An Adenine Code for DNA: a Second Life for N6-Methyladenine
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View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Leading Edge Minireview An Adenine Code for DNA: A Second Life for N6-Methyladenine Holger Heyn1 and Manel Esteller1,2,3,* 1Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain 2Department of Physiological Sciences II, School of Medicine, University of Barcelona, 08036 Barcelona, Catalonia, Spain 3Institucio´ Catalana de Recerca i Estudis Avanc¸ ats (ICREA), 08010 Barcelona, Catalonia, Spain *Correspondence: [email protected] http://dx.doi.org/10.1016/j.cell.2015.04.021 DNA N6-methyladenine (6mA) protects against restriction enzymes in bacteria. However, isolated reports have suggested additional activities and its presence in other organisms, such as unicellular eukaryotes. New data now find that 6mA may have a gene regulatory function in green alga, worm, and fly, suggesting m6A as a potential ‘‘epigenetic’’ mark. The Origins of Adenine Methylation initiated in the presence of methylated adenine at replication Genetic constraints hamper the response of cells to the changing origin (Wion and Casadesu´ s, 2006). Dam-mediated methylation environment and represent a hurdle to adaptations that charac- also regulates replication initiator factors. terize living organisms. Thus, dynamic modifications that expand 6mA guides the discrimination between original and newly the genetic code beyond A, G, C, and T are necessary. Among the synthesized DNA strand after replication. As de novo adenine most studied, 5-methylcytosine (5mC) exerts a predominant role methylation is delayed during the cell cycle, the newly synthe- due to its important activities in mammals to establish the epige- sized strand is recognized by repair enzymes and the Dam motif netic setting and its relevance in human disorders, particularly enables endonuclease processing with subsequent repair pro- cancer (Heyn and Esteller, 2012). 5mC has been named the fifth cesses (Wion and Casadesu´ s, 2006). Adenine methylation has base of DNA, and only lately has a second modification in DNA, further functional implication in the cell cycle, repression of 5-hydromethylcytosine (5hmC), emerged as a contender for transposable elements, and gene regulatory processes (Fang human cells (Kohli and Zhang, 2013). Other derivatives, such as et al., 2012). 6mA also reduces the stability of base pairings, 5-formylcytosine and 5-carboxylcytosine, are so far considered hence favoring transcriptional initiation by lowering the energy transitory byproducts of oxidative demethylation (Kohli and to open DNA duplexes. Dam activity can be hindered by binding Zhang, 2013). However, this can be an anthropocentric view. of competing proteins, resulting in the formation of non-methyl- N4-methylcytosine (4mC) is very common in bacteria but absent ated sites. Strikingly, the protection from methylation is an in- in mammals. There is an even more intriguing DNA modification: herited state that, however, can be modified by environmental N6-methyladenine (6mA) (Figure 1A). conditions (Wion and Casadesu´ s, 2006). Thus, adenine methyl- 6mA represents a dominant modification in bacteria, while ation displays similar characteristics in prokaryotes as cytosine 5mC is absent in many prokaryotic genomes (Fang et al., methylation does in eukaryotes, further underscoring its impor- 2012). In bacteria, 6mA was initially reported to be part of restric- tance throughout generations. tion-modification (R-M) systems—bacterial defense mecha- nisms against phages and plasmids that are able to distinguish Adenine Methylation: An Evolutionary Conserved between host and invader DNA (Arber and Dussoix, 1962). Mechanism Specifically, the presence of 6mA in the host prevents the diges- Although some studies hypothesized the presence of 6mA tion of its genome by DNA methylation-sensitive restriction in eukaryotic genomes decades ago, its implication in epigenetics enzymes. In contrast, foreign unmethylated DNA lacks the pro- in eukaryotes remains elusive (Ratel et al., 2006). Compared to the tection and is readily degraded when entering the cells. R-M sys- highly abundant 5mC in the eukaryotic kingdom, levels of 6mA tem-positive strains are equipped with DNA methyl-transferase were suggested to be minimal and thus only detectable by highly and endonuclease counterparts with common sequence recog- sensitive technologies. Nevertheless, several studies reported the nition motifs. presence of 6mA in eukaryotic genomes, particularly in ciliates, However, the fact that other methyl-transferases lack a chlorophyte algae, and dinoflagellates (Achwal et al., 1983; Gom- restriction enzyme counterpart and that m6A is important mers-Ampt and Borst, 1995; Ratel et al., 2006). In certain cases, for viability in specific bacterial strains suggests a defense-in- 6mA exists in substantial amounts, with 0.5%–10% of adenines dependent function. Specifically, adenine methylation is estab- being methylated. lished as a bacterial epigenetic mark. Exemplary, solitary Sequence analysis predicted the presence of adenine methyl- adenine methylases, such as Dam in E. coli, are involved in transferases and demethylases in several eukaryotic organisms DNA replication, wherein sister-strand synthesis can only be (Iyer et al., 2011)(Figure 1A). The presence of methyl-transferase 710 Cell 161, May 7, 2015 ª2015 Elsevier Inc. Figure 1. Processing and Detection of N6-Methyladenine (A) Adenine bases of DNA are modified by N6-methyladenine (6mA) methyl-transferases and 6mA demethylases. The modifying enzymes are conserved in all super-kingdoms of life, with putative activity also in Homo sapiens (TET1–3 proteins have so far proven activities as 5mC oxidases). (B) Methyladenine is detectable by chromatog- raphy-based technologies, such as the ultra- high performance liquid chromatography-triple quadrupole mass spectrometry coupled with multiple-reaction monitoring (UHPLC-MRM-MS/ MS) method or sequencing approaches. For the specific quantification of methyladenine, next- generation sequencing (NGS)-based strategies are coupled with immunoprecipitation of 6mA (6mA-IPseq) or restriction enzyme guidance (6mA-REseq). Direct quantification at base-pair resolution is enabled by third-generation seq- uencing methods, such as the single-molecule real-time (SMRT) technology, wherein variant enzyme kinetics identify modified DNA bases. had yet to be identified (Hattman et al., 1978). Using sequencing-based mapping strategies, Fu et al. produce the first genome-wide reference map for methyla- denine in C. reinhardtii (Fu et al., 2015). Moreover, the authors provide evidence for an epigenetic function in transcrip- tional regulation. After confirming abun- dant 6mA levels by highly sensitive liquid-chromatography and mass-spec- trometry methodologies (Figure 1B), they show that 6mA levels are stable and in- herited during multiple replication phases. Immunoprecipitation-based sequencing strategies (Figure 1B) identify sequence motifs susceptible to undergo adenine methylation, which are different from the prokaryotic consensus sequences. Sub- sequently, restriction enzyme-guided re- sequencing produces a 6mA reference methylome of C. reinhardtii at base-pair orthologs within transposable elements led to the hypothesis of a resolution (Figure 1B). Intriguingly, although the methyl-trans- cis-acting control mechanism to secure host genome integrity. ferase consensus sequence is equally distributed in the genome, Consistently, such a mechanism was identified in E. coli, sug- 6mA is highly enriched at gene promoters but depleted at the tran- gesting a conserved function of 6mA as safeguard of the genome scription start sites. Consistently, 6mA profiles reveal periodic (Roberts et al., 1985). patterns of 130–140 bp distances and hence a potential associa- Now, three studies in this issue of Cell report the presence of tion to nucleosome positioning at promoter regions. The presence 6mA in three different eukaryotic genomes—Chlamydomonas of 6mA at gene promoters is positively correlated with increased reinhardtii, Caenorhabditis elegans, and Drosophila mela- transcriptional activity. nogaster—with putative epigenetic function (Zhang et al., While adenine methylation has been previously described 2015; Greer et al., 2015; Fu et al., 2015). The authors present ev- in C. reinhardtii, its presence in 6mA C. elegans has not been re- idence for spatiotemporal-regulated 6mA modifications during ported despite the presence of putatively active methyl-transfer- development. Moreover, 6mA is associated to gene regulatory ases in the worm genome. Greer et al. now report 6mA to be events. present in C. elegans and functionally involved in epigenetic The green alga C. reinhardtii has long been reported to harbor transgenerational inheritance (Greer et al., 2015). In C. elegans, substantial levels of 6mA, but its spatial distribution and function mutants lacking histone demethylase spr-5, responsible for Cell 161, May 7, 2015 ª2015 Elsevier Inc. 711 dimethylation of the histone H3 at lysine 4, represent a paradigm 5mC in D. melanogaster DNA sequence (Raddatz et al., 2013). of inheritance. Although no phenotype is detectable in early Hence, the studies by Greer et al. and Zhang et al. suggest generations, the mutant worms become progressively infertile 6mA as the unique DNA methylation modification and potentially in later generations, accompanied by increasing histone H3 functional