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Why does methylation not occur in viral DNA?

Why does methylation not occur in viral DNA?


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Why does methylation not occur in viral DNA? Can viral DNA undergo the process of methylation? If not then why does this process does not occur in viruses?


Contrary to the question title, viral DNA can be methylated. See for example Bonvicini et al. 2012. (1) and Hoelzer et al. 2008 (2).

Hoelzer et al. give a review of the presence and role of cytosine methylation in DNA viruses of animals:

To understand the impact of cytosine methylation on the viral life cycle and the evolution of base composition, the particularities of each virus will need to be considered. Differences will inevitably exist between actively replicating viral DNA and that which is integrated into the host genome. The type of viral persistence will also be of importance. The integration of adeno- or polyomavirus DNA into the host genome is usually a terminal process since the viruses cannot liberate their genomes and are therefore no longer infectious. The evolutionary roles of methylation in these cases will likely differ from those seen in other viruses, such as Herpesviruses, which can liberate their genome after periods of latency. But differences may also exist between large and small viruses-with many larger viruses encoding their own replication machinery and additional proteins which modify host cell processes and immune responses. The susceptibility of the viral genome to methylation and immune recognition will also be affected by other factors, such as the location of replication within the cell and the specific intracellular trafficking route.

Viral DNA methylation has mostly been studied in large DNA virii, and the extent of methylation may be related to repression of viral replication. Bonvicini et al. writes that

Epigenetic mechanisms, and in particular the impact of cytosine methylation at CpG dinucleotides on the viral life cycle have been mainly studied for viruses that can establish latency and undergo reactivation, such as viruses in the Herpesviridae family, or for viruses that can integrate their genome into the host genome such as Retroviridae or Papillomaviridae. In general, a correlation has been found between the extent of CpG dinucleotides methylation of viral genomes and viral quiescence [24]. Scarce information is on the contrary available on the possible occurrence and role of methylation for actively replicating viruses


Methylation played different roles for different types of organisms throughout evolution. For bacteria, methylation protects against self-digestion of DNA by restriction enzymes. In eukaryotes, methylation assumes many different roles (e.g., mutation-rate regulator, gene expression regulator, chromatin structure regulator, etc.). Insects have very little methylation and it is not entirely clear what they use it for. Viruses don't encode for methyltransferases that modify DNA. However, when a virus integrates into a host genome that is methylated, the viral DNA usually assumes the methylation pattern of the integration locus.


Histone Methylation

Julia Yue Cui , . Joseph Dempsey , in Toxicoepigenetics , 2019

Abstract

Histone methylation is important in modulating the accessibility of transcription factors to target genes and the subsequent changes in transcription. The site-specific methylation and demethylation of histone residues are catalyzed by methyltransferases and demethylases, respectively. In general, transcriptional activation marks increase the permissibility of gene transcription, whereas transcriptional silencing marks promote heterochromatin formation. These processes are tightly regulated by methyltransferases and demethylases. Human diseases and toxicological responses from exposure to environmental chemicals are associated with aberrant histone methylation patterns and increased risks of adverse effects. In this chapter, we will introduce various histone methylation marks and their functions on gene transcription, writers and erasers that regulate specific sites of histone methylation patterns, cofactors and other regulators, and human diseases and environmental chemicals associated with dysregulation of histone methylation.


MTHFR (methyletetrahydrofolate reductase) is an enzyme that converts folate into a usable form that our bodies need. It is a key enzyme in an important detoxification reaction in the body – one that converts homocysteine (toxic) to methionine (benign). If the enzyme is impaired, this detoxification reaction is impaired, leading to high homocysteine blood levels. Homocysteine is abrasive to blood vessels, essentially scratching them, leaving damage that causes heart attacks, stroke, dementia, and a host of other problems.

MTHFR converts 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate. It is the 5-methyltetrahydrofolate that converts homocysteine to methionine by the enzyme methionine synthase. Homocysteine can also be converted to methionine by betaine-homocysteine methyltransferase. This enzyme does not require folic acid.

Additionally, when the enzyme MTHFR is impaired, other methylation reactions are compromised. Some of these methylation reactions affect neurotransmitters, which is why impaired MTHFR activity is linked with depression. Inefficiency of the MTHFR enzyme is also linked to migraines, autism, fertility, cancer, and birth defects, all of which depend on proper methylation.


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Methylation

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Methylation, the transfer of a methyl group (―CH3) to an organic compound. Methyl groups may be transferred through addition reactions or substitution reactions in either case, the methyl group takes the place of a hydrogen atom on the compound. Methylation can be divided into two basic types: chemical and biological.

Chemical methylation is studied in the area of organic chemistry, where the term alkylation is used to define the addition of a ―CH3 group. Alkylation is performed using electrophilic (“electron-loving”) compounds such as dimethyl sulfate and iodomethane, which react in a nucleophilic substitution. For example, ethers may be produced by methylation of alkoxides, and ketones may be produced by methylation of ketone enolates. In another type of chemical methylation, known as Irvine–Purdie methylation, hydroxyl groups on polysaccharides undergo methylation to yield monosaccharides.

Biological methylation occurs in various ways. In epigenetic inheritance, methylation can occur as DNA methylation or protein methylation. In DNA methylation, there is an addition of a methyl group to a cytosine residue, causing cytosine to become 5-methylcytosine. DNA methylation occurs at CpG sites—that is, sites where a cytosine is immediately in front of a guanine. This type of methylation controls gene expression or activity. In protein methylation, a lysine amino acid or an arginine residue is methylated in the reaction. Arginine may be methylated one or two times, and lysine may be methylated anywhere from one to three times. Histones can also be methylated by an enzyme called histone methyltransferase, which transfers methyl groups from s -adenosyl methionine to the histone. Protein methylation is also used to control gene expression by activating or deactivating a gene.

Eukaryotic embryos also undergo methylation. Eukaryotic DNA is unmethylated from fertilization to the eight-cell stage. It then undergoes de novo methylation from the eight-cell stage to morula, during which epigenetic information is modified and added to the genome. Methylation is complete by blastula stage. If embryonic methylation fails to occur, the embryo dies. Methylation continues to occur in postnatal development and plays an important role in the interaction of gene expression and environmental factors.

Methylation also plays an important role in tumour formation. Tumours begin with abnormal localized hypermethylation, genome-wide hypomethylation, and increased expression of DNA methyltransferase. Research shows that genome-wide hypomethylation leads to increased mutation rates and instability of chromosomes.

Bacteria use methylation as a tool for self-defense. Bacterial cells protect their DNA through the methylation of adenine or cytosine bases. Foreign DNA that enters the bacteria remains unmethylated and therefore is prone to destruction by the bacteria’s restriction enzymes.


Methylation

DNA methylation is one of the most common types of DNA modification found in both eukaryotes and prokaryotes. In bacteria, it is part of the restriction-modification (R-M) defense system against phage infection (see Restriction enzyme basics), whereby host bacteria protect their own DNA against cleavage by their endogenous restriction enzymes. Methylation commonly occurs at cytosine (C) and adenine (A) bases, and predominantly forms 5-methylcytosine ( m 5C), N 4 -methylcytosine ( m 4C), and N 6 -methyladenine ( m 6A) derivatives.

DNA methyltransferases drive the methylation reaction by transferring a methyl group from a donor to the acceptor bases (e.g., A and C). The most common types of DNA methyltransferases found in laboratory strains of bacteria include:

  • Dam: stands for deoxyadenosine methyltransferase and converts the sequence 5′-GATC-3′ to 5′-G( m 6A)TC-3′
  • Dcm: stands for deoxycytosine methyltransferase and converts the sequence 5′-CCWGG-3′ to 5′-C( m 5C)WGG-3′ (where W is either A or T)
  • EcoKI: stands for the Type I R-M system in the E. coli K12 strain and modifies adenosines in the sequence 5′-AAC(N)6GTGC-3′
  • EcoBI: stands for the Type I R-M system in the E. coli B strain and modifies adenosines in the sequence 5′-TGA(N)8TGCT-3′

In mammalian and plant systems, CpG or CpNpG methylation is a common DNA modification with implications in biological processes, making it a major focus of epigenetic studies.

Sensitivity of restriction enzymes towards methylated DNA recognition sites depends on the restriction enzymes. For example, as illustrated in Figure 4, Dam methylation at GATC completely blocks MboI but activates DpnI. On the other hand, CpG methylation at 5′-CCGG-3′ blocks HpaII activity but has no effect on MspI. In some cases, restriction enzyme activity is only partially inhibited by methylation (e.g., XhoI).

Figure 4. Varying sensitivity of restriction enzymes towards substrate DNA methylation.

When propagating plasmids in bacteria, the effects of methylation on restriction enzymes of interest must be considered. To prevent methylation at 5′-GATC-3′ and 5′-CCWGG-3′, competent cells that lack Dam and Dcm methylases (dam – /dcm – ) should be chosen for plasmid transformation. Most E. coli cells do not possess a CpG methylation system, so CpG methylation is not a concern for DNA isolated from bacteria. If genomic DNA is extracted from plants and mammals, methylation may occur at the CpG sites and impact direct restriction digestion by some methylation-sensitive enzymes.


Epigenetic reprogramming in preimplantation embryos: selective DNA methylation maintenance

The second wave of global epigenetic reprogramming occurs during early embryogenesis and is crucial to establishing pluripotency. The newly formed embryo undergoes massive, global DNA demethylation such that by the time the early blastocyst stage (32–64 cells) is reached, methylation levels are at their lowest (Fig. 4A). However, the process in embryos differs from that in PGCs. First, demethylation is close to absolute in PGCs, with the exception of a few resistant retroelements, while DNA methylation of imprinted gene regions is preserved in embryos, enabling parent-of-origin-specific gene expression in later tissues. Also, the imprinted paternal X inactivation found in early mouse embryos is not reversed until the late epiblast stage. Second, the genome of the zygote (which contains haploid contributions from the oocyte and sperm genome, each with their own specific chromatin properties) follows different DNA demethylation kinetics after fertilization (Fig. 4A Mayer et al. 2000 Oswald et al. 2000 Santos et al. 2002 Santos and Dean 2004).

DNA demethylation dynamics and imprinting maintenance in preimplantation embryos. (A) Distinct characteristics of maternal and paternal genomes impose an epigenetic asymmetry in the zygote. The maternal genome (red pronucleus red line) undergoes passive DNA demethylation throughout several rounds of DNA replication. The paternal genome (blue pronucleus blue lines) undergoes active demethylation before DNA replication in the zygote ensues. Concomitant with global loss of paternal 5mC, 5hmC (blue dotted line) and the further oxidation derivatives (5fC and 5caC blue dashed line) are enriched. Although selected loci are restored to unmodified cytosines, the bulk of paternal 5hmC is passively diluted, paralleling demethylation of the maternal genome. (B) In the zygote, STELLA prevents TET3-dependent oxidation of 5mC through binding to H3K9me2-marked chromatin (maternal genome and paternally imprinted regions) and subsequent active restoration of cytosine by BER (or other pathways). (C) Throughout early cleavage stages, DNMT1 is largely excluded from the nucleus and requires noncanonical targeting to imprinted regions by the ZFP57/TRIM28 complex binding to its methylated consensus sequence found at most ICRs. Nonimprinted regions are efficiently demethylated through replication, while ICRs are maintained by DNMT1 and DNMT3A/B. (D) At later stages of embryogenesis and in adult tissues, high DNMT1/NP95 levels during replication maintain DNA methylation by targeting hemimethylated DNA in a canonical fashion.

Active DNA demethylation of the paternal genome

The mature sperm genome shows 80%–90% overall CpG methylation, the highest global DNA methylation level of any cell in the mouse (Popp et al. 2010), yet the paternal genome is apparently completely demethylated shortly after zygote formation (Fig. 4A, blue line Mayer et al. 2000 Oswald et al. 2000). This loss must be due to an active demethylation mechanism, as it is completed before the onset of DNA replication at the pronuclear stage 3 (PN3). Conversely, the maternal genome shows lower global methylation levels (∼40%) and undergoes replication-dependent demethylation (Fig. 4A, red line), thereby establishing a significant epigenetic asymmetry in the early embryo (Fig. 4 Mayer et al. 2000 Oswald et al. 2000 Santos et al. 2002).

Conflicting observations made by IF analysis in zygotes and DNA sequencing after BSC created a conundrum regarding DNA demethylation and reprogramming. While the loss of 5mC in the paternal pronucleus was evident by IF, BSC analysis did not wholly support this observation (Hajkova et al. 2008 Wossidlo et al. 2010). It was only after the description of 5hmC, the oxidation product of 5mC by TET enzymes, that a unifying explanation came to hand (Gu et al. 2011 Iqbal et al. 2011 Wossidlo et al. 2011). BSC cannot distinguish between 5mC and 5hmC, whereas oxidation of 5mC removes the epitope recognized in IF.

Indeed, TET3 specifically localizes to the paternal pronucleus (Gu et al. 2011), where it was shown to be responsible for 5mC to 5hmC conversion (Fig. 4A, dotted blue line). In its absence, 5hmC is not detectable (Gu et al. 2011 Wossidlo et al. 2011), thus excluding functional redundancy with other TET proteins in the zygote. Lack of TET3 may result in the delayed activation of paternal alleles of genes required for embryonic development and establishment of the pluripotent epiblast (e.g., Nanog and Oct4), potentially causing the reduced fecundity and partial developmental failure of maternal TET3-null offspring (Gu et al. 2011).

The fate of paternal 5hmC

The bulk of 5mCs in the paternal genome is hydroxylated in the late zygote, but only a few regions were shown to completely revert to unmodified cytosine before the first cleavage division. BER activity could account for this loss of 5mC and the hypomethylation of the Nanog and Oct4 promoters (Gu et al. 2011). Several components of the BER pathway are specifically localized to the paternal pronucleus i.e., XRCC1 (X-ray repair cross-complementing protein 1) tightly binds to paternal, but not maternal, DNA (Hajkova et al. 2010 Wossidlo et al. 2010). Concomitant with 5hmC, higher oxidation products of 5mC (5fC and 5caC), which can be direct targets for the TDG/BER pathway (He et al. 2011 Maiti and Drohat 2011), were also observed in the zygote (Fig. 4A, dotted/dashed blue lines Inoue et al. 2011). However, this route of demethylation requires further investigation, since TDG was not detected in zygotes (Hajkova 2010). Certainly, other enzymes with similar activity could perform glycosylation. Alternatively, direct decarboxylation of 5caC has been described in other systems (Schiesser et al. 2012).

However, there is also compelling evidence that paternal 5mC is actively converted to 5hmC (and possibly further to 5fC and 5caC), which then undergoes replication-mediated dilution throughout subsequent cleavage divisions (Fig. 4A, dotted/dashed blue lines Inoue and Zhang 2011 Inoue et al. 2011). Fittingly, the maintenance methyltransferase DNMT1 shows very limited affinity to oxidized 5mC derivatives (Hashimoto et al. 2012) and is generally excluded from the nucleus of preimplantation embryos (Howell et al. 2001 Hirasawa et al. 2008).

Distinction of parental pronuclei

How is TET3 targeted to the paternal genome without affecting the maternal genome? Prior to description of 5hmC dynamics in the zygote, the protein STELLA (Payer et al. 2003) was found to convey specificity to the, then elusive, active demethylation machinery in the early zygote (Fig. 4B Nakamura et al. 2006). In its absence, loss of 5mC is observed in both pronuclei, accompanied by 5hmC accumulation in the maternal pronucleus (Wossidlo et al. 2011). Thus, the divergent demethylation dynamics in maternal and paternal genomes in the zygote are the consequence of specific protection of the maternal genome from TET3-mediated 5mC oxidation by STELLA. Although STELLA appeared to localize to both pronuclei in the zygote, its binding to the paternal genome is weak (Nakamura et al. 2012). The protective function is specifically mediated by STELLA’s interaction with dimethylated histone H3 Lys9-marked chromatin (H3K9me2), which is enriched in the maternal but not paternal pronucleus (Santos et al. 2005). This interaction of STELLA and H3K9me2 nucleosomes alters chromatin configuration, preventing TET3 binding and activity (Nakamura et al. 2012). Aside from its global function in the maternal genome, STELLA also protects at least two paternally methylated, imprinted gene loci (Rasgrf1 and H19, but not the IG-DMR) from aberrant demethylation (Nakamura et al. 2006). These loci retain H3K9me2-marked chromatin during spermatogenesis and protamine exchange, which mediates their protection after fertilization (Nakamura et al. 2012). However, not all paternally or maternally imprinted regions are affected equally, and possibly other mechanisms (described below) act in partial redundancy with STELLA (Messerschmidt 2012). Remarkably, in the absence of STELLA, the loss of DNA methylation at imprinted gene loci in the zygote is complete (Nakamura et al. 2006). Thus, at least the imprinted gene regions undergo active removal of 5hmC or rapidly iterated oxidations to 5caC by TET3 (Wu and Zhang 2010). Interestingly, the BER component XRCC1, which ordinarily exclusively localizes to the paternal genome, is found in both pronuclei in STELLA mutants (Hajkova 2010).

Embryos lacking STELLA display severe phenotypes, rarely developing past the four-cell stage, with few embryos surviving to birth. Remarkably, though, STELLA-deficient oocytes show neither methylation nor developmental defects prior to fertilization (Nakamura et al. 2006). This is particularly intriguing, as TET3 is present in the oocyte but only affects (in the absence of STELLA) the maternal genome after fertilization, in the zygotic context (Nakamura et al. 2006 Gu et al. 2011). The interplay of these two antagonistic factors must be addressed in more detail to define whether TET3 is merely prevented from acting on the maternal genome or must be molecularly targeted to its paternal substrates.

Is active DNA demethylation of the paternal genome required?

It is undisputed that global demethylation in the early mouse embryo is required to impose an open, totipotent or pluripotent state in the forming epiblast. However, it is not clear why only the paternal genome is targeted for active demethylation or, indeed, whether active demethylation is at all required. Although TET3-mediated demethylation of Nanog and Oct4 promoters was linked to embryo viability, loss of TET3 is nonetheless compatible with normal development (Gu et al. 2011). In fact, embryos derived from round spermatid-injected oocytes (containing histone-bound paternal DNA, which is not actively demethylated in the zygote) can develop into viable pups (Polanski et al. 2008). In other mammalian species, active demethylation of the paternal genome is followed by immediate de novo remethylation before parallel, passive demethylation of the maternal and paternal genomes occurs (Fulka et al. 2004 Park et al. 2007 Abdalla et al. 2009). Thus, while active demethylation of the paternal genome is beneficial, perhaps it simply provides an additional measure to ensure efficient reprogramming. Another hypothesis is that the oocyte is programmed to remove distinguishing paternal epigenetic features, which may provide a developmental advantage to any individual embryo. It is in the “interest of the mother” to distribute resources equally among her progeny, necessitating the removal of any unique paternal epigenetic marks that would favor a particular embryo (Moore and Haig 1991). More detailed investigations addressing 5hmC and locus-specific demethylation in round spermatid injection-derived embryos, coupled with a base-resolution view of the dynamics of 5mC and its oxidation products, are required to deepen our understanding of these processes.

Passive DNA demethylation and maintenance of parental imprints

The maternal genome is, at least globally, resistant to hydroxylation by TET3 yet nonetheless loses the bulk of its oocyte-specific DNA methylation pattern by replication-mediated 5mC dilution during preimplantation development (Fig. 4A, red line). Here, passive loss of 5mC is achieved by nuclear exclusion of DNMT1 (Howell et al. 2001 Ratnam et al. 2002 Branco et al. 2008 Hirasawa et al. 2008) rather than by down-regulation of NP95, as proposed in PGCs (Kagiwada et al. 2013).

Nuclear exclusion of DNMT1, however, poses a problem for the required maintenance of genomic imprints and other sequences that must retain their DNA methylation patterns throughout development. Although zygotic deletion of DNMT1 was known to cause massive loss of DNA methylation both globally and at imprinted gene loci and to be embryonic-lethal (Li et al. 1992, 1993), the role of DNMT1 in early preimplantation embryos was only recently resolved. The oocyte-specific form of DNMT1 (DNMT1o) was shown to be required for imprint maintenance only during one cell cycle at the eight-cell stage, where DNMT1o was found to transiently translocate into the nucleus (Carlson et al. 1992 Howell et al. 2001 Ratnam et al. 2002). Because the somatic form of DNMT1 (DNMT1s) was not detected until the blastocyst stage, the maintenance of imprints during early cleavage divisions was attributed to unidentified DNA methyltransferases. Re-examination of DNMT3A, DNMT3B, and DNMT1o/s expression and function finally resolved the issue by first excluding the de novo DNA methyltransferases from general imprinting maintenance in the embryo (Hirasawa et al. 2008). Complete (maternal and zygotic) knockout of DNMT1, however, completely abolished DNA methylation at all imprinted gene loci (Cirio et al. 2008 Hirasawa et al. 2008 Kurihara et al. 2008). Thus, both DNMT1o and DNMT1s contribute to DNA methylation maintenance at imprinted regions even though the vast amount of protein is excluded from the nucleus (Branco et al. 2008).

Noncanonical targeting of DNMT1 to imprinted regions in preimplantation embryos

DNMT1 is required to maintain imprints, yet, at the same time, its nuclear protein levels are drastically reduced to allow global demethylation. How is DNMT1 targeted to imprinted gene loci? STELLA is required for imprinting maintenance. However, STELLA’s global binding and protection of the whole maternal genome from active demethylation makes it an unlikely candidate for DNA methylation maintenance at specific loci. ZFP57, a Krueppel-associated box (KRAB) domain zinc finger protein, has also been associated with imprinting maintenance (Fig. 4C Li et al. 2008 Mackay et al. 2008). Loss of ZFP57 in mouse embryos and ESCs causes hypomethylation of both paternal and maternal ICRs and misregulation of imprinted genes (Li et al. 2008 Quenneville et al. 2011 Zuo et al. 2012). This function of ZFP57 is evolutionarily conserved in humans, loss-of-function mutations also result in ICR hypomethylation, ultimately causing transient, neonatal diabetes (Mackay et al. 2006, 2008).

KRAB zinc finger proteins often act as epigenetic repressors through their interaction with TRIM28. TRIM28 is a component of a multifunctional repressor complex comprised of, at least in this instance, the nucleosome remodeling and histone deacetylation (NuRD) complex, the H3K9me3-catalyzing histone methyltransferase SETDB1, the heterochromatin protein 1 (HP1), and DNA methyltransferases DNMT1, DNMT3A, and DNMT3B (Fig. 4C Schultz et al. 2001, 2002 Iyengar and Farnham 2011 Quenneville et al. 2011 Zuo et al. 2012). While the DNA methylation maintenance defects are less pronounced in zygotic ZFP57 mutants and the lack of maternal ZFP57 is rescued by expression of paternal Zfp57 (Li et al. 2008), loss of maternal Trim28 alone is embryonic-lethal (Messerschmidt et al. 2012). The times of death and the embryonic phenotypes of maternal Trim28 mutants are highly variable, as is the occurrence of hypomethylation at several maternal and paternal ICRs (Messerschmidt et al. 2012). DNA methylation analysis of individual blastomeres confirmed that stochastic, random methylation defects (and phenotypes) are based on the mosaic composition of early Trim28 maternal null embryos carrying normally and aberrantly imprinted gene loci (Messerschmidt 2012 Messerschmidt et al. 2012 Lorthongpanich et al. 2013).

Binding of both proteins and the presence of H3K9me3, the product of the TRIM28 complex, were detected at imprinted loci in embryos (Messerschmidt et al. 2012) and mESCs (Quenneville et al. 2011). Being a DNA-binding transcription factor, ZFP57 localization to ICRs opens the exciting prospect of sequence-specific recognition and maintenance of imprinted loci. Indeed, sequence analysis of loci enriched for H3K9me3, TRIM28, and ZFP57, as identified by chromatin immunoprecipitation (ChIP) combined with deep sequencing (ChIP-seq) in mESCs, revealed a hexanucleotide consensus ZFP57 recognition site (TGCCGC), which is highly conserved in 81 of 91 identified (H3K9me3/TRIM28/ZFP57) sites (Quenneville et al. 2011). Remarkably, binding of TRIM28 to the hypomethylated sites was abrogated in Trim28 maternal null embryos and was not restored by TRIM28 re-expression from the paternal allele in the two- to four-cell stage embryo, indicating the DNA methylation-dependent binding of the ZFP57/TRIM28 complex. In fact, ZFP57 displays much higher binding affinity for its methylated consensus binding site in vitro (Quenneville et al. 2011 Liu et al. 2012). Once lost, DNA methylation cannot be restored via the ZFP57/TRIM28 complex in vivo (Messerschmidt et al. 2012) or ectopic re-expression of ZFP57 in Zfp57-deficient ESCs (Zuo et al. 2012). To a point, the interaction of TRIM28 with DNMT1/NP95 suggests the noncanonical, ZFP57-mediated targeting of the DNA methylation maintenance machinery to ICRs in the preimplantation embryo (Fig. 4C). This targeting mode would compensate for the drastic reduction of nuclear DNMT1 during early cleavage divisions and thus enable DNA methylation maintenance at imprinted regions (Messerschmidt 2012). Only at later embryonic stages, after DNMT1 levels are significantly increased in the nuclei, does canonical DNA methylation maintenance ensue (Fig. 4D).

The maintenance of methylation at imprinted regions in preimplantation embryos was thought to be very robust until genome-wide methylation analysis showed that even ICRs are partially demethylated, particularly at peripheral regions (Tomizawa et al. 2011 Kobayashi et al. 2012). Such loss, however, would be of little to no consequence as long as the ZFP57-binding site itself remains methylated and targeted by the ZFP57/TRIM28 complex. De novo methylation enzymes DNMT3A and DNMT3B, which are also found in the ZFP57/TRIM28 complex (Quenneville et al. 2011 Zuo et al. 2012), may account for the recovery of DNA methylation at these peripheral regions at later stages of development (Tomizawa et al. 2011 Kobayashi et al. 2012).

Finally, given that DNA demethylation mechanisms act during early embryonic development, a drastic reduction of methylation levels is expected and in fact found at later preimplantation stages. Surprisingly, in addition to imprinted genes and retrotransposons, a substantial quantity of differentially methylated CGIs in oocyte-specific and a subset of sperm-specific methylated regions retain DNA methylation at much higher levels than expected if unhindered passive demethylation were to take place (Smallwood et al. 2011 Kobayashi et al. 2012). It remains to be seen whether these CGIs, as has been shown for ICRs, are targeted and protected by ZFP57/TRIM28, other KRAB zinc finger proteins, or entirely different mechanisms.


Take 5 Daily

WHAT IS METHYLATION?

The topic of methylation is getting its fair share of attention lately, and rightly so. Methylation is a simple biochemical process &ndash it is the transfer of four atoms - one carbon atom and three hydrogen atoms (CH3) &ndash from one substance to another.

When optimal methylation occurs, it has a significant positive impact on many biochemical reactions in the body that regulate the activity of the cardiovascular, neurological, reproductive, and detoxification systems, including those relating to:

WHY IS METHYLATION IMPORTANT?

The body is a very complex machine, with various gears and switches that need to be all functioning properly to operate optimally. Think of methylation, and the opposite action, demethylation, as the mechanism that allows the gears to turn, and turns biological switches on and off for a host of systems in the body.

HOW DOES METHYLATION HAPPEN?

CH3 is provided to the body through a universal methyl donor known as SAMe (S-adenosylmethionine). SAMe readily gives away its methyl group to other substances in the body, which enables the cardiovascular, neurological, reproductive, and detoxification systems to perform their functions.

Unfortunately, the system that produces SAMe is reliant on one switch being turned on by a critical B vitamin, 5-MTHF (also known as active folate or methylfolate).

Simply put, if enough 5-MTHF is present, the methylation cycle will work efficiently.

Unfortunately, approximately 60% of people in the United States have a genetic mutation that makes it challenging for their bodies to create enough 5-MTHF.

When the methylation switch is turned off and isn&rsquot creating enough SAMe, then a number of important molecules cannot be efficiently produced, including:

THE GOOD NEWS

First, you can have a simple and easy genetic test to find out if you have a problem with your methylation cycle. This test looks at specific enzymes that are affected by your genetic makeup, including the enzyme MTHFR (methylenetetrahydrofolate reductase), which is the most important enzyme involved in creating 5-MTHF.

IMPROVING THE METHYLATION CYCLE

In addition to a healthy, whole-food, non-processed food diet, make sure you are eating a lot of these foods:

Lifestyle changes include:

  • Engage in regular physical exercise
  • Avoid excessive alcohol consumption
  • Don&rsquot smoke
  • Avoid excessive coffee consumption (not more than five cups daily)

SEVEN ESSENTIAL NUTRIENTS FOR METHYLATION

There are seven specific nutrients that can help the methylation cycle achieve optimal performance, even if an individual has the genetic mutation that slows down the methylation cycle.

Proper methylation influences so many systems in our bodies that it often gets overlooked, which can severely impact how well your body functions. Ask your health-care practitioner for advice if you have any concerns about your CH3 cycle.


Our DNA Changes as we get Older

A study just out shows that as we get older, our DNA changes. A lot.

Researchers in Iceland and the U.S. showed that over a period of 10-16 years, some people's DNA changed as much as 20%. These differences aren't in the famous A, T, C, and G's of DNA though. Instead, they are changes in something called DNA methylation.

Methylation can affect how genes are used. So a change in methylation might cause a change in how someone's genes are used.

How big is a number like 20%? There are millions of spots on human DNA that are methylated. So a 20% change represents tens or even hundreds of thousands of changes.

These changes also tended to cluster in families. In other words, if a dad had less methylation as he got older, chances are his son or daughter would have less methylation too. So people pass on whether or not their methylation will change with age. And if it does, they also pass on whether their kids are more likely to end up with more or less methylation.

These findings matter because changes in methylation have been linked to diseases like cancer and autoimmune disorders. It might be that some cases of these diseases are the result of this change in methylation. This would also mean that some people might inherit an increased risk for these diseases.

People are Different Partly Because of DNA Differences

DNA is made up of a repeating set of chemicals usually abbreviated as A, G, C, and T. These letters are the raw stuff of genes. Each gene has a certain number of these letters in a certain order.

A gene has the instructions for making a specific protein. Each of these proteins then does a specific job in the cell. They carry oxygen, help digest our food, and let us see, hear, breathe and even think.

One way that people are different is in the letters of their DNA. On average, one person has around 6 million different letters (out of 6 billion) compared to someone else.

If one of these differences is in a gene, it can cause the protein to be made to act differently. For example, this kind of change can cause one person to make a protein that causes brown eyes. Or it can cause another person to make a protein that gives him or her blue eyes.

Another reason people are different is in how they use their genes. Some people might have a certain gene turned way up so that it makes lots of protein. Others might have the same gene turned down so they make less protein.

Part of this can come from differences in letters. But part can come from differences in methylation too.

Methylation can hide a gene from the cell making it harder to read. This means that a methylated gene gets read less often or not at all. Which means little or even no protein gets made. So changes in methylation might cause changes in how some genes are used.

How DNA Can Change

The letters of DNA that we are born with don't change much over our lifetime. There is an occasional change but it is pretty rare.

Methylation is thought to be a different matter though. Scientists think that methylation can change a lot in the DNA of any cell.


DNA letters can change like this.
Methylation can change as well.

Scientists know that as a fertilized egg develops into a human, different genes get methylated and unmethylated. The new patterns of methylation are a big part of determining whether a cell turns into skin, muscle, nerve, etc.

Scientists also know that at least in mice, what mom eats can affect how a pup's DNA is methylated. The same is thought to be true in people too.

So there are definitely methylation changes that can happen in the womb. But what about afterwards?

A recent study showed that each twin in an identical twin pair has different DNA methylation. What this suggests is that the environment we live in can affect how our DNA works. It also suggests that as we age, our DNA methylation pattern changes. Now this new report confirms it.

The researchers showed that methylation can change with age by looking at two different groups. The first was a group of 111 Icelanders. The second was 126 people from Utah.

We are different
because we all have
different DNA.

The 111 Icelanders were part of a group who gave DNA samples in 1991 and then again sometime between 2002 and 2005. What the researchers found was that when they looked at an average of all 111, it looked like there were little or no methylation differences over time. It was a different story when they looked at each person's DNA separately though.

Of the 111 people, 70 showed at least a 5% change in methylation. Another 33 showed at least a 10% change and 9 showed a whopping 20%. Some people had more methylation and others had less. Which is why the average was zero.

So DNA methylation can definitely change with age. The researchers next looked at people from Utah to confirm these results in another group.

They found that some of these people also experienced big changes in DNA methylation over time. They also found that the tendencies of these changes ran in families too.


Methylation (shown in green)
can change as we age.

The researchers looked at the DNA from a group of 126 people from Utah (Utahns). This group contained many multigenerational families.

The Utahns were sampled twice over a period of 16 years. The researchers found similar results to those found with the Icelanders.

Of the 126 Utahns, 50 showed at least a 5% change in methylation. Another 23 showed at least a 10% change and 13 showed a 20% change. Again, some people had more methylation and others had less.

When the researchers looked at families, they found that if a parent's methylation went up, the kids' usually did too. And if the parent's went down, the kids' often went down as well.

Many of these were families who did not live together over the 16 year period (grown children, for example). So it is unlikely that the environment would have similar effects on their methylation. It is more likely that something about their genes causes their methylation to increase or decrease with age.

How to Inherit Methylation Tendencies

Methylation really just means putting a methyl group on a C in DNA. (Usually the C is next to a G.) That methyl group is put there by certain proteins. And can also be removed by different proteins.

Like any other protein, the instructions for these methylating proteins are found in genes. These genes can also come in different versions like other genes.

Imagine that someone has a gene for a powerful methylating protein. This person might end up with more methylation than someone with a weaker version. This person could also pass the gene to his or her kids. Now the kids would end up with more methylation too.

A big part of who we are is in our genes. Differences in how our genes are used are going to affect this. Perhaps this is one reason why we change so much as we get older. Or perhaps what we do causes the DNA changes.

Another important detail is that some diseases are caused by changes in methylation. For example, cancer is caused by changes in how genes are used.

Sometimes the cancer results from a change in the letters of DNA. And sometimes they are caused by changes in methylation.

It is well known that older people get cancer more often than younger people. Part of this almost certainly comes from environmental abuse of their DNA over time. This abuse changes the letters of DNA to turn on genes that should be off and vice versa.

Methylation changes can do the same thing. It might be that the changes in methylation turn on a gene that should be off and that causes cancer. And maybe that increased risk was passed down from a person's parents.


Virus Classification

Viruses are classified by factors such as their core content, capsid structure, presence of outer envelope, and how mRNA is produced.

Learning Objectives

Describe how viruses are classified

Key Takeaways

Key Points

  • The type of genetic material, either DNA or RNA, and whether its structure is single- or double-stranded, linear or circular, and segmented or non-segmented are factors for classification.
  • Virus capsids can be classified as naked icosahedral, enveloped icosahedral, enveloped helical, naked helical, and complex.
  • Virus can either have an envelope or not.
  • A more recent system, the Baltimore classification scheme, groups viruses into seven classes according to how the mRNA is produced during the replicative cycle of the virus.

Key Terms

  • Baltimore classification: a classification scheme that groups viruses into seven classes according to how the mRNA is produced during the replicative cycle of the virus
  • messenger RNA: Messenger RNA (mRNA) is a molecule of RNA that encodes a chemical “blueprint” for a protein product.

Virus Classification

To understand the features shared among different groups of viruses, a classification scheme is necessary. However, most viruses are not thought to have evolved from a common ancestor, so the methods that scientists use to classify living things are not very useful. Biologists have used several classification systems in the past, based on the morphology and genetics of the different viruses. However, these earlier classification methods grouped viruses based on which features of the virus they were using to classify them. The most commonly-used classification method today is called the Baltimore classification scheme which is based on how messenger RNA (mRNA) is generated in each particular type of virus. The surface structure of virions can be observed by both scanning and transmission electron microscopy, whereas the internal structures of the virus can only be observed in images from a transmission electron microscope.

Past Systems of Classification

Viruses are classified in several ways: by factors such as their core content, the structure of their capsids, and whether they have an outer envelope. Viruses may use either DNA or RNA as their genetic material. The virus core contains the genome or total genetic content of the virus. Viral genomes tend to be small, containing only those genes that encode proteins that the virus cannot obtain from the host cell. This genetic material may be single- or double-stranded. It may also be linear or circular. While most viruses contain a single nucleic acid, others have genomes that have several, which are called segments. The type of genetic material (DNA or RNA) and its structure (single- or double-stranded, linear or circular, and segmented or non-segmented) are used to classify the virus core structures.

Virus classification by genome structure and core: The type of genetic material (DNA or RNA) and its structure (single- or double-stranded, linear or circular, and segmented or non-segmented) are used to classify the virus core structures.

Viruses can also be classified by the design of their capsids. Isometric viruses have shapes that are roughly spherical, such as poliovirus or herpesviruses. Enveloped viruses have membranes surrounding capsids. Animal viruses, such as HIV, are frequently enveloped. Head and tail viruses infect bacteria and have a head that is similar to icosahedral viruses and a tail shape like filamentous viruses. Capsids are classified as naked icosahedral, enveloped icosahedral, enveloped helical, naked helical, and complex. For example, the tobacco mosaic virus has a naked helical capsid. The adenovirus has an icosahedral capsid.

Adenovirus classification: Adenovirus (left) is depicted with a double-stranded DNA genome enclosed in an icosahedral capsid that is 90–100 nm across. The virus, shown clustered in the micrograph (right), is transmitted orally and causes a variety of illnesses in vertebrates, including human eye and respiratory infections.

Transmission electron micrograph of viruses: Transmission electron micrographs of various viruses show their structures. The capsid of the (a) polio virus is naked icosahedral (b) the Epstein-Barr virus capsid is enveloped icosahedral (c) the mumps virus capsid is an enveloped helix (d) the tobacco mosaic virus capsid is naked helical and (e) the herpesvirus capsid is complex.

Virus classification by capsid structure: Viruses can also be classified by the design of their capsids which are classified as naked icosahedral, enveloped icosahedral, enveloped helical, naked helical, and complex.

Example of viruses classified by caspid design: Viruses are classified based on their core genetic material and capsid design. (a) Rabies virus has a single-stranded RNA (ssRNA) core and an enveloped helical capsid, whereas (b) variola virus, the causative agent of smallpox, has a double-stranded DNA (dsDNA) core and a complex capsid.

Baltimore Classification

The most commonly-used system of virus classification was developed by Nobel Prize-winning biologist David Baltimore in the early 1970s. In addition to the differences in morphology and genetics mentioned above, the Baltimore classification scheme groups viruses according to how the mRNA is produced during the replicative cycle of the virus. Viruses can contain double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), double-stranded RNA (dsRNA), single-stranded RNA with a positive polarity (ssRNA), ssRNA with a negative polarity, diploid (two copies) ssRNA, and partial dsDNA genomes. Positive polarity means that the genomic RNA can serve directly as mRNA and a negative polarity means that their sequence is complementary to the mRNA.

Baltimore classification: The Baltimore classification scheme, the most commonly used, was developed by Nobel Prize-winning biologist David Baltimore in the early 1970s. The scheme groups viruses according to how the mRNA is produced during the replicative cycle of the virus, in addition to the differences in morphology and genetics.



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