DNA Methyltransferase

(ps.nsls.bnl.gov)

Introduction

Types of Mammalian DNA Methyltransferase

DNMT 1

     DNMT 1 is the most common mammalian methyltransferase (Bonfils et al., 2000).  It is thought to be primarily responsible for the maintenance of methylation patterns while DNA is being copied and repaired, a claim that is supported by the protein's high affinity for hemi-methylated DNA (DNA in which one strand is methylated and the other stand isn't; occuring after replication) (Cheng and Blumenthal, 2008).  However, evidence suggests that it may also play some role in de novo methylation (Cheng and Blumenthal, 2008).  DNMT 1 is constituted of an COOH-terminal domain which has a catalytic effect on methylation and an N-terminal domain which play a regulatory role (Cardoso and Leonhardt, 1999).

DNMT 2

     Human DNMT 2 is thought to methylate RNA, not DNA (OMIM--DNMT2).  It differs significantly from the other DNMT species because it is missing the N-terminal domain (OMIM--DNMT2).

DNMT 3

     (pubmedcentral.nih.gov)

 Function

Mechanism 

     In order to transfer a methyl group onto a cytosine residue, DNMT must work in conjuction with another molecule, S-adenosylmethionine (SAM)(Strathdee and Brown, 2002).   The methyl group attached to SAM is moved to the fifth carbon of cytosine, a reaction catatlyzed by DNMT (Strathdee and Brown, 2002).

(Strathdee and Brown, 2002)

Methylation of CpG dinucleotides

     In mammalian cells the methylaion of cytosine can only occur when a cytosine lies directly on the five prime side of a guanine, referred to as a CpG dinucleotide (Siegfried and Cedar, 2003).  CpC dinucleotides are relatively uncommon (Saxonov, Berg, and Brutlag, 2005).  The most likely explanation for this phenomemon lies in the highly mutable nature of methylated cytosine (it is converted to thymine when it is deaminated) (Saxonov, Berg, and Brutlag, 2005).  Within the genome 70-80% of CpG dinucleotides are methylated (OMIM--DNMT1).  However, there are areas that contain an unusually high number of these dinucleodtides, known as "CpG" islands, which are typically free of methylation (Strathdee and Brown, 2002).  About 50-60% of these CpG islands are found in or near the promotor regions of genes (Strathdee and Brown, 2002).  When an unmethylated CpG island is associated with a gene promoter that gene is usually highly transcribed (OMIM--DNMT1).  Certain islands are very highly methylated, and these are often associated with the silenced genes involved in imprinting (discussed below) and X-chromosome inactivation (OMIM--DNMT1).

Maintenance vs. De novo Methylation

     Maintenance methylation refers to the process of adding methyl groups onto the newly synthesized strand of DNA after replication (Otto and Walbot, 1989).  The placement of these groups must match the pattern along the parent stand.  In this way a relatively stable methylation pattern can be maintained as cells divide (Otto and Walbot, 1989).  Maintenance methyltransferases are highly expressed in adult cells where the main role of methyltranferase activity is to perserve a stable methylation pattern (Benbrahim-Tallaa et al.,2007).

     De novo methylation refers to the methylation of previously unmethylated areas (Benbrahim-Tallaa et al.,2007).  Methyltransferases which carry out de novo methylation are found in high levels in embryonic cells (Benbrahim-Tallaa et al.,2007).

Methylation Causes a Decrease in Transcription

     Contrary to one popular theory, it has become evident that DNMTs do not impede transcription by physically blocking transcription protein (Robertson, 2001).  Instead they recruit other proteins which work togther in order to prime DNA to be transcribed (Robertson, 2001).  Initially, methylated DNA recruits some type of methyl binding protein (MBD) (Robertson, 2001).  MeCP2, for example, is a widely studied methyl binding protein (Robertson, 2001).  It is made of a methyl binding domain which recognizes methylation and a transcriptional repression group which recruits other proteins, including histone deacetylase (HDAC) (Robertson, 2001).  HDAC can then remove acetyl groups from nearby histone tails which tightens these tails around the DNA, making the DNA inaccesible for transcription (Robertson, 2001). 

 Epigenetics and Imprinting

     Beyond the basic genetic sequence of DNA, there is another complex and important layer of information known as the epigenetic code (hopkinsmedicine.org).  This code consists of modifications to the DNA that do not involve altering its sequence (hopkinsmedicine.org).  Since each cell has the same genetic information, a code which controls the expression of these genes is necessary in order to ensure that each cell carries out its proper set of functions (hopkinsmedicine.org). Methylation of DNA is one major form of epigenetic coding (hopkinsmedicine.org).  

For more information, see this recent article published in Discover Magazine: DNA is not destiny.

(neb.com)

Imprinting is a very interesting phenomenon associated with epigenetics (Robertson, 2005).  During gametogenesis, mehtylation patterns are augmented in the genetic material of the eggs and sperm in such a way that a sex specific set of genes are methylated or unmethylated, inactive or active (Robertson, 2005).  When the maternal and paternal DNA come together in an embryo only one allele (either maternal or paternal) of each imprinted gene is expressed (Robertson, 2005).  There are about eighty known imprinted genes and more of these genes are discovered all the time (Robertson, 2005).  The intriguing aspect of this process is that it does not follow traditional Mendalian inheritance (ucalgary.ca).  Effects of environmental factors (such as famine) may show up in the methylation patterns of the individuals that experience them (ucalgary.ca).  These effects can be passed to the next generation through imprinting (ucalgary.ca).

(utah.edu)

Human Disease Associated with DNA Methyltransferase

     Research shows that DNA methylation has an impact on a plethera of human phenotypes.  Everything from our behavioral tendancies to whether or not we develop cancer is partly controlled by methylation.  Researchers are investigating the role of epigenetics in behavioral sex differences (Shepard et al. 2009), suicide (McGowan et al., 2008), and schizophrenia (Grayson et al, 2005).  The link to cancer and the possiblity of new cancer treaments is particularly interesting.

Cancer

     The link between cancer and DNA methylation has been apparent for several decades (Robertson, 2005).  Cancer cells are often found to have especially low levels of methylation (hypometylation) leading to a lack of control of gene expression (Robertson, 2005).  For example, genes in the melanoma antigen (MAGE) family are often found to be unmethylated leading to tumor growth (Robertson, 2005).  Hypermethylation can also lead to cancer growth (Robertson, 2005).  When the CpG islands associated with cycle regulation genes, DNA repair genes, etc. become methylated, these genes are silenced (Robertson, 2005).  This leaves the cell essentially unregualted and unchecked growth and division ensue (Robertson, 2005). 

Imprinting disorders

     The classic is example of the imprinting disorder is the case of two sister disorders: Prader-Willi and Angelman Syndromes (Robertson, 2005).  Both syndromes are caused by problems with chromosome 15 (Robertson, 2005).  One section of this chromosome codes for genes which are methylated on the paternal copy and are unmethyated on the maternal copy (Robertson, 2005).  Another set of genes on chromosome 15 has the opposite imprinting condition (maternal is methylated, paternal is unmethylated) (Robertson, 2005).  In the embryo, only the maternal alleles are expressed for the first set of genes, and only the paternal alleles are expressed for the second set (Robertson, 2005).   These disorders arise when the segment of chromosome 15 containing the genes  is missing in either the egg or the sperm (Robertson, 2005).  Prader-Willi syndrome occurs when the paternally expressed genes are lost (Robertson, 2005).  Common symptoms of this disorder include inactivity during infancy, rapid weight gain, and mental retardation (Robertson, 2005).  Angelman syndrome occurs when the maternally expressed genes are lost (Robertson, 2005).  Its symptoms include developmental delay, mental retardation, characteristic posture, and happy demeanor (geneclinics.org).

Epigenetic Therapy

     The fact that so many disorders seem to be epigentic in nature opens up many possibilities for treatment (Egger et al., 2004).  The methylation state of a genes is reversible; while mutations in the gene sequence is harder to deal with (Egger et al., 2004).  In most cases individuals with these disorders do possess a normal gene;  however, these genes have been methylated or unmethylated to that individuals disadvantage (Egger et al., 2004).  The idea of an epigenetic therapy is to gain control of the silencing or expression of these key genes (Egger et al., 2004).  DNA methylation inhibitors, such as 5-azacytidine, could induce expression of certain silenced genes, especially if the hypermethylation took place under pathological conditions (Egger et al., 2004).  HDAC inhibitors are also being investigated for their potential in treatment of these disorders (Egger et al., 2004). 

For a recap of epigenetics and how they influence humans, watch this NOVA science now special.