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Analysis of Brain Epigenome: A Guide to Epigenetic Methods

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Epigenetic Methods in Neuroscience Research

Part of the book series: Neuromethods ((NM,volume 105))

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Abstract

The brain is the most complex tissue in the body. The development and diversity of different brain regions and cell types, as well as neuronal plasticity is controlled by the epigenetic mechanisms. This chapter describes the key epigenetic events at gene promoters, gene bodies, and 3′-untranslated regions that are critical for control of gene expression especially in the brain. Sections 2–4 of the chapter overview different methods for the analysis of DNA methylation (Sect. 2), histone modifications (Sect. 3) and noncoding RNAs (Sect. 4). Each section briefly introduces the main steps and output, advantages, considerations, and limitations of the methods, as well as some alternative approaches further developed from the original method.

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References

  1. Reik W (2007) Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 447(7143):425–432

    Article  CAS  PubMed  Google Scholar 

  2. Feng S, Jacobsen SE, Reik W (2010) Epigenetic reprogramming in plant and animal development. Science 330(6004):622–627

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  3. Kouzarides T (2007) Chromatin modifications and their function. Cell 128:693–705

    Article  CAS  PubMed  Google Scholar 

  4. Amir RE, Van den Veyver IB, Wan M, Tran CQ, Francke U, Zoghbi HY (1999) Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2. Nat Genet 23(2):185–188

    Article  CAS  PubMed  Google Scholar 

  5. Tsankova NM, Berton O, Renthal W, Kumar A, Neve RL, Nestler EJ (2006) Sustained hippocampal chromatin regulation in a mouse model of depression and antidepressant action. Nat Neurosci 9(4):519–525

    Article  CAS  PubMed  Google Scholar 

  6. Schuettengruber B, Martinez AM, Iovino N, Cavalli G (2011) Trithorax group proteins: switching genes on and keeping them active. Nat Rev Mol Cell Biol 12(12):799–814

    Article  CAS  PubMed  Google Scholar 

  7. Keller C, Buhler M (2013) Chromatin-associated ncRNA activities. Chromosome Res 21(6-7):627–641

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  8. Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA et al (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129(7):1311–1323

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  9. Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F et al (2010) Long noncoding RNA as modular scaffold of histone modification complexes. Science 329(5992):689–693

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  10. Lee MG, Wynder C, Cooch N, Shiekhattar R (2005) An essential role for CoREST in nucleosomal histone 3 lysine 4 demethylation. Nature 437(7057):432–435

    CAS  PubMed  Google Scholar 

  11. Abrajano JJ, Qureshi IA, Gokhan S, Zheng D, Bergman A, Mehler MF (2009) REST and CoREST modulate neuronal subtype specification, maturation and maintenance. PLoS One 4(12):e7936

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  12. Rouaux C, Loeffler JP, Boutillier AL (2004) Targeting CREB-binding protein (CBP) loss of function as a therapeutic strategy in neurological disorders. Biochem Pharmacol 68(6):1157–1164

    Article  CAS  PubMed  Google Scholar 

  13. Masri S, Sassone-Corsi P (2010) Plasticity and specificity of the circadian epigenome. Nat Neurosci 13(11):1324–1329

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  14. Ventskovska O, Porkka-Heiskanen T, Karpova NN (2015) Spontaneous sleep-wake cycle and sleep deprivation differently induce Bdnf1, Bdnf4 and Bdnf9a DNA methylation and transcripts levels in the basal forebrain and frontal cortex in rats. J Sleep Res 24:124

    Article  PubMed  Google Scholar 

  15. Bundo M, Toyoshima M, Okada Y, Akamatsu W, Ueda J, Nemoto-Miyauchi T et al (2014) Increased l1 retrotransposition in the neuronal genome in schizophrenia. Neuron 81(2):306–313

    Article  CAS  PubMed  Google Scholar 

  16. Singer T, McConnell MJ, Marchetto MC, Coufal NG, Gage FH (2010) LINE-1 retrotransposons: mediators of somatic variation in neuronal genomes? Trends Neurosci 33(8):345–354

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  17. Muotri AR, Marchetto MC, Coufal NG, Oefner R, Yeo G, Nakashima K et al (2010) L1 retrotransposition in neurons is modulated by MeCP2. Nature 468(7322):443–446

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  18. Yap K, Makeyev EV (2013) Regulation of gene expression in mammalian nervous system through alternative pre-mRNA splicing coupled with RNA quality control mechanisms. Mol Cell Neurosci 56:420–428

    Article  CAS  PubMed  Google Scholar 

  19. Morikawa T, Manabe T (2010) Aberrant regulation of alternative pre-mRNA splicing in schizophrenia. Neurochem Int 57(7):691–704

    Article  CAS  PubMed  Google Scholar 

  20. Gelfman S, Cohen N, Yearim A, Ast G (2013) DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon-intron structure. Genome Res 23(5):789–799

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  21. Fischer U, Englbrecht C, Chari A (2011) Biogenesis of spliceosomal small nuclear ribonucleoproteins. Wiley Interdiscip Rev RNA 2(5):718–731

    Article  CAS  PubMed  Google Scholar 

  22. Lotti F, Imlach WL, Saieva L, Beck ES, le Hao T, Li DK et al (2012) An SMN-dependent U12 splicing event essential for motor circuit function. Cell 151(2):440–454

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  23. Vucicevic D, Schrewe H, Orom UA (2014) Molecular mechanisms of long ncRNAs in neurological disorders. Front Genet 5:48

    PubMed Central  PubMed  Google Scholar 

  24. Chung DW, Rudnicki DD, Yu L, Margolis RL (2011) A natural antisense transcript at the Huntington’s disease repeat locus regulates HTT expression. Hum Mol Genet 20(17):3467–3477

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  25. Sopher BL, Ladd PD, Pineda VV, Libby RT, Sunkin SM, Hurley JB et al (2011) CTCF regulates ataxin-7 expression through promotion of a convergently transcribed, antisense noncoding RNA. Neuron 70(6):1071–1084

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  26. Faghihi MA, Zhang M, Huang J, Modarresi F, Van der Brug MP, Nalls MA et al (2010) Evidence for natural antisense transcript-mediated inhibition of microRNA function. Genome Biol 11(5):R56

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  27. Bredy TW, Lin Q, Wei W, Baker-Andresen D, Mattick JS (2011) MicroRNA regulation of neural plasticity and memory. Neurobiol Learn Mem 96(1):89–94

    Article  CAS  PubMed  Google Scholar 

  28. Minami Y, Ode KL, Ueda HR (2013) Mammalian circadian clock: the roles of transcriptional repression and delay. Handb Exp Pharmacol 217:359–377

    Article  CAS  PubMed  Google Scholar 

  29. Minami Y, Kasukawa T, Kakazu Y, Iigo M, Sugimoto M, Ikeda S et al (2009) Measurement of internal body time by blood metabolomics. Proc Natl Acad Sci U S A 106(24):9890–9895

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  30. Karpova NN, Lindholm JS, Kulesskaya N, Onishchenko N, Vahter M, Popova D et al (2014) TrkB overexpression in mice buffers against memory deficits and depression-like behavior but not all anxiety- and stress-related symptoms induced by developmental exposure to methylmercury. Front Behav Neurosci 8:315

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  31. Fanelli M, Amatori S, Barozzi I, Minucci S (2011) Chromatin immunoprecipitation and high-throughput sequencing from paraffin-embedded pathology tissue. Nat Protoc 6(12):1905–1919

    Article  CAS  PubMed  Google Scholar 

  32. Amatori S, Ballarini M, Faversani A, Belloni E, Fusar F, Bosari S et al (2014) PAT-ChIP coupled with laser microdissection allows the study of chromatin in selected cell populations from paraffin-embedded patient samples. Epigenetics Chromatin 7:18

    Article  PubMed Central  PubMed  Google Scholar 

  33. Lister R, Ecker JR (2009) Finding the fifth base: genome-wide sequencing of cytosine methylation. Genome Res 19(6):959–966

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  34. Bird A (2007) Perceptions of epigenetics. Nature 447(7143):396–398

    Article  CAS  PubMed  Google Scholar 

  35. Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y et al (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324(5929):930–935

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  36. Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW et al (1992) A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci U S A 89(5):1827–1831

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  37. Herman JG, Graff JR, Myohanen S, Nelkin BD, Baylin SB (1996) Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc Natl Acad Sci U S A 93(18):9821–9826

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  38. Hackler L Jr, Masuda T, Oliver VF, Merbs SL, Zack DJ (2012) Use of laser capture microdissection for analysis of retinal mRNA/miRNA expression and DNA methylation. Methods Mol Biol 884:289–304

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  39. Schillebeeckx M, Schrade A, Lobs AK, Pihlajoki M, Wilson DB, Mitra RD (2013) Laser capture microdissection-reduced representation bisulfite sequencing (LCM-RRBS) maps changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse. Nucleic Acids Res 41(11):e116

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  40. Mikeska T, Bock C, El-Maarri O, Hubner A, Ehrentraut D, Schramm J et al (2007) Optimization of quantitative MGMT promoter methylation analysis using pyrosequencing and combined bisulfite restriction analysis. J Mol Diagn 9(3):368–381

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  41. Labonte B, Suderman M, Maussion G, Lopez JP, Navarro-Sanchez L, Yerko V et al (2013) Genome-wide methylation changes in the brains of suicide completers. Am J Psychiatry 170(5):511–520

    Article  PubMed  Google Scholar 

  42. Boyd VL, Moody KI, Karger AE, Livak KJ, Zon G, Burns JW (2006) Methylation-dependent fragment separation: direct detection of DNA methylation by capillary electrophoresis of PCR products from bisulfite-converted genomic DNA. Anal Biochem 354(2):266–273

    Article  CAS  PubMed  Google Scholar 

  43. Kelley K, Chang SJ, Lin SL (2012) Mechanism of repeat-associated microRNAs in fragile X syndrome. Neural Plast 2012:104796

    PubMed Central  PubMed  Google Scholar 

  44. Santoro MR, Bray SM, Warren ST (2012) Molecular mechanisms of fragile X syndrome: a twenty-year perspective. Annu Rev Pathol 7:219–245

    Article  CAS  PubMed  Google Scholar 

  45. Gonzalgo ML, Jones PA (1997) Rapid quantitation of methylation differences at specific sites using methylation-sensitive single nucleotide primer extension (Ms-SNuPE). Nucleic Acids Res 25(12):2529–2531

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  46. Onishchenko N, Karpova N, Sabri F, Castren E, Ceccatelli S (2008) Long-lasting depression-like behavior and epigenetic changes of BDNF gene expression induced by perinatal exposure to methylmercury. J Neurochem 106(3):1378–1387

    Article  CAS  PubMed  Google Scholar 

  47. Wu Z, Luo J, Ge Q, Lu Z (2008) Microarray-based Ms-SNuPE: near-quantitative analysis for a high-throughput DNA methylation. Biosens Bioelectron 23(9):1333–1339

    Article  CAS  PubMed  Google Scholar 

  48. Xiong Z, Laird PW (1997) COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acids Res 25(12):2532–2534

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  49. Brena RM, Auer H, Kornacker K, Plass C (2006) Quantification of DNA methylation in electrofluidics chips (Bio-COBRA). Nat Protoc 1(1):52–58

    Article  PubMed  Google Scholar 

  50. Brena RM, Plass C (2009) Bio-COBRA: absolute quantification of DNA methylation in electrofluidics chips. Methods Mol Biol 507:257–269

    Article  CAS  PubMed  Google Scholar 

  51. Eads CA, Danenberg KD, Kawakami K, Saltz LB, Blake C, Shibata D et al (2000) MethyLight: a high-throughput assay to measure DNA methylation. Nucleic Acids Res 28(8):E32

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  52. Weisenberger DJ, Trinh BN, Campan M, Sharma S, Long TI, Ananthnarayan S et al (2008) DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight. Nucleic Acids Res 36(14):4689–4698

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  53. Tse MY, Ashbury JE, Zwingerman N, King WD, Taylor SA, Pang SC (2011) A refined, rapid and reproducible high resolution melt (HRM)-based method suitable for quantification of global LINE-1 repetitive element methylation. BMC Res Notes 4:565

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  54. Inaba Y, Schwartz CE, Bui QM, Li X, Skinner C, Field M et al (2014) Early detection of fragile X syndrome: applications of a novel approach for improved quantitative methylation analysis in venous blood and newborn blood spots. Clin Chem 60(7):963–973

    Article  CAS  PubMed  Google Scholar 

  55. Weaver IC, Champagne FA, Brown SE, Dymov S, Sharma S, Meaney MJ et al (2005) Reversal of maternal programming of stress responses in adult offspring through methyl supplementation: altering epigenetic marking later in life. J Neurosci 25(47):11045–11054

    Article  CAS  PubMed  Google Scholar 

  56. Champagne FA, Weaver IC, Diorio J, Dymov S, Szyf M, Meaney MJ (2006) Maternal care associated with methylation of the estrogen receptor-alpha1b promoter and estrogen receptor-alpha expression in the medial preoptic area of female offspring. Endocrinology 147(6):2909–2915

    Article  CAS  PubMed  Google Scholar 

  57. Kobow K, Jeske I, Hildebrandt M, Hauke J, Hahnen E, Buslei R et al (2009) Increased reelin promoter methylation is associated with granule cell dispersion in human temporal lobe epilepsy. J Neuropathol Exp Neurol 68(4):356–364

    Article  CAS  PubMed  Google Scholar 

  58. Tost J, Gut IG (2007) DNA methylation analysis by pyrosequencing. Nat Protoc 2(9):2265–2275

    Article  CAS  PubMed  Google Scholar 

  59. Dejeux E, El abdalaoui H, Gut IG, Tost J (2009) Identification and quantification of differentially methylated loci by the pyrosequencing technology. Methods Mol Biol 507:189–205

    Article  CAS  PubMed  Google Scholar 

  60. Wu L, Wang L, Shangguan S, Chang S, Wang Z, Lu X et al (2013) Altered methylation of IGF2 DMR0 is associated with neural tube defects. Mol Cell Biochem 380(1-2):33–42

    Article  CAS  PubMed  Google Scholar 

  61. Godler DE, Tassone F, Loesch DZ, Taylor AK, Gehling F, Hagerman RJ et al (2010) Methylation of novel markers of fragile X alleles is inversely correlated with FMRP expression and FMR1 activation ratio. Hum Mol Genet 19(8):1618–1632

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  62. Godler DE, Inaba Y, Shi EZ, Skinner C, Bui QM, Francis D et al (2013) Relationships between age and epi-genotype of the FMR1 exon 1/intron 1 boundary are consistent with non-random X-chromosome inactivation in FM individuals, with the selection for the unmethylated state being most significant between birth and puberty. Hum Mol Genet 22(8):1516–1524

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  63. Ehrich M, Nelson MR, Stanssens P, Zabeau M, Liloglou T, Xinarianos G et al (2005) Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry. Proc Natl Acad Sci U S A 102(44):15785–15790

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  64. Abdolmaleky HM, Nohesara S, Ghadirivasfi M, Lambert AW, Ahmadkhaniha H, Ozturk S et al (2014) DNA hypermethylation of serotonin transporter gene promoter in drug naive patients with schizophrenia. Schizophr Res 152(2-3):373–380

    Article  PubMed  Google Scholar 

  65. Oda M, Glass JL, Thompson RF, Mo Y, Olivier EN, Figueroa ME et al (2009) High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers. Nucleic Acids Res 37(12):3829–3839

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  66. Preusser M, Plumer S, Dirnberger E, Hainfellner JA, Mannhalter C (2010) Fixation of brain tumor biopsy specimens with RCL2 results in well-preserved histomorphology, immunohistochemistry and nucleic acids. Brain Pathol 20(6):1010–1020

    Article  CAS  PubMed  Google Scholar 

  67. Pulverer W, Hofner M, Preusser M, Dirnberger E, Hainfellner JA, Weinhaeusel A (2014) A simple quantitative diagnostic alternative for MGMT DNA-methylation testing on RCL2 fixed paraffin embedded tumors using restriction coupled qPCR. Clin Neuropathol 33(1):50–60

    Article  PubMed  Google Scholar 

  68. Melnikov AA, Gartenhaus RB, Levenson AS, Motchoulskaia NA, Levenson Chernokhvostov VV (2005) MSRE-PCR for analysis of gene-specific DNA methylation. Nucleic Acids Res 33(10):e93

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  69. Hellman A, Chess A (2010) Extensive sequence-influenced DNA methylation polymorphism in the human genome. Epigenetics Chromatin 3(1):11

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  70. Szwagierczak A, Bultmann S, Schmidt CS, Spada F, Leonhardt H (2010) Sensitive enzymatic quantification of 5-hydroxymethylcytosine in genomic DNA. Nucleic Acids Res 38(19):e181

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  71. Khulan B, Thompson RF, Ye K, Fazzari MJ, Suzuki M, Stasiek E et al (2006) Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res 16(8):1046–1055

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  72. Rauch T, Pfeifer GP (2005) Methylated-CpG island recovery assay: a new technique for the rapid detection of methylated-CpG islands in cancer. Lab Invest 85(9):1172–1180

    Article  CAS  PubMed  Google Scholar 

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

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  74. Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, Lam WL et al (2005) Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37(8):853–862

    Article  CAS  PubMed  Google Scholar 

  75. Ruzov A, Tsenkina Y, Serio A, Dudnakova T, Fletcher J, Bai Y et al (2011) Lineage-specific distribution of high levels of genomic 5-hydroxymethylcytosine in mammalian development. Cell Res 21(9):1332–1342

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  76. Li W, Liu M (2011) Distribution of 5-hydroxymethylcytosine in different human tissues. J Nucl Acids 2011:870726

    Article  CAS  Google Scholar 

  77. Cortese R, Lewin J, Backdahl L, Krispin M, Wasserkort R, Eckhardt F et al (2011) Genome-wide screen for differential DNA methylation associated with neural cell differentiation in mouse. PLoS One 6(10):e26002

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  78. Melka MG, Laufer BI, McDonald P, Castellani CA, Rajakumar N, O’Reilly R et al (2014) The effects of olanzapine on genome-wide DNA methylation in the hippocampus and cerebellum. Clin Epigenet 6(1):1

    Article  CAS  Google Scholar 

  79. Brinkman AB, Simmer F, Ma K, Kaan A, Zhu J, Stunnenberg HG (2010) Whole-genome DNA methylation profiling using MethylCap-seq. Methods 52(3):232–236

    Article  CAS  PubMed  Google Scholar 

  80. Bock C, Tomazou EM, Brinkman AB, Muller F, Simmer F, Gu H et al (2010) Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol 28(10):1106–1114

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  81. Xiao Y, Camarillo C, Ping Y, Arana TB, Zhao H, Thompson PM et al (2014) The DNA methylome and transcriptome of different brain regions in schizophrenia and bipolar disorder. PLoS One 9(4):e95875

    Article  PubMed Central  PubMed  Google Scholar 

  82. Yegnasubramanian S, Lin X, Haffner MC, DeMarzo AM, Nelson WG (2006) Combination of methylated-DNA precipitation and methylation-sensitive restriction enzymes (COMPARE-MS) for the rapid, sensitive and quantitative detection of DNA methylation. Nucleic Acids Res 34(3):e19

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  83. Lee DH, Tran DA, Singh P, Oates N, Rivas GE, Larson GP et al (2011) MIRA-SNuPE, a quantitative, multiplex method for measuring allele-specific DNA methylation. Epigenetics 6(2):212–223

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  84. Globisch D, Munzel M, Muller M, Michalakis S, Wagner M, Koch S et al (2010) Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PLoS One 5(12):e15367

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  85. Almeida RD, Sottile V, Loose M, De Sousa PA, Johnson AD, Ruzov A (2012) Semi-quantitative immunohistochemical detection of 5-hydroxymethyl-cytosine reveals conservation of its tissue distribution between amphibians and mammals. Epigenetics 7(2):137–140

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  86. Kok RM, Smith DE, Barto R, Spijkerman AM, Teerlink T, Gellekink HJ et al (2007) Global DNA methylation measured by liquid chromatography-tandem mass spectrometry: analytical technique, reference values and determinants in healthy subjects. Clin Chem Lab Med 45(7):903–911

    Article  CAS  PubMed  Google Scholar 

  87. Kaas GA, Zhong C, Eason DE, Ross DL, Vachhani RV, Ming GL et al (2013) TET1 controls CNS 5-methylcytosine hydroxylation, active DNA demethylation, gene transcription, and memory formation. Neuron 79(6):1086–1093

    Article  CAS  PubMed  Google Scholar 

  88. Onishchenko N, Karpova NN, Castren E (2012) Epigenetics of environmental contaminants. In: Current topics neurotoxicity. Springer, New York, NY, pp 199–218

    Google Scholar 

  89. Bernstein BE, Meissner A, Lander ES (2007) The mammalian epigenome. Cell 128(4):669–681

    Article  CAS  PubMed  Google Scholar 

  90. O’Neill LP, Turner BM (2003) Immunoprecipitation of native chromatin: NChIP. Methods 31(1):76–82

    Article  PubMed  CAS  Google Scholar 

  91. Gilfillan GD, Hughes T, Sheng Y, Hjorthaug HS, Straub T, Gervin K et al (2012) Limitations and possibilities of low cell number ChIP-seq. BMC Genomics 13:645

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  92. Karpova NN, Rantamaki T, Di Lieto A, Lindemann L, Hoener MC, Castren E (2010) Darkness reduces BDNF expression in the visual cortex and induces repressive chromatin remodeling at the BDNF gene in both hippocampus and visual cortex. Cell Mol Neurobiol 30(7):1117–1123

    Article  CAS  PubMed  Google Scholar 

  93. Shankaranarayanan P, Mendoza-Parra MA, Walia M, Wang L, Li N, Trindade LM et al (2011) Single-tube linear DNA amplification (LinDA) for robust ChIP-seq. Nat Methods 8(7):565–567

    Article  CAS  PubMed  Google Scholar 

  94. Karpova NN (2014) Role of BDNF epigenetics in activity-dependent neuronal plasticity. Neuropharmacology 76(Pt C):709–718

    Article  CAS  PubMed  Google Scholar 

  95. Liu J, Carmell MA, Rivas FV, Marsden CG, Thomson JM, Song JJ et al (2004) Argonaute2 is the catalytic engine of mammalian RNAi. Science 305(5689):1437–1441

    Article  CAS  PubMed  Google Scholar 

  96. Krol J, Loedige I, Filipowicz W (2010) The widespread regulation of microRNA biogenesis, function and decay. Nat Rev Genet 11(9):597–610

    CAS  PubMed  Google Scholar 

  97. Ma B, Culver BP, Baj G, Tongiorgi E, Chao MV, Tanese N (2010) Localization of BDNF mRNA with the Huntington’s disease protein in rat brain. Mol Neurodegener 5:22

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  98. Nelson PT, De Planell-Saguer M, Lamprinaki S, Kiriakidou M, Zhang P, O’Doherty U et al (2007) A novel monoclonal antibody against human Argonaute proteins reveals unexpected characteristics of miRNAs in human blood cells. RNA 13(10):1787–1792

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  99. Chi SW, Zang JB, Mele A, Darnell RB (2009) Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460(7254):479–486

    PubMed Central  CAS  PubMed  Google Scholar 

  100. Konig J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B et al (2010) iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol 17(7):909–915

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  101. Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P et al (2010) Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141(1):129–141

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  102. Erhard F, Dolken L, Jaskiewicz L, Zimmer R (2013) PARma: identification of microRNA target sites in AGO-PAR-CLIP data. Genome Biol 14(7):R79

    Article  PubMed Central  PubMed  Google Scholar 

  103. Viader A, Chang LW, Fahrner T, Nagarajan R, Milbrandt J (2011) MicroRNAs modulate Schwann cell response to nerve injury by reinforcing transcriptional silencing of dedifferentiation-related genes. J Neurosci 31(48):17358–17369

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  104. Eipper-Mains JE, Eipper BA, Mains RE (2012) Global approaches to the role of miRNAs in drug-induced changes in gene expression. Front Genet 3:109

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  105. Bali KK, Hackenberg M, Lubin A, Kuner R, Devor M (2014) Sources of individual variability: miRNAs that predispose to neuropathic pain identified using genome-wide sequencing. Mol Pain 10:22

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  106. Huang JC, Babak T, Corson TW, Chua G, Khan S, Gallie BL et al (2007) Using expression profiling data to identify human microRNA targets. Nat Methods 4(12):1045–1049

    Article  CAS  PubMed  Google Scholar 

  107. Wang WX, Wilfred BR, Hu Y, Stromberg AJ, Nelson PT (2010) Anti-Argonaute RIP-Chip shows that miRNA transfections alter global patterns of mRNA recruitment to microribonucleoprotein complexes. RNA 16(2):394–404

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  108. Erhard F, Dolken L, Zimmer R (2013) RIP-chip enrichment analysis. Bioinformatics 29(1):77–83

    Article  CAS  PubMed  Google Scholar 

  109. Kloosterman WP, Wienholds E, de Bruijn E, Kauppinen S, Plasterk RH (2006) In situ detection of miRNAs in animal embryos using LNA-modified oligonucleotide probes. Nat Methods 3(1):27–29

    Article  CAS  PubMed  Google Scholar 

  110. Herzer S, Silahtaroglu A, Meister B (2012) Locked nucleic acid-based in situ hybridisation reveals miR-7a as a hypothalamus-enriched microRNA with a distinct expression pattern. J Neuroendocrinol 24(12):1492–1504

    Article  CAS  PubMed  Google Scholar 

  111. Pena JT, Sohn-Lee C, Rouhanifard SH, Ludwig J, Hafner M, Mihailovic A et al (2009) miRNA in situ hybridization in formaldehyde and EDC-fixed tissues. Nat Methods 6(2):139–141

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  112. Soe MJ, Moller T, Dufva M, Holmstrom K (2011) A sensitive alternative for microRNA in situ hybridizations using probes of 2′-O-methyl RNA + LNA. J Histochem Cytochem 59(7):661–672

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  113. Weaver IC, Cervoni N, Champagne FA, D’Alessio AC, Sharma S, Seckl JR et al (2004) Epigenetic programming by maternal behavior. Nat Neurosci 7(8):847–854

    Article  CAS  PubMed  Google Scholar 

  114. Szyf M, Weaver IC, Champagne FA, Diorio J, Meaney MJ (2005) Maternal programming of steroid receptor expression and phenotype through DNA methylation in the rat. Front Neuroendocrinol 26(3–4):139–162

    Article  CAS  PubMed  Google Scholar 

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  1. Neuroscience Center, University of Helsinki, Viikinkaari 4, Helsinki, 00790, Finland

    Nina N. Karpova

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  1. Nina N. Karpova
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Correspondence to Nina N. Karpova .

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  1. Neuroscience Center, University of Helsinki, Helsinki, Finland

    Nina Karpova

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Karpova, N.N. (2016). Analysis of Brain Epigenome: A Guide to Epigenetic Methods. In: Karpova, N. (eds) Epigenetic Methods in Neuroscience Research. Neuromethods, vol 105. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2754-8_2

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  • DOI: https://doi.org/10.1007/978-1-4939-2754-8_2

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2753-1

  • Online ISBN: 978-1-4939-2754-8

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