1
|
Singh BN, Tran H, Kramer J, Kirichenko E, Changela N, Wang F, Feng Y, Kumar D, Tu M, Lan J, Bizet M, Fuks F, Steward R. Tet-dependent 5-hydroxymethyl-Cytosine modification of mRNA regulates axon guidance genes in Drosophila. PLoS One 2024; 19:e0293894. [PMID: 38381741 PMCID: PMC10881007 DOI: 10.1371/journal.pone.0293894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/21/2023] [Indexed: 02/23/2024] Open
Abstract
Modifications of mRNA, especially methylation of adenosine, have recently drawn much attention. The much rarer modification, 5-hydroxymethylation of cytosine (5hmC), is not well understood and is the subject of this study. Vertebrate Tet proteins are 5-methylcytosine (5mC) hydroxylases and catalyze the transition of 5mC to 5hmC in DNA. These enzymes have recently been shown to have the same function in messenger RNAs in both vertebrates and in Drosophila. The Tet gene is essential in Drosophila as Tet knock-out animals do not reach adulthood. We describe the identification of Tet-target genes in the embryo and larval brain by mapping one, Tet DNA-binding sites throughout the genome and two, the Tet-dependent 5hmrC modifications transcriptome-wide. 5hmrC modifications are distributed along the entire transcript, while Tet DNA-binding sites are preferentially located at the promoter where they overlap with histone H3K4me3 peaks. The identified mRNAs are preferentially involved in neuron and axon development and Tet knock-out led to a reduction of 5hmrC marks on specific mRNAs. Among the Tet-target genes were the robo2 receptor and its slit ligand that function in axon guidance in Drosophila and in vertebrates. Tet knock-out embryos show overlapping phenotypes with robo2 and both Robo2 and Slit protein levels were markedly reduced in Tet KO larval brains. Our results establish a role for Tet-dependent 5hmrC in facilitating the translation of modified mRNAs primarily in cells of the nervous system.
Collapse
Affiliation(s)
- Badri Nath Singh
- Waksman Institute, Rutgers University, Piscataway, New Jersey, United States of America
| | - Hiep Tran
- Waksman Institute, Rutgers University, Piscataway, New Jersey, United States of America
| | - Joseph Kramer
- Department of Pathology and Laboratory Medicine, Rutgers Biomedical and Health Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Elmira Kirichenko
- Waksman Institute, Rutgers University, Piscataway, New Jersey, United States of America
| | - Neha Changela
- Waksman Institute, Rutgers University, Piscataway, New Jersey, United States of America
| | - Fei Wang
- Waksman Institute, Rutgers University, Piscataway, New Jersey, United States of America
| | - Yaping Feng
- Waksman Institute, Rutgers University, Piscataway, New Jersey, United States of America
| | - Dibyendu Kumar
- Waksman Institute, Rutgers University, Piscataway, New Jersey, United States of America
| | - Min Tu
- Waksman Institute, Rutgers University, Piscataway, New Jersey, United States of America
| | - Jie Lan
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Ruth Steward
- Waksman Institute, Rutgers University, Piscataway, New Jersey, United States of America
- Department of Molecular Biology and Biochemistry, Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey, United States of America
| |
Collapse
|
2
|
Singh BN, Tran H, Kramer J, Kirichenko E, Changela N, Wang F, Feng Y, Kumar D, Tu M, Lan J, Bizet M, Fuks F, Steward R. Tet-dependent 5-hydroxymethyl-Cytosine modification of mRNA regulates axon guidance genes in Drosophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.03.522592. [PMID: 36711932 PMCID: PMC9881870 DOI: 10.1101/2023.01.03.522592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Modifications of mRNA, especially methylation of adenosine, have recently drawn much attention. The much rarer modification, 5-hydroxymethylation of cytosine (5hmC), is not well understood and is the subject of this study. Vertebrate Tet proteins are 5-methylcytosine (5mC) hydroxylases and catalyze the transition of 5mC to 5hmC in DNA. These enzymes have recently been shown to have the same function in messenger RNAs in both vertebrates and in Drosophila. The Tet gene is essential in Drosophila as Tet knock-out animals do not reach adulthood. We describe the identification of Tet-target genes in the embryo and larval brain by mapping one, Tet DNA-binding sites throughout the genome and two, the Tet-dependent 5hmrC modifications transcriptome-wide. 5hmrC modifications are distributed along the entire transcript, while Tet DNA-binding sites are preferentially located at the promoter where they overlap with histone H3K4me3 peaks. The identified mRNAs are preferentially involved in neuron and axon development and Tet knock-out led to a reduction of 5hmrC marks on specific mRNAs. Among the Tet-target genes were the robo2 receptor and its slit ligand that function in axon guidance in Drosophila and in vertebrates. Tet knock-out embryos show overlapping phenotypes with robo2 and both Robo2 and Slit protein levels were markedly reduced in Tet KO larval brains. Our results establish a role for Tet-dependent 5hmrC in facilitating the translation of modified mRNAs primarily in cells of the nervous system.
Collapse
|
3
|
Tran H, Le L, Singh BN, Kramer J, Steward R. Tet Controls Axon Guidance in Early Brain Development through Glutamatergic Signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.539069. [PMID: 37398066 PMCID: PMC10312521 DOI: 10.1101/2023.05.02.539069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Mutations in human TET proteins have been found in individuals with neurodevelopmental disorders. Here we report a new function of Tet in regulating Drosophila early brain development. We found that mutation in the Tet DNA-binding domain ( Tet AXXC ) resulted in axon guidance defects in the mushroom body (MB). Tet is required in early brain development during the outgrowth of MB β axons. Transcriptomic study shows that glutamine synthetase 2 (Gs2), a key enzyme in glutamatergic signaling, is significantly downregulated in the Tet AXXC mutant brains. CRISPR/Cas9 mutagenesis or RNAi knockdown of Gs2 recapitulates the Tet AXXC mutant phenotype. Surprisingly, Tet and Gs2 act in the insulin-producing cells (IPCs) to control MB axon guidance, and overexpression of Gs2 in these cells rescues the axon guidance defects of Tet AXXC . Treating Tet AXXC with the metabotropic glutamate receptor antagonist MPEP can rescue while treating with glutamate enhances the phenotype confirming Tet function in regulating glutamatergic signaling. Tet AXXC and the Drosophila homolog of Fragile X Messenger Ribonucleoprotein protein mutant ( Fmr1 3 ) have similar axon guidance defects and reduction in Gs2 mRNA levels. Interestingly, overexpression of Gs2 in the IPCs also rescues the Fmr1 3 phenotype, suggesting functional overlapping of the two genes. Our studies provide the first evidence that Tet can control the guidance of axons in the developing brain by modulating glutamatergic signaling and the function is mediated by its DNA-binding domain.
Collapse
|
4
|
Singh BN, Tran H, Kramer J, Kirishenko E, Changela N, Wang F, Feng Y, Kumar D, Tu M, Lan J, Bizet M, Fuks F, Steward R. Tet-dependent 5-hydroxymethyl-Cytosine modification of mRNA regulates the axon guidance genes robo2 and slit in Drosophila. RESEARCH SQUARE 2023:rs.3.rs-2511705. [PMID: 36824980 PMCID: PMC9949232 DOI: 10.21203/rs.3.rs-2511705/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Modifications of mRNA, especially methylation of adenosine, have recently drawn much attention. The much rarer modification, 5-hydroxymethylation of cytosine (5hmC), is not well understood and is the subject of this study. Vertebrate Tet proteins are 5-methylcytosine (5mC) hydroxylases enzymes catalyzing the transition of 5mC to 5hmC in DNA and have recently been shown to have the same function in messenger RNAs in both vertebrates and in Drosophila. The Tet gene is essential in Drosophila because Tet knock-out animals do not reach adulthood. We describe the identification of Tet-target genes in the embryo and larval brain by determining Tet DNA-binding sites throughout the genome and by mapping the Tet-dependent 5hmrC modifications transcriptome-wide. 5hmrC-modified sites can be found along the entire transcript and are preferentially located at the promoter where they overlap with histone H3K4me3 peaks. The identified mRNAs are frequently involved in neuron and axon development and Tet knock-out led to a reduction of 5hmrC marks on specific mRNAs. Among the Tet-target genes were the robo2 receptor and its slit ligand that function in axon guidance in Drosophila and in vertebrates. Tet knock-out embryos show overlapping phenotypes with robo2 and are sensitized to reduced levels of slit. Both Robo2 and Slit protein levels were markedly reduced in Tet KO larval brains. Our results establish a role for Tet-dependent 5hmrC in facilitating the translation of modified mRNAs, primarily in developing nerve cells.
Collapse
Affiliation(s)
| | - Hiep Tran
- Waksman Institute, Rutgers University, Piscataway, NJ 08854
| | - Joseph Kramer
- Department of Pathology and Laboratory Medicine, Rutgers Biomedical and Health Sciences, Rutgers University, New Brunswick
| | | | - Neha Changela
- Waksman Institute, Rutgers University, Piscataway, NJ 08854
| | - Fei Wang
- Waksman Institute, Rutgers University, Piscataway, NJ 08854
| | - Yaping Feng
- Waksman Institute, Rutgers University, Piscataway, NJ 08854
| | - Dibyendu Kumar
- Waksman Institute, Rutgers University, Piscataway, NJ 08854
| | - Min Tu
- Waksman Institute, Rutgers University, Piscataway, NJ 08854
| | - Jie Lan
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
- Present address, Institute for Genetics, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Ruth Steward
- Waksman Institute, Rutgers University, Piscataway, NJ 08854
- Department of Molecular Biology and Biochemistry, Cancer Institute of New Jersey, Rutgers University
| |
Collapse
|
5
|
Dynamic changes in genomic 5-hydroxymethyluracil and N6-methyladenine levels in the Drosophila melanogaster life cycle and in response to different temperature conditions. Sci Rep 2022; 12:17552. [PMID: 36266436 PMCID: PMC9584883 DOI: 10.1038/s41598-022-22490-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/14/2022] [Indexed: 01/13/2023] Open
Abstract
In this study, the level of DNA modifications was investigated in three developmental stages of Drosophila melanogaster (larvae, pupae, imago) and in an in vitro model (Schneider 2 cells). Analysis was carried out using two-dimensional ultra-performance liquid chromatography with tandem mass spectrometry. Our method made it possible, for the first time, to analyze a broad spectrum of DNA modifications in the three stages of Drosophila. Each stage was characterized by a specific modification pattern, and the levels of these compounds fluctuated throughout the D. melanogaster life cycle. The level of DNA modification was also compared between insects bred at 25 °C (optimal temperature) and at 18 °C, and the groups differed significantly. The profound changes in N6-methyladenine and 5-hydroxymethyluracil levels during the Drosophila life cycle and as a result of breeding temperature changes indicate that these DNA modifications can play important regulatory roles in response to environmental changes and/or biological conditions. Moreover, the supplementation of Schneider 2 cells with 1 mM L-ascorbic acid caused a time-dependent increase in the level of 5-(hydroxymethyl)-2'-deoxyuridine. These data suggest that a certain pool of this compound may arise from the enzymatic activity of the dTET protein.
Collapse
|
6
|
Drosophila Tet Is Required for Maintaining Glial Homeostasis in Developing and Adult Fly Brains. eNeuro 2022; 9:ENEURO.0418-21.2022. [PMID: 35396259 PMCID: PMC9045479 DOI: 10.1523/eneuro.0418-21.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 11/21/2022] Open
Abstract
Ten-eleven translocation (TET) proteins are crucial epigenetic regulators highly conserved in multicellular organisms. TETs’ enzymatic function in demethylating 5-methyl cytosine in DNA is required for proper development and TETs are frequently mutated in cancer. Recently, Drosophila melanogaster Tet (dTet) was shown to be highly expressed in developing fly brains and discovered to play an important role in brain and muscle development as well as fly behavior. Furthermore, dTet was shown to have different substrate specificity compared with mammals. However, the exact role dTet plays in glial cells and how ectopic TET expression in glial cells contributes to tumorigenesis and glioma is still not clear. Here, we report a novel role for dTet specifically in glial cell organization and number. We show that loss of dTet affects the organization of a specific glia population in the optic lobe, the “optic chiasm” glia. Additionally, we find irregularities in axon patterns in the ventral nerve cord (VNC) both, in the midline and longitudinal axons. These morphologic glia and axonal defects were accompanied by locomotor defects in developing larvae escalating to immobility in adult flies. Furthermore, glia homeostasis was disturbed in dTet-deficient brains manifesting in gain of glial cell numbers and increased proliferation. Finally, we establish a Drosophila model to understand the impact of human TET3 in glia and find that ectopic expression of hTET3 in dTet-expressing cells causes glia expansion in larval brains and affects sleep/rest behavior and the circadian clock in adult flies.
Collapse
|
7
|
Sappa S, Dey D, Sudhamalla B, Islam K. Catalytic Space Engineering as a Strategy to Activate C-H Oxidation on 5-Methylcytosine in Mammalian Genome. J Am Chem Soc 2021; 143:11891-11896. [PMID: 34323479 DOI: 10.1021/jacs.1c03815] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Conditional remodeling of enzyme catalysis is a formidable challenge in protein engineering. Herein, we have undertaken a unique active site engineering tactic to command catalytic outcomes. With ten-eleven translocation (TET) enzyme as a paradigm, we show that variants with an expanded active site significantly enhance multistep C-H oxidation in 5-methylcytosine (5mC), whereas a crowded cavity leads to a single-step catalytic apparatus. We further identify an evolutionarily conserved residue in the TET family with a remarkable catalysis-directing ability. The activating variant demonstrated its prowess to oxidize 5mC in chromosomal DNA for potentiating expression of genes including tumor suppressors.
Collapse
Affiliation(s)
- Sushma Sappa
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Debasis Dey
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Babu Sudhamalla
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Kabirul Islam
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| |
Collapse
|
8
|
du Preez PH, Breeds K, Burger NFV, Swiegers HW, Truter JC, Botha AM. DNA Methylation and Demethylation Are Regulated by Functional DNA Methyltransferases and DnTET Enzymes in Diuraphis noxia. Front Genet 2020; 11:452. [PMID: 32655611 PMCID: PMC7324797 DOI: 10.3389/fgene.2020.00452] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 04/14/2020] [Indexed: 12/31/2022] Open
Abstract
Aphids are economically important insect pests of crops worldwide. Despite resistant varieties being available, resistance is continuously challenged and eventually broken down, posing a threat to food security. In the current study, the epigenome of two related Russian wheat aphid (Diuraphis noxia, Kurdjumov) biotypes (i.e., SA1 and SAM) that differ in virulence was investigated to elucidate its role in virulence in this species. Whole genome bisulfite sequencing covered a total of 6,846,597,083 cytosine bases for SA1 and 7,397,965,699 cytosine bases for SAM, respectively, of which a total of 70,861,462 bases (SA1) and 74, 073,939 bases (SAM) were methylated, representing 1.126 ± 0.321% (SA1) and 1.105 ± 0.295% (SAM) methylation in their genomes. The sequence reads were analyzed for contexts of DNA methylation and the results revealed that RWA has methylation in all contexts (CpG, CHG and CHH), with the majority of methylation within the CpG context (± 5.19%), while the other contexts show much lower levels of methylation (CHG - ± 0.27%; CHH - ± 0.34%). The top strand was slightly (0.02%) more methylated than the bottom strand. Of the 35,493 genes that mapped, we also analyzed the contexts of methylation of each of these and found that the CpG methylation was much higher in genic regions than in intergenic regions. The CHG and CHH levels did not differ between genic and intergenic regions. The exonic regions of genes were more methylated (±0.56%) than the intronic regions. We also measured the 5mC and 5hmC levels between the aphid biotypes, and found little difference in 5mC levels between the biotypes, but much higher levels of 5hmC in the virulent SAM. RWA had two homologs of each of the DNA methyltransferases 1 (DNMT1a and DNMT1b) and DNMT3s (DNMT3a and DNMT3b), but only a single DNMT2, with only the expression of DNMT3 that differed significantly between the two RWA biotypes. RWA has a single ortholog of Ten eleven translocase (DnTET) in the genome. Feeding studies show that the more virulent RWA biotype SAM upregulate DnDNMT3 and DnTET in response to wheat expressing antibiosis and antixenosis.
Collapse
Affiliation(s)
| | | | | | | | | | - Anna-Maria Botha
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| |
Collapse
|
9
|
Ismail JN, Ghannam M, Al Outa A, Frey F, Shirinian M. Ten-eleven translocation proteins and their role beyond DNA demethylation - what we can learn from the fly. Epigenetics 2020; 15:1139-1150. [PMID: 32419604 DOI: 10.1080/15592294.2020.1767323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Ten-eleven Translocation (TET) proteins have emerged as a family of epigenetic regulators that are important during development and have been implicated in various types of cancers. TET is a highly conserved protein that has orthologues in almost all multicellular organisms. Here, we review recent literature on the novel substrate specificity of this family of DNA 5-methylcytosine demethylases on DNA 6-methyladenine and RNA 5-methylcytosine that were first identified in the invertebrate model Drosophila. We focus on the biological role of these novel epigenetic marks in the fruit fly and mammals and highlight TET proteins' critical function during development specifically in brain development.
Collapse
Affiliation(s)
- Joy N Ismail
- Department of Experimental pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut , Beirut, Lebanon.,Center for Infectious Diseases Research, American University of Beirut Medical Center , Beirut, Lebanon
| | - Mirna Ghannam
- Department of Experimental pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut , Beirut, Lebanon.,Center for Infectious Diseases Research, American University of Beirut Medical Center , Beirut, Lebanon
| | - Amani Al Outa
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut , Beirut, Lebanon
| | - Felice Frey
- Department of Experimental pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut , Beirut, Lebanon.,Center for Infectious Diseases Research, American University of Beirut Medical Center , Beirut, Lebanon
| | - Margret Shirinian
- Department of Experimental pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut , Beirut, Lebanon.,Center for Infectious Diseases Research, American University of Beirut Medical Center , Beirut, Lebanon
| |
Collapse
|
10
|
McGuffin LJ, Adiyaman R, Maghrabi AHA, Shuid AN, Brackenridge DA, Nealon JO, Philomina LS. IntFOLD: an integrated web resource for high performance protein structure and function prediction. Nucleic Acids Res 2020; 47:W408-W413. [PMID: 31045208 PMCID: PMC6602432 DOI: 10.1093/nar/gkz322] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/05/2019] [Accepted: 04/23/2019] [Indexed: 12/14/2022] Open
Abstract
The IntFOLD server provides a unified resource for the automated prediction of: protein tertiary structures with built-in estimates of model accuracy (EMA), protein structural domain boundaries, natively unstructured or disordered regions in proteins, and protein–ligand interactions. The component methods have been independently evaluated via the successive blind CASP experiments and the continual CAMEO benchmarking project. The IntFOLD server has established its ranking as one of the best performing publicly available servers, based on independent official evaluation metrics. Here, we describe significant updates to the server back end, where we have focused on performance improvements in tertiary structure predictions, in terms of global 3D model quality and accuracy self-estimates (ASE), which we achieve using our newly improved ModFOLD7_rank algorithm. We also report on various upgrades to the front end including: a streamlined submission process, enhanced visualization of models, new confidence scores for ranking, and links for accessing all annotated model data. Furthermore, we now include an option for users to submit selected models for further refinement via convenient push buttons. The IntFOLD server is freely available at: http://www.reading.ac.uk/bioinf/IntFOLD/.
Collapse
Affiliation(s)
- Liam J McGuffin
- School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, UK
| | - Recep Adiyaman
- School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, UK
| | - Ali H A Maghrabi
- School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, UK
| | - Ahmad N Shuid
- School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, UK.,Infectomics cluster, Advanced Medical and Dental Institute, University of Science, Malaysia, Bertam, 13200, Kepala Batas, Pulau Pinang, Malaysia
| | | | - John O Nealon
- School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, UK
| | - Limcy S Philomina
- School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, UK
| |
Collapse
|
11
|
Mahmood AM, Dunwell JM. Evidence for novel epigenetic marks within plants. AIMS GENETICS 2019; 6:70-87. [PMID: 31922011 PMCID: PMC6949463 DOI: 10.3934/genet.2019.4.70] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 12/07/2019] [Indexed: 12/21/2022]
Abstract
Variation in patterns of gene expression can result from modifications in the genome that occur without a change in the sequence of the DNA; such modifications include methylation of cytosine to generate 5-methylcytosine (5mC) resulting in the generation of heritable epimutation and novel epialleles. This type of non-sequence variation is called epigenetics. The enzymes responsible for generation of such DNA modifications in mammals are named DNA methyltransferases (DNMT) including DNMT1, DNMT2 and DNMT3. The later stages of oxidations to these modifications are catalyzed by Ten Eleven Translocation (TET) proteins, which contain catalytic domains belonging to the 2-oxoglutarate dependent dioxygenase family. In various mammalian cells/tissues including embryonic stem cells, cancer cells and brain tissues, it has been confirmed that these proteins are able to induce the stepwise oxidization of 5-methyl cytosine to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and finally 5-carboxylcytosine (5caC). Each stage from initial methylation until the end of the DNA demethylation process is considered as a specific epigenetic mark that may regulate gene expression. This review discusses controversial evidence for the presence of such oxidative products, particularly 5hmC, in various plant species. Whereas some reports suggest no evidence for enzymatic DNA demethylation, other reports suggest that the presence of oxidative products is followed by the active demethylation and indicate the contribution of possible TET-like proteins in the regulation of gene expression in plants. The review also summarizes the results obtained by expressing the human TET conserved catalytic domain in transgenic plants.
Collapse
Affiliation(s)
- Asaad M Mahmood
- Department of Biology, College of Education, University of Garmian, Kalar, KRG/Iraq
| | - Jim M Dunwell
- School of School of Agriculture, Policy and Development, University of Reading, Reading, Berkshire, UK
| |
Collapse
|
12
|
Ismail JN, Badini S, Frey F, Abou-Kheir W, Shirinian M. Drosophila Tet Is Expressed in Midline Glia and Is Required for Proper Axonal Development. Front Cell Neurosci 2019; 13:252. [PMID: 31213988 PMCID: PMC6558204 DOI: 10.3389/fncel.2019.00252] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/20/2019] [Indexed: 01/10/2023] Open
Abstract
Ten-Eleven Translocation (TET) proteins are important epigenetic regulators that play a key role in development and are frequently deregulated in cancer. Drosophila melanogaster has a single homologous Tet gene (dTet) that is highly expressed in the central nervous system during development. Here, we examined the expression pattern of dTet in the third instar larval CNS and discovered its presence in a specific set of glia cells: midline glia (MG). Moreover, dTet knockdown resulted in significant lethality, locomotor dysfunction, and alterations in axon patterning in the larval ventral nerve cord. Molecular analyses on dTet knockdown larvae showed a downregulation in genes involved in axon guidance and reduced expression of the axon guidance cue Slit. Our findings point toward a potential role for dTet in midline glial function, specifically the regulation of axon patterning during neurodevelopment.
Collapse
Affiliation(s)
- Joy N Ismail
- Department of Experimental Pathology and Immunology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.,Center for Infectious Diseases Research, American University of Beirut Medical Center, Beirut, Lebanon
| | - Shireen Badini
- Department of Experimental Pathology and Immunology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.,Center for Infectious Diseases Research, American University of Beirut Medical Center, Beirut, Lebanon
| | - Felice Frey
- Department of Experimental Pathology and Immunology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.,Center for Infectious Diseases Research, American University of Beirut Medical Center, Beirut, Lebanon
| | - Wassim Abou-Kheir
- Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Margret Shirinian
- Department of Experimental Pathology and Immunology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.,Center for Infectious Diseases Research, American University of Beirut Medical Center, Beirut, Lebanon
| |
Collapse
|
13
|
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
|
14
|
N6-Methyladenosine in RNA and DNA: An Epitranscriptomic and Epigenetic Player Implicated in Determination of Stem Cell Fate. Stem Cells Int 2018; 2018:3256524. [PMID: 30405719 PMCID: PMC6199872 DOI: 10.1155/2018/3256524] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 07/24/2018] [Indexed: 02/06/2023] Open
Abstract
Vast emerging evidences are linking the base modifications and determination of stem cell fate such as proliferation and differentiation. Among the base modification markers extensively studied, 5-methylcytosine (5-mC) and its oxidative derivatives (5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC), and 5-carboxylcytosine (5-caC)) dynamically occur in DNA and RNA and have been acknowledged as important epigenetic markers involved in regulation of cellular biological processes. N6-Methyladenosine modification in DNA (m6dA), mRNA (m6A), tRNA, and other noncoding RNAs has been defined as another important epigenetic and epitranscriptomic marker in eukaryotes in recent years. The mRNA m6A modification has been characterized biochemically, molecularly, and phenotypically, including elucidation of its methyltransferase complexes (m6A writer), demethylases (m6A eraser), and direct interaction proteins (readers), while limited information on the DNA m6dA is available. The levels and the landscapes of m6A in the epitranscriptomes and epigenomes are precisely and dynamically regulated by the fine-tuned coordination of the writers and erasers in accordance with stages of the growth, development, and reproduction as naturally programmed during the lifespan. Additionally, progress has been made in appreciation of the link between aberrant m6A modification in stem cells and diseases, like cancers and neurodegenerative disorders. These achievements are inspiring scientists to further uncover the epigenetic mechanisms for stem cell development and to dissect pathogenesis of the multiple diseases conferred by development aberration of the stem cells. This review article will highlight the research advances in the role of m6A methylation modifications of DNA and RNA in the regulation of stem cell and genesis of the closely related disorders. Additionally, this article will also address the research directions in the future.
Collapse
|
15
|
Yao B, Li Y, Wang Z, Chen L, Poidevin M, Zhang C, Lin L, Wang F, Bao H, Jiao B, Lim J, Cheng Y, Huang L, Phillips BL, Xu T, Duan R, Moberg KH, Wu H, Jin P. Active N 6-Methyladenine Demethylation by DMAD Regulates Gene Expression by Coordinating with Polycomb Protein in Neurons. Mol Cell 2018; 71:848-857.e6. [PMID: 30078725 DOI: 10.1016/j.molcel.2018.07.005] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 06/05/2018] [Accepted: 07/03/2018] [Indexed: 12/22/2022]
Abstract
A ten-eleven translocation (TET) ortholog exists as a DNA N6-methyladenine (6mA) demethylase (DMAD) in Drosophila. However, the molecular roles of 6mA and DMAD remain unexplored. Through genome-wide 6mA and transcriptome profiling in Drosophila brains and neuronal cells, we found that 6mA may epigenetically regulate a group of genes involved in neurodevelopment and neuronal functions. Mechanistically, DMAD interacts with the Trithorax-related complex protein Wds to maintain active transcription by dynamically demethylating intragenic 6mA. Accumulation of 6mA by depleting DMAD coordinates with Polycomb proteins and contributes to transcriptional repression of these genes. Our findings suggest that active 6mA demethylation by DMAD plays essential roles in fly CNS by orchestrating through added epigenetic mechanisms.
Collapse
Affiliation(s)
- Bing Yao
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
| | - Yujing Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Zhiqin Wang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Li Chen
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Biostatistics and Bioinformatics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Mickael Poidevin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Can Zhang
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Li Lin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Feng Wang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Han Bao
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Bin Jiao
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Junghwa Lim
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ying Cheng
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Luoxiu Huang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | - Tianlei Xu
- Department of Biostatistics and Bioinformatics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ranhui Duan
- State Key Laboratory of Medical Genetics, School of Life Science, Central South University, Changsha, Hunan 410078, China
| | - Kenneth H Moberg
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
| |
Collapse
|
16
|
DNA methylation is not involved in dietary restriction induced lifespan extension in adult Drosophila. Genet Res (Camb) 2018; 100:e1. [PMID: 29386085 DOI: 10.1017/s0016672317000064] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dietary restriction (DR) is widely regarded as a viable intervention to extend lifespan and healthspan in diverse organisms. The precise molecular regulatory mechanisms are largely unknown. Epigenetic modifications are not stable upon DR and also keep changing with age. Here, we employed whole genome bisulfite sequencing to determine the DNA methylation changes upon DR in adult Drosophila. Our results indicate that although a low level of DNA methylation exists in the adult Drosophila genome, there is no significant difference in DNA methylation levels upon DR when compared to unrestricted flies. This suggests that other epigenetic components such as histone modifications might be altered by DR.
Collapse
|
17
|
Abstract
The TET (Ten-eleven translocation) 1, 2 and 3 proteins have been shown to function as DNA hydroxymethylases in vertebrates and their requirements have been documented extensively. Recently, the Tet proteins have been shown to also hydroxylate 5-methylcytosine in RNA. 5-hydroxymethylcytosine (5hmrC) is enriched in messenger RNA but the function of this modification has yet to be elucidated. Because Cytosine methylation in DNA is barely detectable in Drosophila, it serves as an ideal model to study the biological function of 5hmrC. Here, we characterized the temporal and spatial expression and requirement of Tet throughout Drosophila development. We show that Tet is essential for viability as Tet complete loss-of-function animals die at the late pupal stage. Tet is highly expressed in neuronal tissues and at more moderate levels in somatic muscle precursors in embryos and larvae. Depletion of Tet in muscle precursors at early embryonic stages leads to defects in larval locomotion and late pupal lethality. Although Tet knock-down in neuronal tissue does not cause lethality, it is essential for neuronal function during development through its affects upon locomotion in larvae and the circadian rhythm of adult flies. Further, we report the function of Tet in ovarian morphogenesis. Together, our findings provide basic insights into the biological function of Tet in Drosophila, and may illuminate observed neuronal and muscle phenotypes observed in vertebrates.
Collapse
|
18
|
Abstract
This paper provides a brief introductory review of the most recent advances in our knowledge about the structural and functional aspects of two transcriptional regulators: MeCP2, a protein whose mutated forms are involved in Rett syndrome; and CTCF, a constitutive transcriptional insulator. This is followed by a description of the PTMs affecting these two proteins and an analysis of their known interacting partners. A special emphasis is placed on the recent studies connecting these two proteins, focusing on the still poorly understood potential structural and functional interactions between the two of them on the chromatin substrate. An overview is provided for some of the currently known genes that are dually regulated by these two proteins. Finally, a model is put forward to account for their possible involvement in their regulation of gene expression.
Collapse
Affiliation(s)
- Juan Ausió
- a Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada.,b Center for Biomedical Research, University of Victoria, Victoria, BC V8W 3N5, Canada
| | - Philippe T Georgel
- c Department of Biological Sciences, Marshall University, Huntington, WV 25755, USA.,d Cell Differentiation and Development Center, Marshall University, Huntington, WV 25755, USA
| |
Collapse
|
19
|
|
20
|
Rasmussen EMK, Vågbø CB, Münch D, Krokan HE, Klungland A, Amdam GV, Dahl JA. DNA base modifications in honey bee and fruit fly genomes suggest an active demethylation machinery with species- and tissue-specific turnover rates. Biochem Biophys Rep 2016; 6:9-15. [PMID: 28955859 PMCID: PMC5600429 DOI: 10.1016/j.bbrep.2016.02.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/15/2016] [Accepted: 02/19/2016] [Indexed: 12/19/2022] Open
Abstract
Well-known epigenetic DNA modifications in mammals include the addition of a methyl group and a hydroxyl group to cytosine, resulting in 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) respectively. In contrast, the abundance and the functional implications of these modifications in invertebrate model organisms such as the honey bee (Apis mellifera) and the fruit fly (Drosophila melanogaster) are not well understood. Here we show that both adult honey bees and fruit flies contain 5mC and also 5hmC. Using a highly sensitive liquid chromatography/tandem mass spectrometry (LC/MS/MS) technique, we quantified 5mC and 5hmC in different tissues of adult honey bee worker castes and in adult fruit flies. A comparison of our data with reports from human and mouse shed light on notable differences in 5mC and 5hmC levels between tissues and species. Reporting cytosine modifications in uncharacterized tissues, phenotypes and species. Quantification of 5mC and 5hmC suggests species-specific roles and turnover. Low levels of 5hmC relative to 5mC and cytosine in honey bees compared to mammals. Honey bee abdominal tissues are richer in5hmC than the brain. We found a higher 5hmC to 5mC ratio in fruit flies as compared to the honey bee.
Collapse
Affiliation(s)
- Erik M K Rasmussen
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, NO-1432 Aas, Norway
| | - Cathrine B Vågbø
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Daniel Münch
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, NO-1432 Aas, Norway
| | - Hans E Krokan
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Arne Klungland
- Department of Microbiology, Division of diagnostics and intervention, Institute of Clinical Medicine, Oslo University Hospital, Rikshospitalet, NO-0027 Oslo, Norway
| | - Gro V Amdam
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, NO-1432 Aas, Norway.,School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - John Arne Dahl
- Department of Microbiology, Division of diagnostics and intervention, Institute of Clinical Medicine, Oslo University Hospital, Rikshospitalet, NO-0027 Oslo, Norway
| |
Collapse
|
21
|
Delatte B, Wang F, Ngoc LV, Collignon E, Bonvin E, Deplus R, Calonne E, Hassabi B, Putmans P, Awe S, Wetzel C, Kreher J, Soin R, Creppe C, Limbach PA, Gueydan C, Kruys V, Brehm A, Minakhina S, Defrance M, Steward R, Fuks F. RNA biochemistry. Transcriptome-wide distribution and function of RNA hydroxymethylcytosine. Science 2016; 351:282-5. [PMID: 26816380 DOI: 10.1126/science.aac5253] [Citation(s) in RCA: 303] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Hydroxymethylcytosine, well described in DNA, occurs also in RNA. Here, we show that hydroxymethylcytosine preferentially marks polyadenylated RNAs and is deposited by Tet in Drosophila. We map the transcriptome-wide hydroxymethylation landscape, revealing hydroxymethylcytosine in the transcripts of many genes, notably in coding sequences, and identify consensus sites for hydroxymethylation. We found that RNA hydroxymethylation can favor mRNA translation. Tet and hydroxymethylated RNA are found to be most abundant in the Drosophila brain, and Tet-deficient fruitflies suffer impaired brain development, accompanied by decreased RNA hydroxymethylation. This study highlights the distribution, localization, and function of cytosine hydroxymethylation and identifies central roles for this modification in Drosophila.
Collapse
Affiliation(s)
- Benjamin Delatte
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Fei Wang
- Waksman Institute, Department of Molecular Biology and Biochemistry, Cancer Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Long Vo Ngoc
- Laboratory of Molecular Biology of the Gene, Faculty of Sciences, Université Libre de Bruxelles, Gosselies, Belgium
| | - Evelyne Collignon
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Elise Bonvin
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Bouchra Hassabi
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Pascale Putmans
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Stephan Awe
- Institut für Molekularbiologie und Tumorforschung, Philipps-Universität Marburg, Marburg, Germany
| | - Collin Wetzel
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Judith Kreher
- Institut für Molekularbiologie und Tumorforschung, Philipps-Universität Marburg, Marburg, Germany
| | - Romuald Soin
- Laboratory of Molecular Biology of the Gene, Faculty of Sciences, Université Libre de Bruxelles, Gosselies, Belgium
| | - Catherine Creppe
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Patrick A Limbach
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Cyril Gueydan
- Laboratory of Molecular Biology of the Gene, Faculty of Sciences, Université Libre de Bruxelles, Gosselies, Belgium
| | - Véronique Kruys
- Laboratory of Molecular Biology of the Gene, Faculty of Sciences, Université Libre de Bruxelles, Gosselies, Belgium
| | - Alexander Brehm
- Institut für Molekularbiologie und Tumorforschung, Philipps-Universität Marburg, Marburg, Germany
| | - Svetlana Minakhina
- Waksman Institute, Department of Molecular Biology and Biochemistry, Cancer Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Matthieu Defrance
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Ruth Steward
- Waksman Institute, Department of Molecular Biology and Biochemistry, Cancer Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Université Libre de Bruxelles (ULB), Brussels, Belgium.
| |
Collapse
|
22
|
Abstract
Protein tertiary structure prediction algorithms aim to predict, from amino acid sequence, the tertiary structure of a protein. In silico protein structure prediction methods have become extremely important, as in vitro-based structural elucidation is unable to keep pace with the current growth of sequence databases due to high-throughput next-generation sequencing, which has exacerbated the gaps in our knowledge between sequences and structures.Here we briefly discuss protein tertiary structure prediction, the biennial competition for the Critical Assessment of Techniques for Protein Structure Prediction (CASP) and its role in shaping the field. We also discuss, in detail, our cutting-edge web-server method IntFOLD2-TS for tertiary structure prediction. Furthermore, we provide a step-by-step guide on using the IntFOLD2-TS web server, along with some real world examples, where the IntFOLD server can and has been used to improve protein tertiary structure prediction and aid in functional elucidation.
Collapse
Affiliation(s)
- Daniel Barry Roche
- Institut de Biologie Computationnelle, LIRMM, CNRS, Université de Montpellier, Montpellier, France.
- CEA, DSV, IG, Genoscope, Évry, France.
- CNRS-UMR8030, Évry, France.
- Université d'Évry Val d'Essonne, Évry, France.
- PRES UniverSud Paris, Saint-Aubin, France.
| | | |
Collapse
|
23
|
Epigenetic mechanisms of dietary restriction induced aging in Drosophila. Exp Gerontol 2015; 72:38-44. [DOI: 10.1016/j.exger.2015.08.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 08/04/2015] [Accepted: 08/25/2015] [Indexed: 01/07/2023]
|
24
|
Disruption of Methionine Metabolism in Drosophila melanogaster Impacts Histone Methylation and Results in Loss of Viability. G3-GENES GENOMES GENETICS 2015; 6:121-32. [PMID: 26546310 PMCID: PMC4704710 DOI: 10.1534/g3.115.024273] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Histone methylation levels, which are determined by the action of both histone demethylases and methyltransferases, impact multiple biological processes by affecting gene expression activity. Methionine metabolism generates the major methyl donor S-adenosylmethionine (SAM) for histone methylation. The functions of methionine metabolic enzymes in regulating biological processes as well as the interaction between the methionine pathway and histone methylation, however, are still not fully understood. Here, we report that reduced levels of some enzymes involved in methionine metabolism and histone demethylases lead to lethality as well as wing development and cell proliferation defects in Drosophila melanogaster. Additionally, disruption of methionine metabolism can directly affect histone methylation levels. Reduction of little imaginal discs (LID) histone demethylase, but not lysine-specific demethylase 2 (KDM2) demethylase, is able to counter the effects on histone methylation due to reduction of SAM synthetase (SAM-S). Taken together, these results reveal an essential role of key enzymes that control methionine metabolism and histone methylation. Additionally, these findings are an indication of a strong connection between metabolism and epigenetics.
Collapse
|
25
|
Dunwell TL, Pfeifer GP. Drosophila genomic methylation: new evidence and new questions. Epigenomics 2015; 6:459-61. [PMID: 25431937 DOI: 10.2217/epi.14.46] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Thomas L Dunwell
- Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | | |
Collapse
|
26
|
Hashimoto H, Zhang X, Vertino PM, Cheng X. The Mechanisms of Generation, Recognition, and Erasure of DNA 5-Methylcytosine and Thymine Oxidations. J Biol Chem 2015; 290:20723-20733. [PMID: 26152719 DOI: 10.1074/jbc.r115.656884] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
One of the most fundamental questions in the control of gene expression in mammals is how the patterns of epigenetic modifications of DNA are generated, recognized, and erased. This includes covalent cytosine methylation of DNA and its associated oxidation states. An array of AdoMet-dependent methyltransferases, Fe(II)- and α-ketoglutarate-dependent dioxygenases, base excision glycosylases, and sequence-specific transcription factors is responsible for changing, maintaining, and interpreting the modification status of specific regions of chromatin. This review focuses on recent developments in characterizing the functional and structural links between the modification status of two DNA bases 5-methylcytosine and thymine (5-methyluracil).
Collapse
Affiliation(s)
- Hideharu Hashimoto
- Departments of Biochemistry, Emory University School of Medicine, Emory University, Atlanta, Georgia 30322
| | - Xing Zhang
- Departments of Biochemistry, Emory University School of Medicine, Emory University, Atlanta, Georgia 30322
| | - Paula M Vertino
- Departments of Radiation Oncology, Emory University School of Medicine, Emory University, Atlanta, Georgia 30322; Winship Cancer Institute, Emory University, Atlanta, Georgia 30322
| | - Xiaodong Cheng
- Departments of Biochemistry, Emory University School of Medicine, Emory University, Atlanta, Georgia 30322; Winship Cancer Institute, Emory University, Atlanta, Georgia 30322.
| |
Collapse
|
27
|
Stegemann R, Buchner DA. Transgenerational inheritance of metabolic disease. Semin Cell Dev Biol 2015; 43:131-140. [PMID: 25937492 PMCID: PMC4626440 DOI: 10.1016/j.semcdb.2015.04.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 04/20/2015] [Accepted: 04/22/2015] [Indexed: 02/05/2023]
Abstract
Metabolic disease encompasses several disorders including obesity, type 2 diabetes, and dyslipidemia. Recently, the incidence of metabolic disease has drastically increased, driven primarily by a worldwide obesity epidemic. Transgenerational inheritance remains controversial, but has been proposed to contribute to human metabolic disease risk based on a growing number of proof-of-principle studies in model organisms ranging from Caenorhabditis elegans to Mus musculus to Sus scrofa. Collectively, these studies demonstrate that heritable risk is epigenetically transmitted from parent to offspring over multiple generations in the absence of a continued exposure to the triggering stimuli. A diverse assortment of initial triggers can induce transgenerational inheritance including high-fat or high-sugar diets, low-protein diets, various toxins, and ancestral genetic variants. Although the mechanistic basis underlying the transgenerational inheritance of disease risk remains largely unknown, putative molecules mediating transmission include small RNAs, histone modifications, and DNA methylation. Due to the considerable impact of metabolic disease on human health, it is critical to better understand the role of transgenerational inheritance of metabolic disease risk to open new avenues for therapeutic intervention and improve upon the current methods for clinical diagnoses and treatment.
Collapse
Affiliation(s)
- Rachel Stegemann
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, United States
| | - David A Buchner
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, United States; Department of Biological Chemistry, Case Western Reserve University, Cleveland, OH 44106, United States.
| |
Collapse
|
28
|
Rasmussen EMK, Amdam GV. Cytosine modifications in the honey bee (Apis mellifera) worker genome. Front Genet 2015; 6:8. [PMID: 25705215 PMCID: PMC4319462 DOI: 10.3389/fgene.2015.00008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 01/09/2015] [Indexed: 01/05/2023] Open
Abstract
Epigenetic changes enable genomes to respond to changes in the environment, such as altered nutrition, activity, or social setting. Epigenetic modifications, thereby, provide a source of phenotypic plasticity in many species. The honey bee (Apis mellifera) uses nutritionally sensitive epigenetic control mechanisms in the development of the royal caste (queens) and the workers. The workers are functionally sterile females that can take on a range of distinct physiological and/or behavioral phenotypes in response to environmental changes. Honey bees have a wide repertoire of epigenetic mechanisms which, as in mammals, include cytosine methylation, hydroxymethylated cytosines, together with the enzymatic machinery responsible for these cytosine modifications. Current data suggests that honey bees provide an excellent system for studying the “social repertoire” of the epigenome. In this review, we elucidate what is known so far about the honey bee epigenome and its mechanisms. Our discussion includes what may distinguish honey bees from other model animals, how the epigenome can influence worker behavioral task separation, and how future studies can answer central questions about the role of the epigenome in social behavior.
Collapse
Affiliation(s)
- Erik M K Rasmussen
- Department of Chemistry, Biotechnology and Food Science, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences Aas, Norway
| | - Gro V Amdam
- Department of Chemistry, Biotechnology and Food Science, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences Aas, Norway ; School of Life Sciences, Arizona State University Tempe, AZ, USA
| |
Collapse
|
29
|
Boffelli D, Takayama S, Martin DIK. Now you see it: genome methylation makes a comeback in Drosophila. Bioessays 2014; 36:1138-44. [PMID: 25220261 DOI: 10.1002/bies.201400097] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Drosophila melanogaster is often considered to lack genomic 5-methylcytosine (m(5) C), an opinion reinforced by two whole genome bisulfite-sequencing studies that failed to find m(5) C. New evidence, however, indicates that genomic methylation is indeed present in the fly, albeit in small quantities and in unusual patterns. At embryonic stage 5, m(5) C occurs in short strand-specific regions that cover ∼1% of the genome, at tissue levels suggesting a distribution restricted to a subset of nuclei. Its function is not obvious, but methylation in subsets of nuclei would obscure functional associations since transcript levels and epigenetic modifications are assayed in whole embryos. Surprisingly, Mt2, the fly's only candidate DNA methyltransferase, is not necessary for the observed methylation. Full evaluation of the functions of genome methylation in Drosophila must await discovery and experimental inactivation of the DNA methyltransferase, as well as a better understanding of the pattern and developmental regulation of genomic m(5) C.
Collapse
Affiliation(s)
- Dario Boffelli
- Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | | | | |
Collapse
|
30
|
Fu L, Guerrero CR, Zhong N, Amato NJ, Liu Y, Liu S, Cai Q, Ji D, Jin SG, Niedernhofer LJ, Pfeifer GP, Xu GL, Wang Y. Tet-mediated formation of 5-hydroxymethylcytosine in RNA. J Am Chem Soc 2014; 136:11582-5. [PMID: 25073028 PMCID: PMC4140497 DOI: 10.1021/ja505305z] [Citation(s) in RCA: 262] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Oxidation of 5-methylcytosine
in DNA by ten-eleven translocation
(Tet) family of enzymes has been demonstrated to play a significant
role in epigenetic regulation in mammals. We found that Tet enzymes
also possess the activity of catalyzing the formation of 5-hydroxymethylcytidine
(5-hmrC) in RNA in vitro. In addition, the catalytic
domains of all three Tet enzymes as well as full-length Tet3 could
induce the formation of 5-hmrC in human cells. Moreover, 5-hmrC was
present at appreciable levels (∼1 per 5000 5-methylcytidine)
in RNA of mammalian cells and tissues. Our results suggest the involvement
of this oxidation in RNA biology.
Collapse
Affiliation(s)
- Lijuan Fu
- Environmental Toxicology Graduate Program and ‡Department of Chemistry, University of California , Riverside, California 92521, United States
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Head JA. Patterns of DNA methylation in animals: an ecotoxicological perspective. Integr Comp Biol 2014; 54:77-86. [PMID: 24785828 DOI: 10.1093/icb/icu025] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
DNA methylation refers to the addition of a methyl group to nucleotides within DNA. As with other epigenetic endpoints, patterns of DNA methylation are susceptible to alterations due to exposure to environmental stressors, including contaminants. These alterations can persist in the absence of the initial stressor as cells divide, and can even be inherited between generations if they occur in the germ line. Although our knowledge concerning patterns of DNA methylation in animals is increasing, there remains a gap in the literature when it comes to species outside of those typically used for biomedical research. Here, I review the literature relating to DNA methylation in an array of taxa (mammals, fish, birds, amphibians, reptiles, and invertebrates) and discuss these data from an ecotoxicological perspective. The pattern and extent of DNA methylation is well conserved across species of vertebrates; methylation appears mainly on cytosine residues within a CpG context, and much of the genome is methylated, with the notable exception of cytosines within CpG islands in the promoters of genes. Highly methylated genes in vertebrates tend to be transcriptionally repressed. However, large differences occur between classes of vertebrates in terms of the timing and nature of reprogramming and genomic imprinting: epigenetic processes that establish patterns of DNA methylation in the early embryo and which are sensitive to environmental stress. In invertebrates, patterns of DNA methylation are extremely variable and differ significantly from the condition observed in vertebrates. Some invertebrate genomes exhibit no DNA methylation while others are methylated to a level that is comparable to vertebrates. Additionally, DNA methylation may have different functions in invertebrates, e.g., alternative splicing. This variability in basic patterns of DNA methylation among species during sensitive periods of development suggests that responses to epigenetically active environmental contaminants may be similarly variable. For example, the timing of exposure to a contaminant may be a critical factor when considered in the light of variable reprogramming schedules among species. With this in mind, I review data relating to the effects of contaminants on DNA methylation in animals, focusing on non-model organisms and on exposures in natural environments, when possible. An ecotoxicological perspective on patterns of DNA methylation in animals may improve our understanding of the range and diversity of epigenetic phenomena in the natural world.
Collapse
Affiliation(s)
- Jessica A Head
- School of Natural Resources and Environment, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|