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Advances in Epigenetics and Epigenomics for Neurodegenerative Diseases

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Abstract

In the post-genomic era, epigenetic factors—literally those that are “over” or “above” genetic ones and responsible for controlling the expression and function of genes—have emerged as important mediators of development and aging; gene-gene and gene-environmental interactions; and the pathophysiology of complex disease states. Here, we provide a brief overview of the major epigenetic mechanisms (ie, DNA methylation, histone modifications and chromatin remodeling, and non-coding RNA regulation). We highlight the nearly ubiquitous profiles of epigenetic dysregulation that have been found in Alzheimer’s and other neurodegenerative diseases. We also review innovative methods and technologies that enable the characterization of individual epigenetic modifications and more widespread epigenomic states at high resolution. We conclude that, together with complementary genetic, genomic, and related approaches, interrogating epigenetic and epigenomic profiles in neurodegenerative diseases represent important and increasingly practical strategies for advancing our understanding of and the diagnosis and treatment of these disorders.

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References

Papers of particular interest, published recently, have been highlighted as: • Of importance •• Of major importance

  1. Lander ES, Linton LM, Birren B, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409:860–921.

    Article  PubMed  CAS  Google Scholar 

  2. Gandhi S, Wood NW. Genome-wide association studies: the key to unlocking neurodegeneration? Nat Neurosci. 2010;13:789–94.

    Article  PubMed  CAS  Google Scholar 

  3. Mehler MF. Epigenetic principles and mechanisms underlying nervous system functions in health and disease. Prog Neurobiol. 2008;86:305–41.

    Article  PubMed  CAS  Google Scholar 

  4. Feinberg AP. Phenotypic plasticity and the epigenetics of human disease. Nature. 2007;447:433–40.

    Article  PubMed  CAS  Google Scholar 

  5. Berdasco M, Esteller M. Aberrant epigenetic landscape in cancer: how cellular identity goes awry. Dev Cell. 2010;19:698–711.

    Article  PubMed  CAS  Google Scholar 

  6. Meda F, Folci M, Baccarelli A, Selmi C. The epigenetics of autoimmunity. Cell Mol Immunol. 2011.

  7. Atadja PW. HDAC inhibitors and cancer therapy. Prog Drug Res. 2011;67:175–95.

    PubMed  CAS  Google Scholar 

  8. Kurdistani SK. Histone modifications in cancer biology and prognosis. Prog Drug Res. 2011;67:91–106.

    PubMed  CAS  Google Scholar 

  9. Taberlay PC, Jones PA. DNA methylation and cancer. Prog Drug Res. 2011;67:1–23.

    PubMed  CAS  Google Scholar 

  10. Wu SC, Zhang Y. Active DNA demethylation: many roads lead to Rome. Nat Rev Mol Cell Biol. 2010;11:607–20.

    Article  PubMed  CAS  Google Scholar 

  11. Qureshi IA, Mehler MF. Impact of nuclear organization and dynamics on epigenetic regulation in the central nervous system: implications for neurological disease states. Ann NY Acad Sci. 2010;1204(Suppl):E20–37.

    Article  PubMed  Google Scholar 

  12. Jenuwein T, Allis CD. Translating the histone code. Science. 2001;293:1074–80.

    Article  PubMed  CAS  Google Scholar 

  13. Ruthenburg AJ, Li H, Patel DJ, Allis CD. Multivalent engagement of chromatin modifications by linked binding modules. Nat Rev Mol Cell Biol. 2007;8:983–94.

    Article  PubMed  CAS  Google Scholar 

  14. •• Kapranov P, St Laurent G, Raz T, et al. The majority of total nuclear-encoded non-ribosomal RNA in a human cell is ‘dark matter’ un-annotated RNA. BMC Biol. 2010;8:149. This paper utilized single molecule sequencing to estimate the relative mass of dark matter RNA, RNA that are either unannotated or whose function is not understood, present in various cell types. It concluded that the majority of total nonribosomal RNA in a human cell is dark matter RNA.

    Article  PubMed  CAS  Google Scholar 

  15. Mattick JS, Taft RJ, Faulkner GJ. A global view of genomic information–moving beyond the gene and the master regulator. Trends Genet. 2010;26:21–8.

    Article  PubMed  CAS  Google Scholar 

  16. Qureshi IA, Mattick JS, Mehler MF. Long non-coding RNAs in nervous system function and disease. Brain Res. 2010;1338:20–35.

    Article  PubMed  CAS  Google Scholar 

  17. Mattick JS, Amaral PP, Dinger ME, et al. RNA regulation of epigenetic processes. Bioessays. 2009;31:51–9.

    Article  PubMed  CAS  Google Scholar 

  18. Krol J, Loedige I, Filipowicz W. The widespread regulation of microRNA biogenesis, function and decay. Nat Rev Genet. 2010;11:597–610.

    PubMed  CAS  Google Scholar 

  19. Mercer TR, Dinger ME, Mattick JS. Long non-coding RNAs: insights into functions. Nat Rev Genet. 2009;10:155–9.

    Article  PubMed  CAS  Google Scholar 

  20. Chuang DM, Leng Y, Marinova Z, et al. Multiple roles of HDAC inhibition in neurodegenerative conditions. Trends Neurosci. 2009;32:591–601.

    Article  PubMed  CAS  Google Scholar 

  21. Lee J, Ryu H. Epigenetic modification is linked to Alzheimer’s disease: is it a maker or a marker? BMB Rep. 2010;43:649–55.

    Article  PubMed  CAS  Google Scholar 

  22. Tohgi H, Utsugisawa K, Nagane Y, et al. The methylation status of cytosines in a tau gene promoter region alters with age to downregulate transcriptional activity in human cerebral cortex. Neurosci Lett. 1999;275:89–92.

    Article  PubMed  CAS  Google Scholar 

  23. Tohgi H, Utsugisawa K, Nagane Y, et al. Reduction with age in methylcytosine in the promoter region −224 approximately −101 of the amyloid precursor protein gene in autopsy human cortex. Brain Res Mol Brain Res. 1999;70:288–92.

    Article  PubMed  CAS  Google Scholar 

  24. West RL, Lee JM, Maroun LE. Hypomethylation of the amyloid precursor protein gene in the brain of an Alzheimer’s disease patient. J Mol Neurosci. 1995;6:141–6.

    Article  PubMed  CAS  Google Scholar 

  25. Mastroeni D, Grover A, Delvaux E, et al. Epigenetic changes in Alzheimer’s disease: decrements in DNA methylation. Neurobiol Aging. 2010;31:2025–37.

    Article  PubMed  CAS  Google Scholar 

  26. Mastroeni D, McKee A, Grover A, et al. Epigenetic differences in cortical neurons from a pair of monozygotic twins discordant for Alzheimer’s disease. PLoS One. 2009;4:e6617.

    Article  PubMed  Google Scholar 

  27. Wang SC, Oelze B, Schumacher A. Age-specific epigenetic drift in late-onset Alzheimer’s disease. PLoS One. 2008;3:e2698.

    Article  PubMed  Google Scholar 

  28. Chen KL, Wang SS, Yang YY, et al. The epigenetic effects of amyloid-beta(1–40) on global DNA and neprilysin genes in murine cerebral endothelial cells. Biochem Biophys Res Commun. 2009;378:57–61.

    Article  PubMed  CAS  Google Scholar 

  29. Wu J, Basha MR, Brock B, et al. Alzheimer’s disease (AD)-like pathology in aged monkeys after infantile exposure to environmental metal lead (Pb): evidence for a developmental origin and environmental link for AD. J Neurosci. 2008;28:3–9.

    Article  PubMed  CAS  Google Scholar 

  30. Cao X, Sudhof TC. A transcriptionally [correction of transcriptively] active complex of APP with Fe65 and histone acetyltransferase Tip60. Science. 2001;293:115–20.

    Article  PubMed  CAS  Google Scholar 

  31. Marambaud P, Wen PH, Dutt A, et al. A CBP binding transcriptional repressor produced by the PS1/epsilon-cleavage of N-cadherin is inhibited by PS1 FAD mutations. Cell. 2003;114:635–45.

    Article  PubMed  CAS  Google Scholar 

  32. Rouaux C, Jokic N, Mbebi C, et al. Critical loss of CBP/p300 histone acetylase activity by caspase-6 during neurodegeneration. EMBO J. 2003;22:6537–49.

    Article  PubMed  CAS  Google Scholar 

  33. Saura CA, Choi SY, Beglopoulos V, et al. Loss of presenilin function causes impairments of memory and synaptic plasticity followed by age-dependent neurodegeneration. Neuron. 2004;42:23–36.

    Article  PubMed  CAS  Google Scholar 

  34. Cogswell JP, Ward J, Taylor IA, et al. Identification of miRNA changes in Alzheimer’s disease brain and CSF yields putative biomarkers and insights into disease pathways. J Alzheimers Dis. 2008;14:27–41.

    PubMed  CAS  Google Scholar 

  35. Guo JH, Cheng HP, Yu L, Zhao S. Natural antisense transcripts of Alzheimer’s disease associated genes. DNA Seq. 2006;17:170–3.

    PubMed  CAS  Google Scholar 

  36. Faghihi MA, Modarresi F, Khalil AM, et al. Expression of a noncoding RNA is elevated in Alzheimer’s disease and drives rapid feed-forward regulation of beta-secretase. Nat Med. 2008;14:723–30.

    Article  PubMed  CAS  Google Scholar 

  37. Buckley NJ, Johnson R, Zuccato C, et al. The role of REST in transcriptional and epigenetic dysregulation in Huntington’s disease. Neurobiol Dis. 2010;39:28–39.

    Article  PubMed  CAS  Google Scholar 

  38. • Seong IS, Woda JM, Song JJ, et al. Huntingtin facilitates polycomb repressive complex 2. Hum Mol Genet. 2010;19:573–583. This paper investigated the structure of the HTT and the role of huntingtin in modulating the polycomb repressive complex 2. It demonstrated that huntingtin stimulates histone H3 lysine 27 methyltransferase activity.

    Article  PubMed  CAS  Google Scholar 

  39. Shimojo M. Huntingtin regulates RE1-silencing transcription factor/neuron-restrictive silencer factor (REST/NRSF) nuclear trafficking indirectly through a complex with REST/NRSF-interacting LIM domain protein (RILP) and dynactin p150 Glued. J Biol Chem. 2008;283:34880–6.

    Article  PubMed  CAS  Google Scholar 

  40. Johnson R, Zuccato C, Belyaev ND, et al. A microRNA-based gene dysregulation pathway in Huntington’s disease. Neurobiol Dis. 2008;29:438–45.

    Article  PubMed  CAS  Google Scholar 

  41. Packer AN, Xing Y, Harper SQ, et al. The bifunctional microRNA miR-9/miR-9* regulates REST and CoREST and is downregulated in Huntington’s disease. J Neurosci. 2008;28:14341–6.

    Article  PubMed  CAS  Google Scholar 

  42. •• Marti E, Pantano L, Banez-Coronel M, et al. A myriad of miRNA variants in control and Huntington’s disease brain regions detected by massively parallel sequencing. Nucleic Acids Res. 2010. This paper performed massively parallel sequencing to analyze small RNAs expressed in the frontal cortex and striatum of patients with HD and controls. It found that the vast majority are miRNAs with significant sequence and length variability in both populations and, further, that these isomiRs are strongly deregulated in HD.

  43. • Johnson R, Richter N, Jauch R, et al. The Human Accelerated Region 1 noncoding RNA is repressed by REST in Huntington’s disease. Physiol Genomics. 2010. This paper identified an lncRNA that is abnormally repressed by REST in the striatum of patients with HD.

  44. Marullo M, Valenza M, Mariotti C, et al. Analysis of the repressor element-1 silencing transcription factor/neuron-restrictive silencer factor occupancy of non-neuronal genes in peripheral lymphocytes from patients with Huntington’s disease. Brain Pathol. 2010;20:96–105.

    Article  PubMed  CAS  Google Scholar 

  45. Jowaed A, Schmitt I, Kaut O, Wullner U. Methylation regulates alpha-synuclein expression and is decreased in Parkinson’s disease patients’ brains. J Neurosci. 2010;30:6355–9.

    Article  PubMed  CAS  Google Scholar 

  46. Matsumoto L, Takuma H, Tamaoka A, et al. CpG demethylation enhances alpha-synuclein expression and affects the pathogenesis of Parkinson’s disease. PLoS One. 2010;5:e15522.

    Article  PubMed  Google Scholar 

  47. Junn E, Lee KW, Jeong BS, et al. Repression of alpha-synuclein expression and toxicity by microRNA-7. Proc Natl Acad Sci USA. 2009;106:13052–7.

    Article  PubMed  CAS  Google Scholar 

  48. • Desplats P, Spencer B, Coffee E, et al. Alpha-synuclein sequesters DNMT1 from the nucleus: a novel mechanism for epigenetic alterations in Lewy body diseases. J Biol Chem. 2011. This paper studied DNMT1 levels in postmortem brains from PD and dementia with Lewy bodies patients. It determined that DNMT1 is sequestered in the cytoplasm and that α-synuclein might mediate this aberrant subcellular localization.

  49. Kontopoulos E, Parvin JD, Feany MB. Alpha-synuclein acts in the nucleus to inhibit histone acetylation and promote neurotoxicity. Hum Mol Genet. 2006;15:3012–23.

    Article  PubMed  CAS  Google Scholar 

  50. Santosh PS, Arora N, Sarma P, et al. Interaction map and selection of microRNA targets in Parkinson’s disease-related genes. J Biomed Biotechnol. 2009;2009:363145.

    Google Scholar 

  51. •• Gehrke S, Imai Y, Sokol N, Lu B. Pathogenic LRRK2 negatively regulates microRNA-mediated translational repression. Nature. 2010;466:637–641. This paper showed that pathogenic LRRK2 antagonizes the let-7 and miR-184* miRNAs and leads to the deregulation of E2F1/DP.

    Article  PubMed  CAS  Google Scholar 

  52. Simpson CL, Lemmens R, Miskiewicz K, et al. Variants of the elongator protein 3 (ELP3) gene are associated with motor neuron degeneration. Hum Mol Genet. 2009;18:472–81.

    Article  PubMed  CAS  Google Scholar 

  53. • Okada Y, Yamagata K, Hong K, et al. A role for the elongator complex in zygotic paternal genome demethylation. Nature. 2010;463:554–558. This paper demonstrated that knocking down Elp3, a gene linked to ALS, impairs paternal DNA demethylation.

    Article  PubMed  CAS  Google Scholar 

  54. Winkler GS, Kristjuhan A, Erdjument-Bromage H, et al. Elongator is a histone H3 and H4 acetyltransferase important for normal histone acetylation levels in vivo. Proc Natl Acad Sci USA. 2002;99:3517–22.

    Article  PubMed  CAS  Google Scholar 

  55. Matsumoto T, Yun CS, Yoshikawa H, Nishida H. Comparative studies of genome-wide maps of nucleosomes between deletion mutants of elp3 and hos2 genes of Saccharomyces cerevisiae. PLoS One. 2011;6:e16372.

    Article  PubMed  CAS  Google Scholar 

  56. Han Q, Lu J, Duan J, et al. Gcn5- and Elp3-induced histone H3 acetylation regulates hsp70 gene transcription in yeast. Biochem J. 2008;409:779–88.

    Article  PubMed  CAS  Google Scholar 

  57. Lagier-Tourenne C, Polymenidou M, Cleveland DW. TDP-43 and FUS/TLS: emerging roles in RNA processing and neurodegeneration. Hum Mol Genet. 2010;19:R46–64.

    Article  PubMed  CAS  Google Scholar 

  58. • Ling SC, Albuquerque CP, Han JS, et al. ALS-associated mutations in TDP-43 increase its stability and promote TDP-43 complexes with FUS/TLS. Proc Natl Acad Sci USA. 2010; 107:13318–13323. This paper found that TDP-43 mutant polypeptides are more stable than those of the wild-type. Further, using mass spectrometry, it identified TDP-43 complexes containing components of the Drosha microprocessor, suggesting roles in mediating microRNA biogenesis, and also TDP-43 complexes containing FUS/TLS.

    Article  PubMed  CAS  Google Scholar 

  59. Freibaum BD, Chitta RK, High AA, Taylor JP. Global analysis of TDP-43 interacting proteins reveals strong association with RNA splicing and translation machinery. J Proteome Res. 2010;9:1104–20.

    Article  PubMed  CAS  Google Scholar 

  60. Buratti E, De Conti L, Stuani C, et al. Nuclear factor TDP-43 can affect selected microRNA levels. FEBS J. 2010;277:2268–81.

    Article  PubMed  CAS  Google Scholar 

  61. •• Williams AH, Valdez G, Moresi V, et al.: MicroRNA-206 delays ALS progression and promotes regeneration of neuromuscular synapses in mice. Science 2009, 326:1549–1554. This paper determined that miR-206 is significantly upregulated in a mouse model of ALS and that deficiency of miR-206 accelerates disease progression.

    Article  PubMed  CAS  Google Scholar 

  62. Birney E, Stamatoyannopoulos JA, Dutta A, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007;447:799–816.

    Article  PubMed  CAS  Google Scholar 

  63. Lister R, Pelizzola M, Dowen RH, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 2009;462:315–22.

    Article  PubMed  CAS  Google Scholar 

  64. Gu H, Smith ZD, Bock C, et al. Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat Protoc. 2011;6:468–81.

    Article  PubMed  CAS  Google Scholar 

  65. Ball MP, Li JB, Gao Y, et al. Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol. 2009;27:361–8.

    Article  PubMed  CAS  Google Scholar 

  66. Rauch TA, Pfeifer GP. The MIRA method for DNA methylation analysis. Methods Mol Biol. 2009;507:65–75.

    Article  PubMed  CAS  Google Scholar 

  67. Suzuki M, Greally JM. DNA methylation profiling using HpaII tiny fragment enrichment by ligation-mediated PCR (HELP). Methods. 2010;52:218–22.

    Article  PubMed  CAS  Google Scholar 

  68. Bock C, Tomazou EM, Brinkman AB, et al. Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol. 2010;28:1106–14.

    Article  PubMed  CAS  Google Scholar 

  69. Harris RA, Wang T, Coarfa C, et al. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol. 2010;28:1097–105.

    Article  PubMed  CAS  Google Scholar 

  70. Wang Z, Zang C, Rosenfeld JA, et al. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet. 2008;40:897–903.

    Article  PubMed  CAS  Google Scholar 

  71. Barski A, Cuddapah S, Cui K, et al. High-resolution profiling of histone methylations in the human genome. Cell. 2007;129:823–37.

    Article  PubMed  CAS  Google Scholar 

  72. Boyle AP, Davis S, Shulha HP, et al. High-resolution mapping and characterization of open chromatin across the genome. Cell. 2008;132:311–22.

    Article  PubMed  CAS  Google Scholar 

  73. Hesselberth JR, Chen X, Zhang Z, et al. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods. 2009;6:283–9.

    Article  PubMed  CAS  Google Scholar 

  74. Auerbach RK, Euskirchen G, Rozowsky J, et al. Mapping accessible chromatin regions using Sono-Seq. Proc Natl Acad Sci USA. 2009;106:14926–31.

    Article  PubMed  CAS  Google Scholar 

  75. Giresi PG, Kim J, McDaniell RM, et al. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res. 2007;17:877–85.

    Article  PubMed  CAS  Google Scholar 

  76. Schones DE, Cui K, Cuddapah S, et al. Dynamic regulation of nucleosome positioning in the human genome. Cell. 2008;132:887–98.

    Article  PubMed  CAS  Google Scholar 

  77. Kaplan N, Moore IK, Fondufe-Mittendorf Y, et al. The DNA-encoded nucleosome organization of a eukaryotic genome. Nature. 2009;458:362–6.

    Article  PubMed  CAS  Google Scholar 

  78. • Deal RB, Henikoff JG, Henikoff S. Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones. Science. 2010;328:1161–1164. This paper describes a novel method for measurement of the kinetics of nucleosome turnover.

    Article  PubMed  CAS  Google Scholar 

  79. Branton D, Deamer DW, Marziali A, et al. The potential and challenges of nanopore sequencing. Nat Biotechnol. 2008;26:1146–53.

    Article  PubMed  CAS  Google Scholar 

  80. Hwang do W, Song IC, Lee DS, Kim S. Smart magnetic fluorescent nanoparticle imaging probes to monitor microRNAs. Small. 2010;6:81–8.

    Article  PubMed  Google Scholar 

  81. Lendvai G, Estrada S, Bergstrom M. Radiolabelled oligonucleotides for imaging of gene expression with PET. Curr Med Chem. 2009;16:4445–61.

    Article  PubMed  CAS  Google Scholar 

  82. Chen AK, Rhee WJ, Bao G, Tsourkas A. Delivery of molecular beacons for live-cell imaging and analysis of RNA. Methods Mol Biol. 2011;714:159–74.

    Article  PubMed  CAS  Google Scholar 

  83. Liu CH, Kim YR, Ren JQ, et al. Imaging cerebral gene transcripts in live animals. J Neurosci. 2007;27:713–22.

    Article  PubMed  CAS  Google Scholar 

  84. Jirtle RL, Skinner MK. Environmental epigenomics and disease susceptibility. Nat Rev Genet. 2007;8:253–62.

    Article  PubMed  CAS  Google Scholar 

  85. Jones PA, Archer TK, Baylin SB, et al. Moving AHEAD with an international human epigenome project. Nature. 2008;454:711–715.

    Google Scholar 

  86. Jain S, Heutink P. From single genes to gene networks: high-throughput-high-content screening for neurological disease. Neuron. 2010;68:207–17.

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

M. F. Mehler is supported by grants from the National Institutes of Health (NS38902, MH66290, NS071571), as well as by the Roslyn and Leslie Goldstein, Harold and Isabel Feld, Mildred and Bernard H. Kayden, F. M. Kirby, and Alpern Family Foundations.

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Qureshi, I.A., Mehler, M.F. Advances in Epigenetics and Epigenomics for Neurodegenerative Diseases. Curr Neurol Neurosci Rep 11, 464–473 (2011). https://doi.org/10.1007/s11910-011-0210-2

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