1
|
Wang Y, Sheng Y, Liu Y, Pan B, Huang J, Warren A, Gao S. N 6 -methyladenine DNA modification in the unicellular eukaryotic organism Tetrahymena thermophila. Eur J Protistol 2017; 58:94-102. [DOI: 10.1016/j.ejop.2016.12.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 12/08/2016] [Accepted: 12/12/2016] [Indexed: 01/30/2023]
|
2
|
O'Brown ZK, Greer EL. N6-Methyladenine: A Conserved and Dynamic DNA Mark. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:213-246. [PMID: 27826841 DOI: 10.1007/978-3-319-43624-1_10] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Chromatin, consisting of deoxyribonucleic acid (DNA) wrapped around histone proteins, facilitates DNA compaction and allows identical DNA codes to confer many different cellular phenotypes. This biological versatility is accomplished in large part by posttranslational modifications to histones and chemical modifications to DNA. These modifications direct the cellular machinery to expand or compact specific chromatin regions and mark regions of the DNA as important for cellular functions. While each of the four bases that make up DNA can be modified (Iyer et al. 2011), this chapter will focus on methylation of the sixth position on adenines (6mA), as this modification has been poorly characterized in recently evolved eukaryotes, but shows promise as a new conserved layer of epigenetic regulation. 6mA was previously thought to be restricted to unicellular organisms, but recent work has revealed its presence in metazoa. Here, we will briefly describe the history of 6mA, examine its evolutionary conservation, and evaluate the current methods for detecting 6mA. We will discuss the enzymes that bind and regulate this mark and finally examine known and potential functions of 6mA in eukaryotes.
Collapse
Affiliation(s)
- Zach Klapholz O'Brown
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Eric Lieberman Greer
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA. .,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
| |
Collapse
|
3
|
Sun Q, Huang S, Wang X, Zhu Y, Chen Z, Chen D. N6-methyladenine functions as a potential epigenetic mark in eukaryotes. Bioessays 2015; 37:1155-62. [PMID: 26293475 DOI: 10.1002/bies.201500076] [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: 11/06/2022]
Abstract
N(6)-methyladenine (6mA) is one of the most abundant types of DNA methylation, and plays an important role in bacteria; however, its roles in higher eukaryotes, such as plants, insects, and mammals, have been considered less important. Recent studies highlight that 6mA does indeed occur, and that it plays an important role in eukaryotes, such as worm, fly, and green algae, and thus the regulation of 6mA has emerged as a novel epigenetic mechanism in higher eukaryotes. Despite this intriguing development, a number of important issues regarding its biological roles are yet to be addressed. In this review, we focus on the 5mC and 6mA modifications in terms of their production, distribution, and the erasure of 6mA in higher eukaryotes including mammals. We perform an analysis of the potential functions of 6mA, hence widening understanding of this new epigenetic mark in higher eukaryotes, and suggesting future studies in this field.
Collapse
Affiliation(s)
- Qinmiao Sun
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shoujun Huang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Center for Developmental Biology, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xiaona Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yuanxiang Zhu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhenping Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Dahua Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
4
|
Huang W, Xiong J, Yang Y, Liu SM, Yuan BF, Feng YQ. Determination of DNA adenine methylation in genomes of mammals and plants by liquid chromatography/mass spectrometry. RSC Adv 2015. [DOI: 10.1039/c5ra05307b] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Determination of DNA adenine methylation in genomes of mammals and plants.
Collapse
Affiliation(s)
- Wei Huang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- Department of Chemistry
- Wuhan University
- Wuhan 430072
- P.R. China
| | - Jun Xiong
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- Department of Chemistry
- Wuhan University
- Wuhan 430072
- P.R. China
| | - Ying Yang
- Center for Gene Diagnosis
- Zhongnan Hospital of Wuhan University
- Wuhan
- P.R. China
| | - Song-Mei Liu
- Center for Gene Diagnosis
- Zhongnan Hospital of Wuhan University
- Wuhan
- P.R. China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- Department of Chemistry
- Wuhan University
- Wuhan 430072
- P.R. China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education)
- Department of Chemistry
- Wuhan University
- Wuhan 430072
- P.R. China
| |
Collapse
|
5
|
Abstract
Contrary to mammalian DNA, which is thought to contain only 5-methylcytosine (m5C), bacterial DNA contains two additional methylated bases, namely N6-methyladenine (m6A), and N4-methylcytosine (m4C). However, if the main function of m5C and m4C in bacteria is protection against restriction enzymes, the roles of m6A are multiple and include, for example, the regulation of virulence and the control of many bacterial DNA functions such as the replication, repair, expression and transposition of DNA. Interestingly, even if adenine methylation is usually considered a bacterial DNA feature, the presence of m6A has been found in protist and plant DNAs. Furthermore, indirect evidence suggests the presence of m6A in mammal DNA, raising the possibility that this base has remained undetected due to the low sensitivity of the analytical methods used. This highlights the importance of considering m6A as the sixth element of DNA.
Collapse
Affiliation(s)
- David Ratel
- Neurosciences précliniques
INSERM : U318Université Joseph Fourier - Grenoble ICHU Grenoble 38043 Grenoble Cedex 9,FR
| | | | - François Berger
- Neurosciences précliniques
INSERM : U318Université Joseph Fourier - Grenoble ICHU Grenoble 38043 Grenoble Cedex 9,FR
| | - Didier Wion
- Neurosciences précliniques
INSERM : U318Université Joseph Fourier - Grenoble ICHU Grenoble 38043 Grenoble Cedex 9,FR
- * Correspondence should be adressed to: Didier Wion
| |
Collapse
|
6
|
Abstract
DNA methylation in lower eukaryotes, in contrast to vertebrates, can involve modification of adenine to N6-methyladenine (m6A). While DNA-[cytosine] methylation in higher eukaryotes has been implicated in many important cellular processes, the function(s) of DNA-[adenine] methylation in lower eukaryotes remains unknown. I have chosen to study the ciliate Tetrahymena thermophila as a model system, since this organism is known to contain m6A, but not m5C, in its macronuclear DNA. A BLAST analysis revealed an open reading frame (ORF) that appears to encode for the Tetrahymena DNA-[adenine] methyltransferase (MTase), based on the presence of motifs characteristic of the enzymes in prokaryotes. Possible biological roles for DNA-[adenine] methylation in Tetrahymena are discussed. Experiments to test these hypotheses have begun with the cloning of the gene. Orthologous ORFs are also present in three species of the malarial parasite Plasmodium. They are compared to one another and to the putative Tetrahymena DNA-[adenine] MTase. The gene from the human parasite P. falciparum has been cloned.
Collapse
Affiliation(s)
- S Hattman
- Department of Biology, University of Rochester, Rochester, NY 14627-0211, USA.
| |
Collapse
|
7
|
Abstract
Nucleosome positioning in the somatic macronuclear genome of the ciliated protozoan Tetrahymena thermophila was analyzed by indirect end labeling. Nucleosomes were positioned nonrandomly in three different regions of the Tetrahymena genome. Nucleosome repeat length varied between adjacent nucleosomes. Nucleosome positioning in a histone H1 knockout strain was indistinguishable from that in a strain with wild type histone H1.
Collapse
Affiliation(s)
- K M Karrer
- Department of Biology, Marquette University, Milwaukee, Wisconsin 53201-1881, USA. kathleen,
| | | |
Collapse
|
8
|
Affiliation(s)
- K M Karrer
- Department of Biology, Marquette University, Milwaukee, Wisconsin 53201, USA
| |
Collapse
|
9
|
Karrer KM, VanNuland TA. Position effect takes precedence over target sequence in determination of adenine methylation patterns in the nuclear genome of a eukaryote, Tetrahymena thermophila. Nucleic Acids Res 1998; 26:4566-73. [PMID: 9753722 PMCID: PMC147886 DOI: 10.1093/nar/26.20.4566] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Approximately 0.8% of the adenine residues in the macronuclear DNA of the ciliated protozoan Tetrahymena thermophila are modified to N 6-methyladenine. DNA methylation is site specific and the pattern of methylation is constant between clonal cell lines. In vivo, modification of adenine residues appears to occur exclusively in the sequence 5'-NAT-3', but no consensus sequence for modified sites has been found. In this study, DNA fragments containing a site that is uniformly methylated on the 50 copies of the macronuclear chromosome were cloned into the extrachromosomal rDNA. In the novel location on the rDNA minichromosome, the site was unmethylated. The result was the same whether the sequences were introduced in a methylated or unmethylated state and regardless of the orientation of the sequence with respect to the origin of DNA replication. The data show that sequence is insufficient to account for site-specific methylation in Tetrahymena and argue that other factors determine the pattern of DNA methylation.
Collapse
Affiliation(s)
- K M Karrer
- Department of Biology, Marquette University, Milwaukee, WI 53201-1881, USA.
| | | |
Collapse
|
10
|
Patil NS, Hempen PM, Udani RA, Karrer KM. Alternate junctions and microheterogeneity of Tlr1, a developmentally regulated DNA rearrangement in Tetrahymena thermophila. J Eukaryot Microbiol 1997; 44:518-22. [PMID: 9304822 DOI: 10.1111/j.1550-7408.1997.tb05733.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A large number of developmentally regulated DNA rearrangements occur during the development of the macronucleus in Tetrahymena thermophila. Tlr1 is a deletion element which has large inverted repeats near the rearrangement junctions and deletes more than 13 kbp of internal DNA. Previous analysis of caryonidal lines revealed alternate left junctions for the Tlr1 rearrangement in B strain cells. We show here that C2 strain Tetrahymena also use alternate rearrangement junctions. We have mapped and sequenced two additional rearrangement variants and find that both the left and right junctions can vary over a range of approximately 200 bp. We also demonstrate the presence of sequence microheterogeneity in the most commonly found Tlr1 rearrangement product.
Collapse
Affiliation(s)
- N S Patil
- Department of Biology, Marquette University, Milwaukee, Wisconsin 53201-1881, USA
| | | | | | | |
Collapse
|
11
|
Van Nuland TA, Capowski EE, Karrer KM. Position effect for adenine methylation in the macronuclear DNA of Tetrahymena. Gene X 1995; 157:235-7. [PMID: 7607498 DOI: 10.1016/0378-1119(94)00546-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The macronucleus of the ciliate Tetrahymena contains about 45 copies of the genome. The fraction of the molecules on which an adenine residue is modified to N6-methyladenine is characteristic of the specific site, and consistent between clones. A fragment of DNA containing a site that is uniformly methylated on the macronuclear chromosome was moved to a new location on the extrachromosomal rDNA. The methylation pattern of the fragment on the rDNA was different from that on the chromosome. The data suggest that DNA sequence is not sufficient to determine the level of methylation.
Collapse
Affiliation(s)
- T A Van Nuland
- Department of Biology, Marquette University, Milwaukee, WI 53233, USA
| | | | | |
Collapse
|
12
|
Karrer KM, Stein-Gavens S. Constancy of adenine methylation in Tetrahymena macronuclear DNA. THE JOURNAL OF PROTOZOOLOGY 1990; 37:409-14. [PMID: 2213654 DOI: 10.1111/j.1550-7408.1990.tb01165.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Macronuclear DNA from Tetrahymena was examined in order to determine whether the pattern of adenine methylation changed with the transcriptional activity of nearby genes. The DNA from growing, starved and conjugating cells was digested with six restriction enzymes which are sensitive to methylation of adenine within their recognition site. Southern blots of the restricted DNAs were probed with seven cDNA clones and one genomic clone which are homologous to polyA+ RNAs, whose transcriptional activity varies with the physiological state of the cell. One of the cDNA clones, BC11, had not been described previously. It hybridized to a 1.3 kb transcript which was present in populations of starved and conjugating, but not in growing cells. On Southern blots of genomic DNA it hybridized to a complex pattern of bands which was highly polymorphic between the DNAs of closely related strains. It was estimated that between 137 and 272 sites were assayed for changes in methylation, including at least 27 sites which were known to be methylated. No differences were seen in the size of restriction fragments from cells in different physiological states. The data suggested that the methylation pattern, which is determined during macronuclear development, does not vary with the physiological state of the cell.
Collapse
Affiliation(s)
- K M Karrer
- Department of Biology, Marquette University, Milwaukee, Wisconsin 53233
| | | |
Collapse
|
13
|
Au KY, Yao CM, Cowan R, Ng SF. Programming of the macronucleus of Paramecium during asexual and sexual reproduction: A further study with cytidine analogues, dimethylsulfoxide, L-ethionine and N-butyric acid. Eur J Protistol 1990. [DOI: 10.1016/s0932-4739(11)80386-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
|