ReviewActive DNA demethylation in post-mitotic neurons: A reason for optimism
Introduction
Approximately 70–80% of cytosines in CpG dinucleotides are methylated in human somatic cells. Generally, CpG methylation in gene promoter or enhancer regions is associated with repressed transcription (Razin and Riggs, 1980), while gene body methylation is positively correlated with gene expression (Laurent et al., 2010, Lister et al., 2009, Rauch et al., 2009). This highly stable covalent modification to DNA in mammals produces potentially lifelong changes in gene expression making it integral to maintaining stable cellular identities When a CpG dinucleotide is not methylated on either DNA strand the de novo DNA methyltransferases, DNMT3a and DNMT3b, are primarily responsible for adding a methyl group. When one strand is already methylated the complementary strand is methylated via a maintenance DNMT, primarily DNMT1 (Sharma et al., 2010). While the factors that guide a DNMT to a specific CpG have not been fully elucidated, it is generally believed that DNMTs are recruited through their interactions with transcription factors, chromatin proteins (see Section 2 below), as well as other proteins. In cultured cell lines, transcription factors shown to promote the targeting of DNMTs include DNMT1 and 3a by PML-RAR (Di Croce et al., 2002) and DNMT1 by Daxx (Muromoto et al., 2004) and E2F6 (Velasco et al., 2010).
DNA methylation gene silencing has been shown to be important not only for maintaining cellular subtypes, but also contributes to sustaining functional identities, including stabilizing neuronal interactions (Bird, 2002, Cortese et al., 2011, De Carvalho et al., 2010, Deaton et al., 2011, Iwamoto et al., 2011, Levenson et al., 2006). This is best exemplified by its contribution to long-term memory. DNA methylation silencing of the memory suppressor gene, protein phosphatase 1 (PP1), in combination with reduced methylation of the synaptic plasticity gene reelin have been shown to be associated with new memory formation (Miller and Sweatt, 2007). The same group has also shown that cortical DNA methylation changes at specific genes are associated with consolidating and maintaining memory, and that established memories can be weakened using DNMT inhibitors (Miller et al., 2010). Similarly, DNMT1 and DNMT3a double knockout mice have been shown to have deficits in learning and memory (Feng et al., 2010), while restoration of DNMT3a2 levels in aged mice leads to improved memory (Oliveira et al., 2012). Based on these studies it appears that in general DNA methylation changes are important for memory formation. However, it has not yet been determined which methylation changes at specific genomic loci are functionally involved in memory formation and which are passive events perhaps not even affecting gene transcription.
While neurotransmitters largely constitute the message neurons communicate to each other the neurons to which they communicate may be largely hard-wired using DNA methylation and histone modifications (Sharma et al., 2012). With few exceptions all current psychopharmacological agents target neurotransmitter levels or their receptors and not these more profound factors. In mental disorders, such as schizophrenia, presumably there are abnormalities in both domains.
Without the existence of active DNA demethylation neurons once misprogrammed could never be reprogrammed as the DNA methyl mark can persist across a lifetime as well as be passed to subsequent generations (Anway et al., 2006, Heijmans et al., 2008, Morgan et al., 1999, Rakyan et al., 2003). The potential to pharmacologically alter this code would then be minimal due to the stability of the covalent bonds that link methyl groups to cytosines. The importance of recent insights into the DNA demethylation pathway cannot be understated as this raises the possibility that neurons containing a gene expression profile that contributes to mental illness encoded by DNA methylation can be reprogrammed using epigenetic tools.
Section snippets
DNA methylation and histone modifications
Restrictive epigenetic changes such as DNA methylation and histone modifications have been implicated in a variety of mental disorders. The process of chromatin condensation or ‘heterochromatization’ involves the accumulation of certain histone modifications, such as methylated lysines 9 (H3K9) and 27 (H3K27) of histone 3, and DNA CpG methylation at a gene promoter leading to reduced gene expression. These histone modifications and the enzymes that catalyze their formation are known to interact
DNA demethylation
Until recently the existence of active DNA demethylation remained somewhat controversial (Ooi and Bestor, 2008). While it was known that DNA can become demethylated passively as cells divide, when a maintenance DNMT does not act prior to cell division, active removal of methyl groups from cytosine or removal of the 5-methylcytosine (5MC) molecule itself was thought to be a rare occurrence (Ooi and Bestor, 2008). However, there are several reasons, beyond recent direct evidence, that suggest the
Base excision repair (BER)
In plants, active DNA demethylation is a well-characterized process in which the accepted mechanism involves BER (Gehring et al., 2009). Over the last four years there is increasing support that a similar BER pathway is involved in active DNA demethylation in animals as well. Recent studies indicate that in the adult mouse brain and in embryonic stem cells 5MC is first oxidized to form 5-hydroxymethylcytosine (5HMC) catalyzed by ten-eleven translocation (TET) enzymes (Guo et al., 2011, Ito
Schizophrenia and DNA demethylation
In a genomewide experiment abnormal DNA methylation networks have been demonstrated in psychotic patients (Mill and Petronis, 2009). Also, a wide variety of DNA methylation alterations at individual gene promoters has been reported, including GAD1, reelin, BDNF, Catechol-O-methyltransferase (COMT), and SOX10 (Abdolmaleky et al., 2006, Guidotti et al., 2011, Iwamoto et al., 2005). We recently reported that the reduction of BDNF expression in the parietal cortex of schizophrenia patients was
Utilizing DNA demethylation to reprogram neurons
Aberrant connections maintained by restrictive histone modifications and DNA methylation have been hypothesized to contribute to the maintenance of psychopathology (Guidotti et al., 2011, Sharma et al., 2012). One means of reversing this state could be accomplished by inhibiting the participants of the transcription silencing process of heterochromatization (Sharma et al., 2012). However, merely inhibiting the spread of restrictive chromatin cannot alone reactivate previously silenced genes.
Conclusion
DNA methylation is the most stable of all epigenetic modifications, leading to the belief that it was irreversible. Recent evidence indicates that the BER pathway is the most likely method of active DNA demethylation. Mental disorders, including schizophrenia, have been shown to be characterized by a variety of epigenetic abnormalities. Some have reported these to be present at specific gene loci, while others have reported more generalized abnormalities. The chronic nature of most psychiatric
Acknowledgments
This work was supported in part by a NARSAD Young Investigator Award donation from The Family of Joseph M. Evans and the Department of Veterans Affairs (Merit Review Grant; Career Development Award (CDA-2)) (DPG) and National Institutes of Health (NIH) R01 MH094358 grant (RPS).
References (202)
- et al.
Molecular and cellular mechanisms of altered GAD1/GAD67 expression in schizophrenia and related disorders
Brain Research Reviews
(2006) - et al.
Molecular evidence for increased expression of genes related to immune and chaperone function in the prefrontal cortex in schizophrenia
Biological Psychiatry
(2007) - et al.
Induction and superinduction of growth arrest and DNA damage gene 45 (GADD45) alpha and beta messenger RNAs by histone deacetylase inhibitors trichostatin A (TSA) and butyrate in SW620 human colon carcinoma cells
Cancer Letters
(2002) - et al.
Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair
Cell
(2011) - et al.
Tet1 is dispensable for maintaining pluripotency and its loss is compatible with embryonic and postnatal development
Cell Stem Cell
(2011) - et al.
DNA methylation and cellular reprogramming
Trends in Cell Biology
(2010) - et al.
Genes modulated by histone acetylation as new effectors of butyrate activity
FEBS Letters
(2001) - et al.
Valproate induces replication-independent active DNA demethylation
The Journal of Biological Chemistry
(2003) - et al.
Promoter-specific activation and demethylation by MBD2/demethylase
The Journal of Biological Chemistry
(2002) - et al.
Reduced baseline acetylated histone 3 levels, and a blunted response to HDAC inhibition in lymphocyte cultures from schizophrenia subjects
Schizophrenia Research
(2008)
Histone deacetylase inhibitors and candidate gene expression: an in vivo and in vitro approach to studying chromatin remodeling in a clinical population
Journal of Psychiatric Research
HDAC inhibitors: clinical update and mechanism-based potential
Biochemical Pharmacology
Epigenetic GABAergic targets in schizophrenia and bipolar disorder
Neuropharmacology
Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain
Cell
Dynamics of 5-hydroxymethylcytosine and chromatin marks in mammalian neurogenesis
Cell Reports
Acetylation of poly(ADP-ribose) polymerase-1 by p300/CREB-binding protein regulates coactivation of NF-kappaB-dependent transcription
The Journal of Biological Chemistry
Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells
Cell Stem Cell
Local DNA demethylation in vertebrates: how could it be performed and targeted?
FEBS Letters
PARP-1 regulates chromatin structure and transcription through a KDM5B-dependent pathway
Molecular Cell
Histone H3 lysine 4 demethylation is a target of nonselective antidepressive medications
Chemistry & Biology
Hypomethylation of MB-COMT promoter is a major risk factor for schizophrenia and bipolar disorder
Human Molecular Genetics
Hypermethylation of the reelin (RELN) promoter in the brain of schizophrenic patients: a preliminary report
American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics: The Official Publication of the International Society of Psychiatric Genetics
Solution structure of the nonmethyl-CpG-binding CXXC domain of the leukaemia-associated MLL histone methyltransferase
The EMBO Journal
Endocrine disruptor vinclozolin induced epigenetic transgenerational adult-onset disease
Endocrinology
Binding to nonmethylated CpG DNA is essential for target recognition, transactivation, and myeloid transformation by an MLL oncoprotein
Molecular and Cellular Biology
A novel histone deacetylase 8 (HDAC8)-specific inhibitor PCI-34051 induces apoptosis in T-cell lymphomas
Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
Gadd45a promotes epigenetic gene activation by repair-mediated DNA demethylation
Nature
Regulation of chromatin structure by poly(ADP-ribosyl)ation
Frontiers in Genetics
Regulation of the GABA cell phenotype in hippocampus of schizophrenics and bipolars
Proceedings of the National Academy of Sciences of the United States of America
Site-specific regulation of cell cycle and DNA repair in post-mitotic GABA cells in schizophrenic versus bipolars
Proceedings of the National Academy of Sciences of the United States of America
The expression of proapoptosis genes is increased in bipolar disorder, but not in schizophrenia
Molecular Psychiatry
DNA fragmentation decreased in schizophrenia but not bipolar disorder
Archives of General Psychiatry
A mammalian protein with specific demethylase activity for mCpG DNA
Nature
DNA methylation patterns and epigenetic memory
Genes & Development
The MT domain of the proto-oncoprotein MLL binds to CpG-containing DNA and discriminates against methylation
Nucleic Acids Research
Reprogramming towards pluripotency requires AID-dependent DNA demethylation
Nature
Efficacy of MS-275, a selective inhibitor of class I histone deacetylases, in human colon cancer models
International Journal of Oncology
The class-I HDAC inhibitor MGCD0103 induces apoptosis in hodgkin lymphoma cell lines and synergizes with proteasome inhibitors by an HDAC6-independent mechanism
British Journal of Haematology
The histone deacetylase inhibitor SAHA arrests cancer cell growth, up-regulates thioredoxin-binding protein-2, and down-regulates thioredoxin
Proceedings of the National Academy of Sciences of the United States of America
The histone deacetylase inhibitor trichostatin A induces GADD45 gamma expression via oct and NF-Y binding sites
Oncogene
Gadd45, a p53-responsive stress protein, modifies DNA accessibility on damaged chromatin
Molecular and Cellular Biology
Nicotinamide adenine dinucleotide (NAD)-regulated DNA methylation alters CCCTC-binding factor (CTCF)/cohesin binding and transcription at the BDNF locus
Proceedings of the National Academy of Sciences of the United States of America
Derepression of BDNF transcription involves calcium-dependent phosphorylation of MeCP2
Science (New York, N.Y.)
Ethanol-mediated DNA damage and PARP-1 apoptotic responses in cultured fetal cortical neurons. Alcoholism
Clinical and Experimental Research
Poly(ADP-ribosyl)ation acts in the DNA demethylation of mouse primordial germ cells also with DNA damage-independent roles
PloS One
KDM1B is a histone H3K4 demethylase required to establish maternal genomic imprints
Nature
Long-term memory requires polyADP-ribosylation
Science (New York, N.Y.)
The AID/APOBEC family of nucleic acid mutators
Genome Biology
Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability
Nature
Genome-wide screen for differential DNA methylation associated with neural cell differentiation in mouse
PloS One
Cited by (61)
Role of PARP-catalyzed ADP-ribosylation in the Crosstalk Between DNA Strand Breaks and Epigenetic Regulation
2020, Journal of Molecular BiologyAltered amygdala DNA methylation mechanisms after adolescent alcohol exposure contribute to adult anxiety and alcohol drinking
2019, NeuropharmacologyCitation Excerpt :DNMT1 functions as a maintenance methyltransferase, whereas DNMT3a and DNMT3b catalyze the ‘de novo’ methylation of previously unmethylated cytosine residues (Feng and Fan, 2009; Krishnan et al., 2014). Additionally, DNA demethylation occurs in a process involving base excision repair (BER) mechanisms (Gavin et al., 2013; Wu and Zhang, 2014). On the contrary, the BER pathway is initiated by the ten-eleven translocation (TET) family of enzymes that catalyzes the conversion of methylcytosine to 5-hydroxymethylcytosine (5-hmC), which is ultimately removed through several enzymatic events coordinated by the growth arrest and DNA damage inducible protein 45 (GADD45) family of co-factors (Krishnan et al., 2014; Wu and Zhang, 2014).
Reactivation of the FMR1 Gene
2017, Fragile X Syndrome: From Genetics to Targeted Treatment