DNA methyltransferase1.
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Affiliation(s)
- Simon Vial-Pradel
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Sumie Keta
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Mika Nomoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Lilan Luo
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Hiro Takahashi
- Graduate School of Medical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, Japan
| | - Masataka Suzuki
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Yuri Yokoyama
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Michiko Sasabe
- Faculty of Agriculture and Life Science, Department of Biology, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Japan
| | - Shoko Kojima
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Yasuomi Tada
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Yasunori Machida
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Chiyoko Machida
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
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96
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Dimitrova E, Kondo T, Feldmann A, Nakayama M, Koseki Y, Konietzny R, Kessler BM, Koseki H, Klose RJ. FBXL19 recruits CDK-Mediator to CpG islands of developmental genes priming them for activation during lineage commitment. eLife 2018; 7:e37084. [PMID: 29809150 PMCID: PMC5997449 DOI: 10.7554/elife.37084] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 05/26/2018] [Indexed: 01/05/2023] Open
Abstract
CpG islands are gene regulatory elements associated with the majority of mammalian promoters, yet how they regulate gene expression remains poorly understood. Here, we identify FBXL19 as a CpG island-binding protein in mouse embryonic stem (ES) cells and show that it associates with the CDK-Mediator complex. We discover that FBXL19 recruits CDK-Mediator to CpG island-associated promoters of non-transcribed developmental genes to prime these genes for activation during cell lineage commitment. We further show that recognition of CpG islands by FBXL19 is essential for mouse development. Together this reveals a new CpG island-centric mechanism for CDK-Mediator recruitment to developmental gene promoters in ES cells and a requirement for CDK-Mediator in priming these developmental genes for activation during cell lineage commitment.
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Affiliation(s)
- Emilia Dimitrova
- Department of BiochemistryUniversity of OxfordOxfordUnited Kingdom
| | - Takashi Kondo
- Laboratory for Developmental GeneticsRIKEN Center for Integrative Medical SciencesYokohamaJapan
| | | | - Manabu Nakayama
- Department of Technology DevelopmentKazusa DNA Research InstituteKisarazuJapan
| | - Yoko Koseki
- Laboratory for Developmental GeneticsRIKEN Center for Integrative Medical SciencesYokohamaJapan
| | - Rebecca Konietzny
- Nuffield Department of MedicineTDI Mass Spectrometry Laboratory, Target Discovery Institute, University of OxfordOxfordUnited Kingdom
| | - Benedikt M Kessler
- Nuffield Department of MedicineTDI Mass Spectrometry Laboratory, Target Discovery Institute, University of OxfordOxfordUnited Kingdom
| | - Haruhiko Koseki
- Laboratory for Developmental GeneticsRIKEN Center for Integrative Medical SciencesYokohamaJapan
- CRESTJapan Science and Technology AgencyKawaguchiJapan
| | - Robert J Klose
- Department of BiochemistryUniversity of OxfordOxfordUnited Kingdom
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97
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Brown DA, Di Cerbo V, Feldmann A, Ahn J, Ito S, Blackledge NP, Nakayama M, McClellan M, Dimitrova E, Turberfield AH, Long HK, King HW, Kriaucionis S, Schermelleh L, Kutateladze TG, Koseki H, Klose RJ. The SET1 Complex Selects Actively Transcribed Target Genes via Multivalent Interaction with CpG Island Chromatin. Cell Rep 2018; 20:2313-2327. [PMID: 28877467 PMCID: PMC5603731 DOI: 10.1016/j.celrep.2017.08.030] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 07/19/2017] [Accepted: 08/06/2017] [Indexed: 12/24/2022] Open
Abstract
Chromatin modifications and the promoter-associated epigenome are important for the regulation of gene expression. However, the mechanisms by which chromatin-modifying complexes are targeted to the appropriate gene promoters in vertebrates and how they influence gene expression have remained poorly defined. Here, using a combination of live-cell imaging and functional genomics, we discover that the vertebrate SET1 complex is targeted to actively transcribed gene promoters through CFP1, which engages in a form of multivalent chromatin reading that involves recognition of non-methylated DNA and histone H3 lysine 4 trimethylation (H3K4me3). CFP1 defines SET1 complex occupancy on chromatin, and its multivalent interactions are required for the SET1 complex to place H3K4me3. In the absence of CFP1, gene expression is perturbed, suggesting that normal targeting and function of the SET1 complex are central to creating an appropriately functioning vertebrate promoter-associated epigenome. The CFP1/SET1 complex engages in dynamic and stable chromatin-binding events CFP1 uses multivalent chromatin interactions to select active CpG island promoters SET1A occupancy at CpG island promoters is predominately defined by CFP1 CFP1 targets SET1 to shape promoter-associated H3K4me3 and gene expression
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Affiliation(s)
- David A Brown
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Vincenzo Di Cerbo
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Angelika Feldmann
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Jaewoo Ahn
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Shinsuke Ito
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-2 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Neil P Blackledge
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Manabu Nakayama
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-2 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Michael McClellan
- Ludwig Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Emilia Dimitrova
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | | | - Hannah K Long
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Hamish W King
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Skirmantas Kriaucionis
- Ludwig Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | | | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-2 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
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98
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Yu C, Fan X, Sha QQ, Wang HH, Li BT, Dai XX, Shen L, Liu J, Wang L, Liu K, Tang F, Fan HY. CFP1 Regulates Histone H3K4 Trimethylation and Developmental Potential in Mouse Oocytes. Cell Rep 2018; 20:1161-1172. [PMID: 28768200 DOI: 10.1016/j.celrep.2017.07.011] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/22/2017] [Accepted: 07/06/2017] [Indexed: 12/18/2022] Open
Abstract
Trimethylation of histone H3 at lysine-4 (H3K4me3) is associated with eukaryotic gene promoters and poises their transcriptional activation during development. To examine the in vivo function of H3K4me3 in the absence of DNA replication, we deleted CXXC finger protein 1 (CFP1), the DNA-binding subunit of the SETD1 histone H3K4 methyltransferase, in developing oocytes. We find that CFP1 is required for H3K4me3 accumulation and the deposition of histone variants onto chromatin during oocyte maturation. Decreased H3K4me3 in oocytes caused global downregulation of transcription activity. Oocytes lacking CFP1 failed to complete maturation and were unable to gain developmental competence after fertilization, due to defects in cytoplasmic lattice formation, meiotic division, and maternal-zygotic transition. Our study highlights the importance of H3K4me3 in continuous histone replacement for transcriptional regulation, chromatin remodeling, and normal developmental progression in a non-replicative system.
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Affiliation(s)
- Chao Yu
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China; Department of Chemistry and Molecular Biology, Goteborg University, Goteborg SE405 30, Sweden
| | - Xiaoying Fan
- Biomedical Institute for Pioneering Investigation via Convergence, Peking University, Beijing 100871, China
| | - Qian-Qian Sha
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Hui-Han Wang
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Bo-Tai Li
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xing-Xing Dai
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Li Shen
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Junping Liu
- Institute of Aging Research, Hangzhou Normal University, Hangzhou 311121, China
| | - Lie Wang
- Institute of Immunology, Zhejiang University Medical School, Hangzhou 310058, China
| | - Kui Liu
- Department of Chemistry and Molecular Biology, Goteborg University, Goteborg SE405 30, Sweden
| | - Fuchou Tang
- Biomedical Institute for Pioneering Investigation via Convergence, Peking University, Beijing 100871, China
| | - Heng-Yu Fan
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China; Institute of Aging Research, Hangzhou Normal University, Hangzhou 311121, China.
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99
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Grayson DR, Guidotti A. DNA Methylation in Animal Models of Psychosis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 157:105-132. [PMID: 29933947 DOI: 10.1016/bs.pmbts.2017.12.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Schizophrenia (SZ) is a debilitating disease that impacts 1% of the population worldwide. Association studies have shown that inherited genetic mutations account for a portion of disease risk. However, environmental factors play an important role in the pathophysiology of the disease by altering cellular epigenetic marks at the level of chromatin. Postmortem brain studies of SZ subjects suggest that the dynamic equilibrium between DNA methylation and demethylation network components is disrupted at the level of individual SZ target genes. Herein, we review the role of DNA methylation and demethylation in the context of what is currently known regarding SZ. Furthermore, we describe the deficits that accompany two mouse models of SZ. The chronic methionine mouse model of SZ is predicated on the administration of methionine to SZ patients and controls in the context of clinical studies that were carried out during the 1960s and 1970s. The prenatal restraint stress model of SZ is based on a prolonged stress paradigm administered to pregnant dams during gestation days 7-21. The adult offspring of these dams show various behavioral and biochemical deficits in adulthood. Both models are epigenetic in origin and mimic the positive and negative symptoms, as well as the cognitive endophenotypes commonly observed in SZ patients. We also discuss the utility of typical and atypical antipsychotic drugs in alleviating these symptoms in each model.
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Affiliation(s)
- Dennis R Grayson
- Center for Alcohol Research in Epigenetics, University of Illinois, Chicago, IL, United States.
| | - Alessandro Guidotti
- Center for Alcohol Research in Epigenetics, University of Illinois, Chicago, IL, United States
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100
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Luong TQ, Keta S, Asai T, Kojima S, Nakagawa A, Micol JL, Xia S, Machida Y, Machida C. A genetic link between epigenetic repressor AS1-AS2 and DNA replication factors in establishment of adaxial-abaxial leaf polarity of Arabidopsis. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2018; 35:39-49. [PMID: 31275036 PMCID: PMC6543732 DOI: 10.5511/plantbiotechnology.18.0129b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 01/29/2018] [Indexed: 05/27/2023]
Abstract
Balanced development of adaxial and abaxial domains in leaf primordia is critical for the formation of flat symmetric leaf lamina. Arabidopsis ASYMMETRIC LEAVES1 (AS1) and AS2 proteins form a complex (AS1-AS2), which acts as key regulators for the adaxial development by the direct repression of expression of the abaxial gene ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3). Many modifier mutations have been identified, which enhance the defect of as1 and as2 mutations to generate abaxialized filamentous leaves without adaxial traits, suggesting that the development of the adaxial domain is achieved by cooperative repression by AS1-AS2 and the wild-type proteins corresponding to the modifiers. Mutations of several genes for DNA replication-related chromatin remodeling factors such as Chromatin Assembly Factor-1 (CAF-1) have been also identified as modifiers. It is still unknown, however, whether mutations in genes involved in DNA replication themselves might act as modifiers. Here we report that as1 and as2 mutants grown in the presence of hydroxyurea, a known inhibitor of DNA replication, form abaxialized filamentous leaves in a concentration-dependent manner. We further show that a mutation of the INCURVATA2 (ICU2) gene, which encodes the putative catalytic subunit of DNA polymerase α, and a mutation of the Replication Factor C Subunit3 (RFC3) gene, which encodes a protein used in replication as a clamp loader, act as modifiers. In addition, as2-1 icu2-1 double mutants showed increased mRNA levels of the genes for leaf abaxialization. These results suggest a tight link between DNA replication and the function of AS1-AS2 in the development of flat leaves.
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Affiliation(s)
- Toan Quy Luong
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - Sumie Keta
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - Toshiharu Asai
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - Shoko Kojima
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - Ayami Nakagawa
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - José Luis Micol
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Alicante, Spain
| | - Shitou Xia
- Hunan Provincial Key Laboratory of Phytohormones and Growth and Development, Hunan Agricultural University, Changsha 410128, China
| | - Yasunori Machida
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Chiyoko Machida
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi 487-8501, Japan
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