Skip to main content
SpringerLink
Log in
Book cover

Environmental Epigenomics in Health and Disease pp 115–165Cite as

Epigenomic and Noncoding RNA Regulation in Addictive Processes

  • Chapter
  • First Online:

  • 1524 Accesses

Part of the book series: Epigenetics and Human Health ((EHH))

Abstract

The phenotypic effects of drugs of abuse are partially mediated by transcriptional and epigenetic regulatory mechanisms. This chapter will provide a brief overview of substance abuse and then focus on the roles of three epigenetic regulatory mechanisms in addictive processes: histone modifications, DNA modifications, and noncoding RNAs. This chapter will conclude with a focus on three other important areas: (1) the potential for long-lasting epigenetic effects due to drugs of abuse, (2) obstacles and opportunities in this scientific area as they pertain to addiction biology, and (3) the potential for translating epigenomic and noncoding RNA discoveries into improvements in human health and the treatment of substance use disorders.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Abbreviations

ADAR:

Adenosine deaminase

Ago2:

Argonaute 2

AML:

Acute myeloid leukemia

BDNF:

Brain-derived neurotrophic factor

BRD4:

Bromodomain-containing protein 4

Brg1:

Brahma-related Gene 1

caC:

5-carboxylcytosine

CBP:

CREB-binding protein

Cdk5:

Cyclin-dependent kinase 5

CHD:

Chromodomain helicase DNA-binding protein

ChIA-PET:

Chromatin interaction analyses – paired end tags

ChIP-seq:

Chromatin immunoprecipitation-sequencing assay

CPP assay:

Conditioned place preference assay

CREB:

cAMP-response element-binding protein

D1R:

Dopamine 1 receptor

DARPP-32:

Dopamine- and cyclic-AMP-regulated phosphoprotein 32

DAT:

Dopamine transporter

DNMT:

DNA methyltransferase

DOHaD:

Developmental origins of health and disease

EMX2OS:

EMX2 opposite strand

ENCODE:

Encyclopedia of DNA elements

eRNA:

Enhancer RNA

EWAS:

Epigenome-wide association studies

fC:

5-formylcytosine

GABA:

Gamma-aminobutyric acid

GAD67:

Glutamic acid decarboxylase 67

GFP:

Green fluorescent protein

GluR2:

Glutamate receptor 2

GWAS:

Genome-wide association studies

HAT:

Histone acetyltransferase

HDAC:

Histone deacetylase

Hi-C:

Chromatin conformation capture assay

Histone modifications:

Example H3K4me3 = histone H3 with trimethylated lysine-4

hmC:

5-hydroxymethylcytosine

HOTAIR:

HOX antisense intergenic RNA

HOTTIP:

HOXA transcript at the distal tip

IGFBP-3:

Insulin-like growth factor binding protein 3

JARID1C:

Jumonji AT-rich interactive domain 1C protein

lincRNA:

Large intervening noncoding RNA

LINE:

Long interspersed nuclear element

MBD:

Methyl-CpG-binding domain protein

mC:

5-methylcytosine

MeCP2:

Methyl CpG-binding protein 2

MEG3:

Maternally expressed Gene 3 ncRNA

methylC-seq:

5-methylcytosine sequencing assay

mGluR5:

Metabotropic glutamate receptor 5

MGMT:

Methyl guanine DNA methyltransferase

MIAT:

Myocardial infarction associated transcript

miRNA:

MicroRNA

MOR:

Mu opioid receptor

mPFC:

Medial prefrontal cortex

MSK1:

Mitogen and stress-activated protein kinase 1

NAc:

Nucleus accumbens

nAChR:

Nicotinic acetylcholine receptor

ncRNA:

Noncoding RNA

NEAT1:

Nuclear paraspeckle assembly transcript 1 ncRNA

NEAT2:

Nuclear paraspeckle assembly transcript 2 ncRNA

PET:

Positron emission tomography

PFC:

Prefrontal cortex

PHD:

Pleckstrin homology domain

piRNA:

Piwi-interacting RNA

PRC2:

Polycomb repressive complex 2

RIP-seq:

RNA immunoprecipitation sequencing assay

SAHA:

Suberoylanilide hydroxamic acid

SINE:

Short interspersed nuclear element

siRNA:

Small interfering RNA

SIRT1:

Sirtuin 1

SNP:

Single-nucleotide polymorphism

SPRED1:

Sprouty-related EVH1 domain containing 1 protein

SUD:

Substance abuse disorder

TORC:

Transducers of regulated CREB

TPH2:

Tryptophan hydroxylase-2

Uhrf1:

Ubiquitin-like containing PHD and RING finger domains 1 protein

VTA:

Ventral tegmental area

WD40 domain:

WD dipeptide-containing domain

References

  • Adrian J, Farrona S, Reimer JJ, Albani MC, Coupland G, Turck F (2010) cis-Regulatory elements and chromatin state coordinately control temporal and spatial expression of FLOWERING LOCUS T in Arabidopsis. Plant Cell 22:1425–1440

    Article  PubMed  CAS  Google Scholar 

  • Akbarian S, Huang HS (2009) Epigenetic regulation in human brain-focus on histone lysine methylation. Biol Psychiatry 65:198–203

    Article  PubMed  CAS  Google Scholar 

  • Allen ND, Logan K, Lally G, Drage DJ, Norris ML, Keverne EB (1995) Distribution of parthenogenetic cells in the mouse brain and their influence on brain development and behavior. Proc Natl Acad Sci U S A 92:10782–10786

    Article  PubMed  CAS  Google Scholar 

  • Almeida AM, Murakami Y, Baker A, Maeda Y, Roberts IA, Kinoshita T, Layton DM, Karadimitris A (2007) Targeted therapy for inherited GPI deficiency. N Engl J Med 356:1641–1647

    Article  PubMed  CAS  Google Scholar 

  • Ambermoon P, Carter A, Hall WD, Dissanayaka NN, O’Sullivan JD (2011) Impulse control disorders in patients with Parkinson’s disease receiving dopamine replacement therapy: evidence and implications for the addictions field. Addiction 106:283–293

    Article  PubMed  Google Scholar 

  • American Psychiatric Association (2000) Diagnostic and statistical manual of mental disorders, 4th edn. American Psychiatric Association, Washington, DC

    Google Scholar 

  • 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 23:185–188

    Article  PubMed  CAS  Google Scholar 

  • Anier K, Malinovskaja K, Aonurm-Helm A, Zharkovsky A, Kalda A (2010) DNA methylation regulates cocaine-induced behavioral sensitization in mice. Neuropsychopharmacology 35:2450–2461

    Article  PubMed  CAS  Google Scholar 

  • Austin CP, Brady LS, Insel TR, Collins FS (2004) NIH molecular libraries initiative. Science 306:1138–1139

    Article  PubMed  CAS  Google Scholar 

  • Avena NM, Rada P, Hoebel BG (2008) Evidence for sugar addiction: behavioral and neurochemical effects of intermittent, excessive sugar intake. Neurosci Biobehav Rev 32:20–39

    Article  PubMed  CAS  Google Scholar 

  • Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K (2007) High-resolution profiling of histone methylations in the human genome. Cell 129:823–837

    Article  PubMed  CAS  Google Scholar 

  • Bellet MM, Sassone-Corsi P (2010) Mammalian circadian clock and metabolism – the epigenetic link. J Cell Sci 123:3837–3848

    Article  PubMed  CAS  Google Scholar 

  • Bernstein BE, Kamal M, Lindblad-Toh K, Bekiranov S, Bailey DK, Huebert DJ, McMahon S, Karlsson EK, Kulbokas EJ III, Gingeras TR, Schreiber SL, Lander ES (2005) Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120:169–181

    Article  PubMed  CAS  Google Scholar 

  • Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker JR, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS, Thomson JA (2010) The NIH roadmap epigenomics mapping consortium. Nat Biotechnol 28:1045–1048

    Article  PubMed  CAS  Google Scholar 

  • Bialer M, Yagen B (2007) Valproic acid: second generation. Neurotherapeutics 4:130–137

    Article  PubMed  CAS  Google Scholar 

  • Birney E (2011) Chromatin and heritability: how epigenetic studies can complement genetic approaches. Trends Genet 27:172–176

    Article  PubMed  CAS  Google Scholar 

  • Bogdanovic O, Veenstra GJ (2009) DNA methylation and methyl-CpG binding proteins: developmental requirements and function. Chromosoma 118:549–565

    Article  PubMed  CAS  Google Scholar 

  • Bonasio R, Lecona E, Reinberg D (2010) MBT domain proteins in development and disease. Semin Cell Dev Biol 21:221–230

    Article  PubMed  CAS  Google Scholar 

  • Bonsch D, Lenz B, Reulbach U, Kornhuber J, Bleich S (2004) Homocysteine associated genomic DNA hypermethylation in patients with chronic alcoholism. J Neural Transm 111:1611–1616

    Article  PubMed  CAS  Google Scholar 

  • Brami-Cherrier K, Valjent E, Herve D, Darragh J, Corvol JC, Pages C, Arthur SJ, Girault JA, Caboche J (2005) Parsing molecular and behavioral effects of cocaine in mitogen- and stress-activated protein kinase-1-deficient mice. J Neurosci 25:11444–11454

    Article  PubMed  CAS  Google Scholar 

  • Bredy TW, Sun YE, Kobor MS (2010) How the epigenome contributes to the development of psychiatric disorders. Dev Psychobiol 52:331–342

    Article  PubMed  CAS  Google Scholar 

  • Briand LA, Blendy JA (2010) Molecular and genetic substrates linking stress and addiction. Brain Res 1314:219–234

    Article  PubMed  CAS  Google Scholar 

  • Brown E, Malakar S, Krebs JE (2007) How many remodelers does it take to make a brain? Diverse and cooperative roles of ATP-dependent chromatin-remodeling complexes in development. Biochem Cell Biol 85:444–462

    Article  PubMed  CAS  Google Scholar 

  • Buckland PR (2008) Will we ever find the genes for addiction? Addiction 103:1768–1776

    Article  PubMed  Google Scholar 

  • Buka SL, Shenassa ED, Niaura R (2003) Elevated risk of tobacco dependence among offspring of mothers who smoked during pregnancy: a 30-year prospective study. Am J Psychiatry 160:1978–1984

    Article  PubMed  Google Scholar 

  • Byrnes EM (2005) Transgenerational consequences of adolescent morphine exposure in female rats: effects on anxiety-like behaviors and morphine sensitization in adult offspring. Psychopharmacology 182:537–544

    Article  PubMed  CAS  Google Scholar 

  • Byrnes JJ, Babb JA, Scanlan VF, Byrnes EM (2011) Adolescent opioid exposure in female rats: transgenerational effects on morphine analgesia and anxiety-like behavior in adult offspring. Behav Brain Res 218:200–205

    Article  PubMed  CAS  Google Scholar 

  • Caldji C, Hellstrom IC, Zhang TY, Diorio J, Meaney MJ (2011) Environmental regulation of the neural epigenome. FEBS Lett 585:2049–2058

    Article  PubMed  CAS  Google Scholar 

  • Campos EI, Reinberg D (2009) Histones: annotating chromatin. Annu Rev Genet 43:559–599

    Article  PubMed  CAS  Google Scholar 

  • Cantara WA, Crain PF, Rozenski J, McCloskey JA, Harris KA, Zhang X, Vendeix FA, Fabris D, Agris PF (2011) The RNA modification database, RNAMDB: 2011 update. Nucleic Acids Res 39:D195–D201

    Article  PubMed  CAS  Google Scholar 

  • Carlezon WA Jr, Duman RS, Nestler EJ (2005) The many faces of CREB. Trends Neurosci 28:436–445

    Article  PubMed  CAS  Google Scholar 

  • Carroll KM, Onken LS (2005) Behavioral therapies for drug abuse. Am J Psychiatry 162:1452–1460

    Article  PubMed  Google Scholar 

  • Caspi A, Moffitt TE, Cannon M, McClay J, Murray R, Harrington H, Taylor A, Arseneault L, Williams B, Braithwaite A, Poulton R, Craig IW (2005) Moderation of the effect of adolescent-onset cannabis use on adult psychosis by a functional polymorphism in the catechol-O-methyltransferase gene: longitudinal evidence of a gene X environment interaction. Biol Psychiatry 57:1117–1127

    Article  PubMed  CAS  Google Scholar 

  • Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, National Center for Chronic Disease Prevention and Health Promotion, Office on Smoking and Health (2007) Best practices for comprehensive tobacco control programs. GPO, Atlanta

    Google Scholar 

  • Champagne FA (2008) Epigenetic mechanisms and the transgenerational effects of maternal care. Front Neuroendocrinol 29:386–397

    Article  PubMed  CAS  Google Scholar 

  • Champagne FA, Meaney MJ (2007) Transgenerational effects of social environment on variations in maternal care and behavioral response to novelty. Behav Neurosci 121:1353–1363

    Article  PubMed  Google Scholar 

  • Chandrasekar V, Dreyer JL (2011) Regulation of MiR-124, Let-7d, and MiR-181a in the accumbens affects the expression, extinction, and reinstatement of cocaine-induced conditioned place preference. Neuropsychopharmacology 36:1149–1164

    Article  PubMed  CAS  Google Scholar 

  • Chao HT, Chen H, Samaco RC, Xue M, Chahrour M, Yoo J, Neul JL, Gong S, Lu HC, Heintz N, Ekker M, Rubenstein JL, Noebels JL, Rosenmund C, Zoghbi HY (2010) Dysfunction in GABA signalling mediates autism-like stereotypies and Rett syndrome phenotypes. Nature 468:263–269

    Article  PubMed  CAS  Google Scholar 

  • Chen WG, Chang Q, Lin Y, Meissner A, West AE, Griffith EC, Jaenisch R, Greenberg ME (2003) Derepression of BDNF transcription involves calcium-dependent phosphorylation of MeCP2. Science 302:885–889

    Article  PubMed  CAS  Google Scholar 

  • Cheung I, Shulha HP, Jiang Y, Matevossian A, Wang J, Weng Z, Akbarian S (2010) Developmental regulation and individual differences of neuronal H3K4me3 epigenomes in the prefrontal cortex. Proc Natl Acad Sci U S A 107:8824–8829

    Article  PubMed  CAS  Google Scholar 

  • Cicero TJ, Adams ML, Giordano A, Miller BT, O’Connor L, Nock B (1991) Influence of morphine exposure during adolescence on the sexual maturation of male rats and the development of their offspring. J Pharmacol Exp Ther 256:1086–1093

    PubMed  CAS  Google Scholar 

  • Cipriany BR, Zhao R, Murphy PJ, Levy SL, Tan CP, Craighead HG, Soloway PD (2010) Single molecule epigenetic analysis in a nanofluidic channel. Anal Chem 82:2480–2487

    Article  PubMed  CAS  Google Scholar 

  • Cortellino S, Xu J, Sannai M, Moore R, Caretti E, Cigliano A, Le CM, Devarajan K, Wessels A, Soprano D, Abramowitz LK, Bartolomei MS, Rambow F, Bassi MR, Bruno T, Fanciulli M, Renner C, Klein-Szanto AJ, Matsumoto Y, Kobi D, Davidson I, Alberti C, Larue L, Bellacosa A (2011) Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair. Cell 146:67–79

    Article  PubMed  CAS  Google Scholar 

  • Crosio C, Heitz E, Allis CD, Borrelli E, Sassone-Corsi P (2003) Chromatin remodeling and neuronal response: multiple signaling pathways induce specific histone H3 modifications and early gene expression in hippocampal neurons. J Cell Sci 116:4905–4914

    Article  PubMed  CAS  Google Scholar 

  • Czech B, Hannon GJ (2011) Small RNA sorting: matchmaking for Argonautes. Nat Rev Genet 12:19–31

    Article  PubMed  CAS  Google Scholar 

  • Dalley JW, Everitt BJ, Robbins TW (2011) Impulsivity, compulsivity, and top-down cognitive control. Neuron 69:680–694

    Article  PubMed  CAS  Google Scholar 

  • Davis TH, Cuellar TL, Koch SM, Barker AJ, Harfe BD, McManus MT, Ullian EM (2008) Conditional loss of Dicer disrupts cellular and tissue morphogenesis in the cortex and hippocampus. J Neurosci 28:4322–4330

    Article  PubMed  CAS  Google Scholar 

  • Day JJ, Sweatt JD (2010) DNA methylation and memory formation. Nat Neurosci 13:1319–1323

    Article  PubMed  CAS  Google Scholar 

  • Day JJ, Sweatt JD (2011) Epigenetic mechanisms in cognition. Neuron 70:813–829

    Article  PubMed  CAS  Google Scholar 

  • de Ibanez CI, Cortes-Sempere M, Moratilla C, Machado-Pinilla R, Rodriguez-Fanjul V, Manguan-Garcia C, Cejas P, Lopez-Rios F, Paz-Ares L, de CastroCarpeño J, Nistal M, Belda-Iniesta C, Perona R (2010) IGFBP-3 hypermethylation-derived deficiency mediates cisplatin resistance in non-small-cell lung cancer. Oncogene 29:1681–1690

    Article  CAS  Google Scholar 

  • Dekker FJ, Haisma HJ (2009) Histone acetyl transferases as emerging drug targets. Drug Discov Today 14:942–948

    Article  PubMed  CAS  Google Scholar 

  • Deng JV, Rodriguiz RM, Hutchinson AN, Kim IH, Wetsel WC, West AE (2010) MeCP2 in the nucleus accumbens contributes to neural and behavioral responses to psychostimulants. Nat Neurosci 13:1128–1136

    Article  PubMed  CAS  Google Scholar 

  • Dietz DM, Laplant Q, Watts EL, Hodes GE, Russo SJ, Feng J, Oosting RS, Vialou V, Nestler EJ (2011) Paternal transmission of stress-induced pathologies. Biol Psychiatry 70:408–414

    Article  PubMed  Google Scholar 

  • Doyle JP, Dougherty JD, Heiman M, Schmidt EF, Stevens TR, Ma G, Bupp S, Shrestha P, Shah RD, Doughty ML, Gong S, Greengard P, Heintz N (2008) Application of a translational profiling approach for the comparative analysis of CNS cell types. Cell 135:749–762

    Article  PubMed  CAS  Google Scholar 

  • Dracheva S, Patel N, Woo DA, Marcus SM, Siever LJ, Haroutunian V (2008) Increased serotonin 2C receptor mRNA editing: a possible risk factor for suicide. Mol Psychiatry 13:1001–1010

    Article  PubMed  CAS  Google Scholar 

  • Dracheva S, Lyddon R, Barley K, Marcus SM, Hurd YL, Byne WM (2009) Editing of serotonin 2C receptor mRNA in the prefrontal cortex characterizes high-novelty locomotor response behavioral trait. Neuropsychopharmacology 34:2237–2251

    Article  PubMed  CAS  Google Scholar 

  • Dulac C (2010) Brain function and chromatin plasticity. Nature 465:728–735

    Article  PubMed  CAS  Google Scholar 

  • Egelhofer TA, Minoda A, Klugman S, Lee K, Kolasinska-Zwierz P, Alekseyenko AA, Cheung MS, Day DS, Gadel S, Gorchakov AA, Gu T, Kharchenko PV, Kuan S, Latorre I, Linder-Basso D, Luu Y, Ngo Q, Perry M, Rechtsteiner A, Riddle NC, Schwartz YB, Shanower GA, Vielle A, Ahringer J, Elgin SC, Kuroda MI, Pirrotta V, Ren B, Strome S, Park PJ, Karpen GH, Hawkins RD, Lieb JD (2011) An assessment of histone-modification antibody quality. Nat Struct Mol Biol 18:91–93

    Article  PubMed  CAS  Google Scholar 

  • Eipper-Mains JE, Kiraly DD, Palakodeti D, Mains RE, Eipper BA, Graveley BR (2011) microRNA-Seq reveals cocaine-regulated expression of striatal microRNAs. RNA 17:1529–1543

    Article  PubMed  CAS  Google Scholar 

  • Ernst J, Kellis M (2010) Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol 28:817–825

    Article  PubMed  CAS  Google Scholar 

  • Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, Ku M, Durham T, Kellis M, Bernstein BE (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473:43–49

    Article  PubMed  CAS  Google Scholar 

  • Eskiw CH, Cope NF, Clay I, Schoenfelder S, Nagano T, Fraser P (2010) Transcription factories and nuclear organization of the genome. Cold Spring Harb Symp Quant Biol 75:501–506

    Article  PubMed  CAS  Google Scholar 

  • Espinoza CA, Ren B (2011) Mapping higher order structure of chromatin domains. Nat Genet 43:615–616

    Article  PubMed  CAS  Google Scholar 

  • Feng J, Fan G (2009) The role of DNA methylation in the central nervous system and neuropsychiatric disorders. Int Rev Neurobiol 89:67–84

    Article  PubMed  CAS  Google Scholar 

  • Ferguson-Smith AC (2011) Genomic imprinting: the emergence of an epigenetic paradigm. Nat Rev Genet 12:565–575

    Article  PubMed  CAS  Google Scholar 

  • Ficz G, Branco MR, Seisenberger S, Santos F, Krueger F, Hore TA, Marques CJ, Andrews S, Reik W (2011) Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature 473:398–402

    Article  PubMed  CAS  Google Scholar 

  • Fischer A, Sananbenesi F, Wang X, Dobbin M, Tsai LH (2007) Recovery of learning and memory is associated with chromatin remodelling. Nature 447:178–182

    Article  PubMed  CAS  Google Scholar 

  • Fischer A, Sananbenesi F, Mungenast A, Tsai LH (2010) Targeting the correct HDAC(s) to treat cognitive disorders. Trends Pharmacol Sci 31:605–617

    Article  PubMed  CAS  Google Scholar 

  • Fiskus W, Wang Y, Sreekumar A, Buckley KM, Shi H, Jillella A, Ustun C, Rao R, Fernandez P, Chen J, Balusu R, Koul S, Atadja P, Marquez VE, Bhalla KN (2009) Combined epigenetic therapy with the histone methyltransferase EZH2 inhibitor 3-deazaneplanocin A and the histone deacetylase inhibitor panobinostat against human AML cells. Blood 114:2733–2743

    Article  PubMed  CAS  Google Scholar 

  • Fleckenstein AE, Volz TJ, Riddle EL, Gibb JW, Hanson GR (2007) New insights into the mechanism of action of amphetamines. Annu Rev Pharmacol Toxicol 47:681–698

    Article  PubMed  CAS  Google Scholar 

  • Fleischman RA, Cambell JL, Richardson CC (1976) Modification and restriction of T-even bacteriophages. In vitro degradation of deoxyribonucleic acid containing 5-hydroxymethylctosine. J Biol Chem 251:1561–1570

    PubMed  CAS  Google Scholar 

  • Franklin TB, Russig H, Weiss IC, Graff J, Linder N, Michalon A, Vizi S, Mansuy IM (2010) Epigenetic transmission of the impact of early stress across generations. Biol Psychiatry 68:408–415

    Article  PubMed  Google Scholar 

  • Frauer C, Hoffmann T, Bultmann S, Casa V, Cardoso MC, Antes I, Leonhardt H (2011) Recognition of 5-hydroxymethylcytosine by the Uhrf1 SRA domain. PLoS One 6:e21306

    Article  PubMed  CAS  Google Scholar 

  • Freed WJ, Chen J, Backman CM, Schwartz CM, Vazin T, Cai J, Spivak CE, Lupica CR, Rao MS, Zeng X (2008) Gene expression profile of neuronal progenitor cells derived from hESCs: activation of chromosome 11p15.5 and comparison to human dopaminergic neurons. PLoS One 3:e1422

    Article  PubMed  CAS  Google Scholar 

  • Friedler G (1978) Pregestational administration of morphine sulfate to female mice: longterm effects on the development of subsequent progeny. J Pharmacol Exp Ther 205:33–39

    PubMed  CAS  Google Scholar 

  • Friedler G, Cochin J (1972) Growth retardation in offspring of female rats treated with morphine prior to conception. Science 175:654–656

    Article  PubMed  CAS  Google Scholar 

  • Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH, Chew EG, Huang PY, Welboren WJ, Han Y, Ooi HS, Ariyaratne PN, Vega VB, Luo Y, Tan PY, Choy PY, Wansa KD, Zhao B, Lim KS, Leow SC, Yow JS, Joseph R, Li H, Desai KV, Thomsen JS, Lee YK, Karuturi RK, Herve T, Bourque G, Stunnenberg HG, Ruan X, Cacheux-Rataboul V, Sung WK, Liu ET, Wei CL, Cheung E, Ruan Y (2009) An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 462:58–64

    Article  PubMed  CAS  Google Scholar 

  • Gao J, Wang WY, Mao YW, Graff J, Guan JS, Pan L, Mak G, Kim D, Su SC, Tsai LH (2010) A novel pathway regulates memory and plasticity via SIRT1 and miR-134. Nature 466:1105–1109

    Article  PubMed  CAS  Google Scholar 

  • Gardner EL (2011) Addiction and brain reward and antireward pathways. Adv Psychosom Med 30:22–60

    Article  PubMed  Google Scholar 

  • Gardner KE, Allis CD, Strahl BD (2011) Operating on chromatin, a colorful language where context matters. J Mol Biol 409:36–46

    Article  PubMed  CAS  Google Scholar 

  • Geng T, Bao N, Litt MD, Glaros TG, Li L, Lu C (2011) Histone modification analysis by chromatin immunoprecipitation from a low number of cells on a microfluidic platform. Lab Chip 11:2842–2848

    Article  PubMed  CAS  Google Scholar 

  • Gkikopoulos T, Schofield P, Singh V, Pinskaya M, Mellor J, Smolle M, Workman JL, Barton GJ, Owen-Hughes T (2011) A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization. Science 333:1758–1760

    Article  PubMed  CAS  Google Scholar 

  • Goren A, Ozsolak F, Shoresh N, Ku M, Adli M, Hart C, Gymrek M, Zuk O, Regev A, Milos PM, Bernstein BE (2010) Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA. Nat Methods 7:47–49

    Article  PubMed  CAS  Google Scholar 

  • Graff J, Mansuy IM (2009) Epigenetic dysregulation in cognitive disorders. Eur J Neurosci 30:1–8

    Article  PubMed  Google Scholar 

  • Grant S (2009) Targeting histone demethylases in cancer therapy. Clin Cancer Res 15:7111–7113

    Article  PubMed  CAS  Google Scholar 

  • Grant JE, Potenza MN, Weinstein A, Gorelick DA (2010) Introduction to behavioral addictions. Am J Drug Alcohol Abuse 36:233–241

    Article  PubMed  Google Scholar 

  • Gregg C, Zhang J, Butler JE, Haig D, Dulac C (2010) Sex-specific parent-of-origin allelic expression in the mouse brain. Science 329:682–685

    Article  PubMed  CAS  Google Scholar 

  • Grohmann M, Hammer P, Walther M, Paulmann N, Buttner A, Eisenmenger W, Baghai TC, Schule C, Rupprecht R, Bader M, Bondy B, Zill P, Priller J, Walther DJ (2010) Alternative splicing and extensive RNA editing of human TPH2 transcripts. PLoS One 5:e8956

    Article  PubMed  CAS  Google Scholar 

  • Gu H, Bock C, Mikkelsen TS, Jager N, Smith ZD, Tomazou E, Gnirke A, Lander ES, Meissner A (2010) Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods 7:133–136

    Article  PubMed  CAS  Google Scholar 

  • Guan JS, Haggarty SJ, Giacometti E, Dannenberg JH, Joseph N, Gao J, Nieland TJ, Zhou Y, Wang X, Mazitschek R, Bradner JE, DePinho RA, Jaenisch R, Tsai LH (2009) HDAC2 negatively regulates memory formation and synaptic plasticity. Nature 459:55–60

    Article  PubMed  CAS  Google Scholar 

  • Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA (2007) A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130:77–88

    Article  PubMed  CAS  Google Scholar 

  • Guo JU, Su Y, Zhong C, Ming GL, Song H (2011) Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell 145:423–434

    Article  PubMed  CAS  Google Scholar 

  • Gurrieri F, Accadia M (2009) Genetic imprinting: the paradigm of Prader-Willi and Angelman syndromes. Endocr Dev 14:20–28

    Article  PubMed  Google Scholar 

  • Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, Cabili MN, Jaenisch R, Mikkelsen TS, Jacks T, Hacohen N, Bernstein BE, Kellis M, Regev A, Rinn JL, Lander ES (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458:223–227

    Article  PubMed  CAS  Google Scholar 

  • Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G, Young G, Lucas AB, Ach R, Bruhn L, Yang X, Amit I, Meissner A, Regev A, Rinn JL, Root DE, Lander ES (2011) lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 477:295–300

    Article  PubMed  CAS  Google Scholar 

  • Haberland M, Montgomery RL, Olson EN (2009) The many roles of histone deacetylases in development and physiology: implications for disease and therapy. Nat Rev Genet 10:32–42

    Article  PubMed  CAS  Google Scholar 

  • Haggarty SJ, Tsai LH (2011) Probing the role of HDACs and mechanisms of chromatin-mediated neuroplasticity. Neurobiol Learn Mem 96:41–52

    Article  PubMed  CAS  Google Scholar 

  • Haigis MC, Sinclair DA (2010) Mammalian sirtuins: biological insights and disease relevance. Annu Rev Pathol 5:253–295

    Article  PubMed  CAS  Google Scholar 

  • Hallam TM, Bourtchouladze R (2006) Rubinstein-Taybi syndrome: molecular findings and therapeutic approaches to improve cognitive dysfunction. Cell Mol Life Sci 63:1725–1735

    Article  PubMed  CAS  Google Scholar 

  • Hamada S, Suzuki T, Mino K, Koseki K, Oehme F, Flamme I, Ozasa H, Itoh Y, Ogasawara D, Komaarashi H, Kato A, Tsumoto H, Nakagawa H, Hasegawa M, Sasaki R, Mizukami T, Miyata N (2010) Design, synthesis, enzyme-inhibitory activity, and effect on human cancer cells of a novel series of jumonji domain-containing protein 2 histone demethylase inhibitors. J Med Chem 53:5629–5638

    Article  PubMed  CAS  Google Scholar 

  • Han JH, Kushner SA, Yiu AP, Cole CJ, Matynia A, Brown RA, Neve RL, Guzowski JF, Silva AJ, Josselyn SA (2007) Neuronal competition and selection during memory formation. Science 316:457–460

    Article  PubMed  CAS  Google Scholar 

  • Hannon GJ, Rivas FV, Murchison EP, Steitz JA (2006) The expanding universe of noncoding RNAs. Cold Spring Harb Symp Quant Biol 71:551–564

    Article  PubMed  CAS  Google Scholar 

  • Hansen KH, Bracken AP, Pasini D, Dietrich N, Gehani SS, Monrad A, Rappsilber J, Lerdrup M, Helin K (2008) A model for transmission of the H3K27me3 epigenetic mark. Nat Cell Biol 10:1291–1300

    Article  PubMed  CAS  Google Scholar 

  • Hargreaves DC, Crabtree GR (2011) ATP-dependent chromatin remodeling: genetics, genomics and mechanisms. Cell Res 21:396–420

    Article  PubMed  CAS  Google Scholar 

  • Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O’Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF (2010) Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol 28:1097–1105

    Article  PubMed  CAS  Google Scholar 

  • Hawkins RD, Hon GC, Lee LK, Ngo Q, Lister R, Pelizzola M, Edsall LE, Kuan S, Luu Y, Klugman S, Antosiewicz-Bourget J, Ye Z, Espinoza C, Agarwahl S, Shen L, Ruotti V, Wang W, Stewart R, Thomson JA, Ecker JR, Ren B (2010) Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 6:479–491

    Article  PubMed  CAS  Google Scholar 

  • He C (2010) Grand challenge commentary: RNA epigenetics? Nat Chem Biol 6:863–865

    Article  PubMed  CAS  Google Scholar 

  • He F, Lidow IA, Lidow MS (2006) Consequences of paternal cocaine exposure in mice. Neurotoxicol Teratol 28:198–209

    Article  PubMed  CAS  Google Scholar 

  • He YF, Li BZ, Li Z, Liu P, Wang Y, Tang Q, Ding J, Jia Y, Chen Z, Li L, Sun Y, Li X, Dai Q, Song CX, Zhang K, He C, Xu GL (2011) Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 333:1303–1307

    Article  PubMed  CAS  Google Scholar 

  • Heiman M, Schaefer A, Gong S, Peterson JD, Day M, Ramsey KE, Suarez-Farinas M, Schwarz C, Stephan DA, Surmeier DJ, Greengard P, Heintz N (2008) A translational profiling approach for the molecular characterization of CNS cell types. Cell 135:738–748

    Article  PubMed  CAS  Google Scholar 

  • Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, Ching KA, Antosiewicz-Bourget JE, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Crawford GE, Kellis M, Ren B (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459:108–112

    Article  PubMed  CAS  Google Scholar 

  • Henikoff S, Shilatifard A (2011) Histone modification: cause or cog? Trends Genet 27:389–396

    Article  PubMed  CAS  Google Scholar 

  • Herranz D, Serrano M (2010) SIRT1: recent lessons from mouse models. Nat Rev Cancer 10:819–823

    Article  PubMed  CAS  Google Scholar 

  • Hill KG, Hawkins JD, Catalano RF, Abbott RD, Guo J (2005) Family influences on the risk of daily smoking initiation. J Adolesc Health 37:202–210

    Article  PubMed  Google Scholar 

  • Hollander JA, Im HI, Amelio AL, Kocerha J, Bali P, Lu Q, Willoughby D, Wahlestedt C, Conkright MD, Kenny PJ (2010) Striatal microRNA controls cocaine intake through CREB signalling. Nature 466:197–202

    Article  PubMed  CAS  Google Scholar 

  • Hooker JM, Kim SW, Alexoff D, Xu Y, Shea C, Reid A, Volkow N, Fowler JS (2010) Histone deacetylase inhibitor, MS-275, exhibits poor brain penetration: PK studies of [C]MS-275 using positron emission tomography. ACS Chem Neurosci 1:65–73

    Article  PubMed  CAS  Google Scholar 

  • Horsthemke B, Wagstaff J (2008) Mechanisms of imprinting of the Prader-Willi/Angelman region. Am J Med Genet A 146A:2041–2052

    Article  PubMed  CAS  Google Scholar 

  • Host L, Dietrich JB, Carouge D, Aunis D, Zwiller J (2011) Cocaine self-administration alters the expression of chromatin-remodelling proteins; modulation by histone deacetylase inhibition. J Psychopharmacol 25:222–229

    Article  PubMed  CAS  Google Scholar 

  • Huang W, Li MD (2009) Differential allelic expression of dopamine D1 receptor gene (DRD1) is modulated by microRNA miR-504. Biol Psychiatry 65:702–705

    Article  PubMed  CAS  Google Scholar 

  • Hwang CK, Kim CS, Kim dK, Law PY, Wei LN, Loh HH (2010) Up-regulation of the mu-opioid receptor gene is mediated through chromatin remodeling and transcriptional factors in differentiated neuronal cells. Mol Pharmacol 78:58–68

    Article  PubMed  CAS  Google Scholar 

  • Ikegami D, Narita M, Imai S, Miyashita K, Tamura R, Narita M, Takagi S, Yokomizo A, Takeshima H, Ando T, Igarashi K, Kanno J, Kuzumaki N, Ushijima T, Suzuki T (2010) Epigenetic modulation at the CCR2 gene correlates with the maintenance of behavioral sensitization to methamphetamine. Addict Biol 15:358–361

    Article  PubMed  CAS  Google Scholar 

  • Im HI, Hollander JA, Bali P, Kenny PJ (2010) MeCP2 controls BDNF expression and cocaine intake through homeostatic interactions with microRNA-212. Nat Neurosci 13:1120–1127

    Article  PubMed  CAS  Google Scholar 

  • Ito S, Shen L, Dai Q, Wu SC, Collins LB, Swenberg JA, He C, Zhang Y (2011) Tet proteins can convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine. Science 333:1300–1303

    Article  PubMed  CAS  Google Scholar 

  • Iwamoto K, Bundo M, Kato T (2009) Serotonin receptor 2C and mental disorders: genetic, expression and RNA editing studies. RNA Biol 6:248–253

    Article  PubMed  CAS  Google Scholar 

  • Iwase S, Lan F, Bayliss P, Torre-Ubieta L, Huarte M, Qi HH, Whetstine JR, Bonni A, Roberts TM, Shi Y (2007) The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. Cell 128:1077–1088

    Article  PubMed  CAS  Google Scholar 

  • Jacquemont S, Curie A, Des Portes V, Torrioli MG, Berry-Kravis E, Hagerman RJ, Ramos FJ, Cornish K, He Y, Paulding C, Neri G, Chen F, Hadjikhani N, Martinet D, Meyer J, Beckmann JS, Delange K, Brun A, Bussy G, Gasparini F, Hilse T, Floesser A, Branson J, Bilbe G, Johns D, Gomez-Mancilla B (2011) Epigenetic modification of the FMR1 gene in fragile X syndrome is associated with differential response to the mGluR5 antagonist AFQ056. Sci Transl Med 3:64ra1

    Article  PubMed  CAS  Google Scholar 

  • Jensen LR, Amende M, Gurok U, Moser B, Gimmel V, Tzschach A, Janecke AR, Tariverdian G, Chelly J, Fryns JP, Van EH, Kleefstra T, Hamel B, Moraine C, Gecz J, Turner G, Reinhardt R, Kalscheuer VM, Ropers HH, Lenzner S (2005) Mutations in the JARID1C gene, which is involved in transcriptional regulation and chromatin remodeling, cause X-linked mental retardation. Am J Hum Genet 76:227–236

    Article  PubMed  CAS  Google Scholar 

  • Jing L, Luo J, Zhang M, Qin WJ, Li YL, Liu Q, Wang YT, Lawrence AJ, Liang JH (2011) Effect of the histone deacetylase inhibitors on behavioural sensitization to a single morphine exposure in mice. Neurosci Lett 494:169–173

    Article  PubMed  CAS  Google Scholar 

  • Jirtle RL, Skinner MK (2007) Environmental epigenomics and disease susceptibility. Nat Rev Genet 8:253–262

    Article  PubMed  CAS  Google Scholar 

  • Johnson EO, van den Bree MB, Uhl GR, Pickens RW (1996) Indicators of genetic and environmental influences in drug abusing individuals. Drug Alcohol Depend 41:17–23

    Article  PubMed  CAS  Google Scholar 

  • Johnson NL, Carini L, Schenk ME, Stewart M, Byrnes EM (2011) Adolescent opiate exposure in the female rat induces subtle alterations in maternal care and transgenerational effects on play behavior. Front Psychiat 2:29

    Google Scholar 

  • Justinova Z, Panlilio LV, Goldberg SR (2009) Drug addiction. Curr Top Behav Neurosci 1:309–346

    Article  PubMed  CAS  Google Scholar 

  • Kaikkonen MU, Lam MT, Glass CK (2011) Non-coding RNAs as regulators of gene expression and epigenetics. Cardiovasc Res 90:430–440

    Article  PubMed  CAS  Google Scholar 

  • Kalda A, Heidmets LT, Shen HY, Zharkovsky A, Chen JF (2007) Histone deacetylase inhibitors modulates the induction and expression of amphetamine-induced behavioral sensitization partially through an associated learning of the environment in mice. Behav Brain Res 181:76–84

    Article  PubMed  CAS  Google Scholar 

  • Kalivas PW, LaLumiere RT, Knackstedt L, Shen H (2009) Glutamate transmission in addiction. Neuropharmacology 56(Suppl 1):169–173

    Article  PubMed  CAS  Google Scholar 

  • Kendler KS, Neale MC, Sullivan P, Corey LA, Gardner CO, Prescott CA (1999) A population-based twin study in women of smoking initiation and nicotine dependence. Psychol Med 29:299–308

    Article  PubMed  CAS  Google Scholar 

  • Khraiwesh B, Arif MA, Seumel GI, Ossowski S, Weigel D, Reski R, Frank W (2010) Transcriptional control of gene expression by microRNAs. Cell 140:111–122

    Article  PubMed  CAS  Google Scholar 

  • Kilgore M, Miller CA, Fass DM, Hennig KM, Haggarty SJ, Sweatt JD, Rumbaugh G (2010) Inhibitors of class 1 histone deacetylases reverse contextual memory deficits in a mouse model of Alzheimer’s disease. Neuropsychopharmacology 35:870–880

    Article  PubMed  CAS  Google Scholar 

  • Kim J, Daniel J, Espejo A, Lake A, Krishna M, Xia L, Zhang Y, Bedford MT (2006) Tudor, MBT and chromo domains gauge the degree of lysine methylation. EMBO Rep 7:397–403

    PubMed  CAS  Google Scholar 

  • Klein CJ, Botuyan MV, Wu Y, Ward CJ, Nicholson GA, Hammans S, Hojo K, Yamanishi H, Karpf AR, Wallace DC, Simon M, Lander C, Boardman LA, Cunningham JM, Smith GE, Litchy WJ, Boes B, Atkinson EJ, Middha S, B Dyck PJ, Parisi JE, Mer G, Smith DI, Dyck PJ (2011) Mutations in DNMT1 cause hereditary sensory neuropathy with dementia and hearing loss. Nat Genet 43:595–600

    Article  PubMed  CAS  Google Scholar 

  • Koche RP, Smith ZD, Adli M, Gu H, Ku M, Gnirke A, Bernstein BE, Meissner A (2011) Reprogramming factor expression initiates widespread targeted chromatin remodeling. Cell Stem Cell 8:96–105

    Article  PubMed  CAS  Google Scholar 

  • Kong A, Steinthorsdottir V, Masson G, Thorleifsson G, Sulem P, Besenbacher S, Jonasdottir A, Sigurdsson A, Kristinsson KT, Jonasdottir A, Frigge ML, Gylfason A, Olason PI, Gudjonsson SA, Sverrisson S, Stacey SN, Sigurgeirsson B, Benediktsdottir KR, Sigurdsson H, Jonsson T, Benediktsson R, Olafsson JH, Johannsson OT, Hreidarsson AB, Sigurdsson G, Ferguson-Smith AC, Gudbjartsson DF, Thorsteinsdottir U, Stefansson K (2009) Parental origin of sequence variants associated with complex diseases. Nature 462:868–874

    Article  PubMed  CAS  Google Scholar 

  • Koob GF, Le MM (1997) Drug abuse: hedonic homeostatic dysregulation. Science 278:52–58

    Article  PubMed  CAS  Google Scholar 

  • Koob GF, Volkow ND (2010) Neurocircuitry of addiction. Neuropsychopharmacology 35:217–238

    Article  PubMed  Google Scholar 

  • Korzus E, Rosenfeld MG, Mayford M (2004) CBP histone acetyltransferase activity is a critical component of memory consolidation. Neuron 42:961–972

    Article  PubMed  CAS  Google Scholar 

  • Kriaucionis S, Heintz N (2009) The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324:929–930

    Article  PubMed  CAS  Google Scholar 

  • Kumar A, Choi KH, Renthal W, Tsankova NM, Theobald DE, Truong HT, Russo SJ, Laplant Q, Sasaki TS, Whistler KN, Neve RL, Self DW, Nestler EJ (2005) Chromatin remodeling is a key mechanism underlying cocaine-induced plasticity in striatum. Neuron 48:303–314

    Article  PubMed  CAS  Google Scholar 

  • Laplant Q, Nestler EJ (2011) CRACKing the histone code: cocaine’s effects on chromatin structure and function. Horm Behav 59:321–330

    Article  PubMed  CAS  Google Scholar 

  • Laplant Q, Vialou V, Covington HE III, Dumitriu D, Feng J, Warren BL, Maze I, Dietz DM, Watts EL, Iniguez SD, Koo JW, Mouzon E, Renthal W, Hollis F, Wang H, Noonan MA, Ren Y, Eisch AJ, Bolanos CA, Kabbaj M, Xiao G, Neve RL, Hurd YL, Oosting RS, Fan G, Morrison JH, Nestler EJ (2010) Dnmt3a regulates emotional behavior and spine plasticity in the nucleus accumbens. Nat Neurosci 13:1137–1143

    Article  PubMed  CAS  Google Scholar 

  • Launay JM, Del PM, Chironi G, Callebert J, Peoc’h K, Megnien JL, Mallet J, Simon A, Rendu F (2009) Smoking induces long-lasting effects through a monoamine-oxidase epigenetic regulation. PLoS One 4:e7959

    Article  PubMed  CAS  Google Scholar 

  • Le FB, Diaz J, Sokoloff P (2005) A single cocaine exposure increases BDNF and D3 receptor expression: implications for drug-conditioning. Neuroreport 16:175–178

    Article  Google Scholar 

  • Lee EJ, Banerjee S, Zhou H, Jammalamadaka A, Arcila M, Manjunath BS, Kosik KS (2011) Identification of piRNAs in the central nervous system. RNA 17:1090–1099

    Article  PubMed  CAS  Google Scholar 

  • Levine AA, Guan Z, Barco A, Xu S, Kandel ER, Schwartz JH (2005) CREB-binding protein controls response to cocaine by acetylating histones at the fosB promoter in the mouse striatum. Proc Natl Acad Sci U S A 102:19186–19191

    Article  PubMed  CAS  Google Scholar 

  • Lewis JD, Meehan RR, Henzel WJ, Maurer-Fogy I, Jeppesen P, Klein F, Bird A (1992) Purification, sequence, and cellular localization of a novel chromosomal protein that binds to methylated DNA. Cell 69:905–914

    Article  PubMed  CAS  Google Scholar 

  • Li G, Reinberg D (2011) Chromatin higher-order structures and gene regulation. Curr Opin Genet Dev 21:175–186

    Article  PubMed  CAS  Google Scholar 

  • Li MD, van der Vaart AD (2011) MicroRNAs in addiction: adaptation’s middlemen? Mol Psychiatry 16:1159–1168

    Article  PubMed  CAS  Google Scholar 

  • Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326:289–293

    Article  PubMed  CAS  Google Scholar 

  • Lin Q, Wei W, Coelho CM, Li X, Baker-Andresen D, Dudley K, Ratnu VS, Boskovic Z, Kobor MS, Sun YE, Bredy TW (2011) The brain-specific microRNA miR-128b regulates the formation of fear-extinction memory. Nat Neurosci 4:1115–1117

    Article  CAS  Google Scholar 

  • Lind GE, Danielsen SA, Ahlquist T, Merok MA, Andresen K, Skotheim RI, Hektoen M, Rognum TO, Meling GI, Hoff G, Bretthauer M, Thiis-Evensen E, Nesbakken A, Lothe RA (2011) Identification of an epigenetic biomarker panel with high sensitivity and specificity for colorectal cancer and adenomas. Mol Cancer 10:85

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462:315–322

    Article  PubMed  CAS  Google Scholar 

  • Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O’Malley R, Castanon R, Klugman S, Downes M, Yu R, Stewart R, Ren B, Thomson JA, Evans RM, Ecker JR (2011) Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature 471:68–73

    Article  PubMed  CAS  Google Scholar 

  • Luscher C, Malenka RC (2011) Drug-evoked synaptic plasticity in addiction: from molecular changes to circuit remodeling. Neuron 69:650–663

    Article  PubMed  CAS  Google Scholar 

  • Ma DK, Jang MH, Guo JU, Kitabatake Y, Chang ML, Pow-Anpongkul N, Flavell RA, Lu B, Ming GL, Song H (2009) Neuronal activity-induced Gadd45b promotes epigenetic DNA demethylation and adult neurogenesis. Science 323:1074–1077

    Article  PubMed  CAS  Google Scholar 

  • Ma DK, Marchetto MC, Guo JU, Ming GL, Gage FH, Song H (2010) Epigenetic choreographers of neurogenesis in the adult mammalian brain. Nat Neurosci 13:1338–1344

    Article  PubMed  CAS  Google Scholar 

  • Mack GS (2006) Epigenetic cancer therapy makes headway. J Natl Cancer Inst 98:1443–1444

    Article  PubMed  Google Scholar 

  • Malvaez M, Sanchis-Segura C, Vo D, Lattal KM, Wood MA (2010) Modulation of chromatin modification facilitates extinction of cocaine-induced conditioned place preference. Biol Psychiatry 67:36–43

    Article  PubMed  CAS  Google Scholar 

  • Margolis DM (2011) Histone deacetylase inhibitors and HIV latency. Curr Opin HIV AIDS 6:25–29

    Article  PubMed  Google Scholar 

  • Marques JT, Carthew RW (2007) A call to arms: coevolution of animal viruses and host innate immune responses. Trends Genet 23:359–364

    Article  PubMed  CAS  Google Scholar 

  • Marutha Ravindran CR, Ticku MK (2004) Changes in methylation pattern of NMDA receptor NR2B gene in cortical neurons after chronic ethanol treatment in mice. Brain Res Mol Brain Res 121:19–27

    Article  PubMed  CAS  Google Scholar 

  • Mattick JS, Mehler MF (2008) RNA editing, DNA recoding and the evolution of human cognition. Trends Neurosci 31:227–233

    Article  PubMed  CAS  Google Scholar 

  • Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R, Qu H, Brody J, Shafer A, Neri F, Lee K, Kutyavin T, Stehling-Sun S, Johnson AK, Canfield TK, Giste E, Diegel M, Bates D, Hansen RS, Neph S, Sabo PJ, Heimfeld S, Raubitschek A, Ziegler S, Cotsapas C, Sotoodehnia N, Glass I, Sunyaev SR, Kaul R, Stamatoyannopoulos JA (2012) Systematic localization of common disease-associated variation in regulatory DNA. Science 337(6099):1190–1195. doi:10.1126/science.1222794, Sep 7, Epub 2012 Sep 5

    Article  PubMed  CAS  Google Scholar 

  • Maze I, Nestler EJ (2011) The epigenetic landscape of addiction. Ann N Y Acad Sci 1216:99–113

    Article  PubMed  CAS  Google Scholar 

  • Maze I, Covington HE III, Dietz DM, Laplant Q, Renthal W, Russo SJ, Mechanic M, Mouzon E, Neve RL, Haggarty SJ, Ren Y, Sampath SC, Hurd YL, Greengard P, Tarakhovsky A, Schaefer A, Nestler EJ (2010) Essential role of the histone methyltransferase G9a in cocaine-induced plasticity. Science 327:213–216

    Article  PubMed  CAS  Google Scholar 

  • Maze I, Feng J, Wilkinson MB, Sun H, Shen L, Nestler EJ (2011) Cocaine dynamically regulates heterochromatin and repetitive element unsilencing in nucleus accumbens. Proc Natl Acad Sci U S A 108:3035–3040

    Article  PubMed  CAS  Google Scholar 

  • McCann DJ (2008) Potential of buprenorphine/naltrexone in treating polydrug addiction and co-occurring psychiatric disorders. Clin Pharmacol Ther 83:627–630

    Article  PubMed  CAS  Google Scholar 

  • McGowan PO, Sasaki A, D’Alessio AC, Dymov S, Labonte B, Szyf M, Turecki G, Meaney MJ (2009) Epigenetic regulation of the glucocorticoid receptor in human brain associates with childhood abuse. Nat Neurosci 12:342–348

    Article  PubMed  CAS  Google Scholar 

  • McGraw CM, Samaco RC, Zoghbi HY (2011) Adult neural function requires MeCP2. Science 333:186

    Article  PubMed  CAS  Google Scholar 

  • McQuown SC, Wood MA (2010) Epigenetic regulation in substance use disorders. Curr Psychiatry Rep 12:145–153

    Article  PubMed  Google Scholar 

  • McQuown SC, Barrett RM, Matheos DP, Post RJ, Rogge GA, Alenghat T, Mullican SE, Jones S, Rusche JR, Lazar MA, Wood MA (2011) HDAC3 is a critical negative regulator of long-term memory formation. J Neurosci 31:764–774

    Article  PubMed  CAS  Google Scholar 

  • Mercer TR, Dinger ME, Sunkin SM, Mehler MF, Mattick JS (2008) Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci U S A 105:716–721

    Article  PubMed  CAS  Google Scholar 

  • Mercer TR, Qureshi IA, Gokhan S, Dinger ME, Li G, Mattick JS, Mehler MF (2010) Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation. BMC Neurosci 11:14

    Article  PubMed  CAS  Google Scholar 

  • Michelhaugh SK, Lipovich L, Blythe J, Jia H, Kapatos G, Bannon MJ (2011) Mining Affymetrix microarray data for long non-coding RNAs: altered expression in the nucleus accumbens of heroin abusers. J Neurochem 116:459–466

    Article  PubMed  CAS  Google Scholar 

  • Mill J, Tang T, Kaminsky Z, Khare T, Yazdanpanah S, Bouchard L, Jia P, Assadzadeh A, Flanagan J, Schumacher A, Wang SC, Petronis A (2008) Epigenomic profiling reveals DNA-methylation changes associated with major psychosis. Am J Hum Genet 82:696–711

    Article  PubMed  CAS  Google Scholar 

  • Miller CA (2011) Forgot your HAT? CBP might be to blame. Neuropsychopharmacology 36:1543–1544

    Article  PubMed  CAS  Google Scholar 

  • Miller CA, Gavin CF, White JA, Parrish RR, Honasoge A, Yancey CR, Rivera IM, Rubio MD, Rumbaugh G, Sweatt JD (2010) Cortical DNA methylation maintains remote memory. Nat Neurosci 13:664–666

    Article  PubMed  CAS  Google Scholar 

  • Miranda TB, Jones PA (2007) DNA methylation: the nuts and bolts of repression. J Cell Physiol 213:384–390

    Article  PubMed  CAS  Google Scholar 

  • Montoya ID, Vocci F (2008) Novel medications to treat addictive disorders. Curr Psychiatry Rep 10:392–398

    Article  PubMed  Google Scholar 

  • Moretti P, Zoghbi HY (2006) MeCP2 dysfunction in Rett syndrome and related disorders. Curr Opin Genet Dev 16:276–281

    Article  PubMed  CAS  Google Scholar 

  • Morris MJ, Karra AS, Monteggia LM (2010) Histone deacetylases govern cellular mechanisms underlying behavioral and synaptic plasticity in the developing and adult brain. Behav Pharmacol 21:409–419

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Muschler MA, Hillemacher T, Kraus C, Kornhuber J, Bleich S, Frieling H (2010) DNA methylation of the POMC gene promoter is associated with craving in alcohol dependence. J Neural Transm 117:513–519

    Article  PubMed  CAS  Google Scholar 

  • Musselman CA, Kutateladze TG (2009) PHD fingers: epigenetic effectors and potential drug targets. Mol Interv 9:314–323

    Article  PubMed  CAS  Google Scholar 

  • Myers RM, Stamatoyannopoulos J, Snyder M, Dunham I, Hardison RC, Bernstein BE, Gingeras TR, Kent WJ, Birney E, Wold B, Crawford GE (2011) A user’s guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 9:e1001046

    Article  CAS  Google Scholar 

  • Namihira M, Kohyama J, Abematsu M, Nakashima K (2008) Epigenetic mechanisms regulating fate specification of neural stem cells. Philos Trans R Soc Lond B Biol Sci 363:2099–2109

    Article  PubMed  CAS  Google Scholar 

  • National Drug Intelligence Center. United States Department of Justice (2010) National drug threat assessment. GPO, Washington

    Google Scholar 

  • Ndlovu N, Denis H, Fuks F (2011) Exposing the DNA methylome iceberg. Trends Biochem Sci 36:381–387

    PubMed  CAS  Google Scholar 

  • Nelson ED, Monteggia LM (2011) Epigenetics in the mature mammalian brain: effects on behavior and synaptic transmission. Neurobiol Learn Mem 96:53–60

    Article  PubMed  CAS  Google Scholar 

  • Nestler EJ (2008) Review. Transcriptional mechanisms of addiction: role of DeltaFosB. Philos Trans R Soc Lond B Biol Sci 363:3245–3255

    Article  PubMed  CAS  Google Scholar 

  • Nestler EJ, Malenka RC (2004) The addicted brain. Sci Am 290:78–85

    Article  PubMed  CAS  Google Scholar 

  • Nestler EJ, Barrot M, Self DW (2001) DeltaFosB: a sustained molecular switch for addiction. Proc Natl Acad Sci U S A 98:11042–11046

    Article  PubMed  CAS  Google Scholar 

  • Newman AH, Kulkarni S (2002) Probes for the dopamine transporter: new leads toward a cocaine-abuse therapeutic–A focus on analogues of benztropine and rimcazole. Med Res Rev 22:429–464

    Article  PubMed  CAS  Google Scholar 

  • Ng RK, Gurdon JB (2008) Epigenetic inheritance of cell differentiation status. Cell Cycle 7:1173–1177

    Article  PubMed  CAS  Google Scholar 

  • Nielsen DA, Yuferov V, Hamon S, Jackson C, Ho A, Ott J, Kreek MJ (2009) Increased OPRM1 DNA methylation in lymphocytes of methadone-maintained former heroin addicts. Neuropsychopharmacology 34:867–873

    Article  PubMed  CAS  Google Scholar 

  • Noushmehr H, Weisenberger DJ, Diefes K, Phillips HS, Pujara K, Berman BP, Pan F, Pelloski CE, Sulman EP, Bhat KP, Verhaak RG, Hoadley KA, Hayes DN, Perou CM, Schmidt HK, Ding L, Wilson RK, Van Den Berg D, Shen H, Bengtsson H, Neuvial P, Cope LM, Buckley J, Herman JG, Baylin SB, Laird PW, Aldape K (2010) Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. Cancer Cell 17:510–522

    Article  PubMed  CAS  Google Scholar 

  • Novikova SI, He F, Bai J, Cutrufello NJ, Lidow MS, Undieh AS (2008) Maternal cocaine administration in mice alters DNA methylation and gene expression in hippocampal neurons of neonatal and prepubertal offspring. PLoS One 3:e1919

    Article  PubMed  CAS  Google Scholar 

  • Nowak SJ, Corces VG (2004) Phosphorylation of histone H3: a balancing act between chromosome condensation and transcriptional activation. Trends Genet 20:214–220

    Article  PubMed  CAS  Google Scholar 

  • Numachi Y, Yoshida S, Yamashita M, Fujiyama K, Naka M, Matsuoka H, Sato M, Sora I (2004) Psychostimulant alters expression of DNA methyltransferase mRNA in the rat brain. Ann N Y Acad Sci 1025:102–109

    Article  PubMed  CAS  Google Scholar 

  • O’Carroll D, Mecklenbrauker I, Das PP, Santana A, Koenig U, Enright AJ, Miska EA, Tarakhovsky A (2007) A Slicer-independent role for Argonaute 2 in hematopoiesis and the microRNA pathway. Genes Dev 21:1999–2004

    Article  PubMed  CAS  Google Scholar 

  • Olde Loohuis NF, Kos A, Martens GJ, Van Bokhoven H, Nadif Kasri N, Aschrafi A (2012) MicroRNA networks direct neuronal development and plasticity. Cell Mol Life Sci 69(1):89–102. doi:10.1007/s00018-011-0788-1, Epub 2011 Aug 11

    Article  PubMed  CAS  Google Scholar 

  • Olsen CM (2011) Natural rewards, neuroplasticity, and non-drug addictions. Neuropharmacology 61:1109–1122

    Article  PubMed  CAS  Google Scholar 

  • Ooi SK, Bestor TH (2008) The colorful history of active DNA demethylation. Cell 133:1145–1148

    Article  PubMed  CAS  Google Scholar 

  • Pandey SC, Ugale R, Zhang H, Tang L, Prakash A (2008) Brain chromatin remodeling: a novel mechanism of alcoholism. J Neurosci 28:3729–3737

    Article  PubMed  CAS  Google Scholar 

  • Pankevich DE, Mueller BR, Brockel B, Bale TL (2009) Prenatal stress programming of offspring feeding behavior and energy balance begins early in pregnancy. Physiol Behav 98:94–102

    Article  PubMed  CAS  Google Scholar 

  • Park PJ (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10:669–680

    Article  PubMed  CAS  Google Scholar 

  • Pastor V, Host L, Zwiller J, Bernabeu R (2011a) Histone deacetylase inhibition decreases preference without affecting aversion for nicotine. J Neurochem 116:636–645

    Article  PubMed  CAS  Google Scholar 

  • Pastor WA, Pape UJ, Huang Y, Henderson HR, Lister R, Ko M, McLoughlin EM, Brudno Y, Mahapatra S, Kapranov P, Tahiliani M, Daley GQ, Liu XS, Ecker JR, Milos PM, Agarwal S, Rao A (2011b) Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature 473:394–397

    Article  PubMed  CAS  Google Scholar 

  • Pembrey ME, Bygren LO, Kaati G, Edvinsson S, Northstone K, Sjostrom M, Golding J (2006) Sex-specific, male-line transgenerational responses in humans. Eur J Hum Genet 14:159–166

    Article  PubMed  Google Scholar 

  • Pennisi E (2011) The biology of genomes. Disease risk links to gene regulation. Science 332:1031

    Article  PubMed  Google Scholar 

  • Perry JL, Carroll ME (2008) The role of impulsive behavior in drug abuse. Psychopharmacology 200:1–26

    Article  PubMed  CAS  Google Scholar 

  • Petrij F, Giles RH, Dauwerse HG, Saris JJ, Hennekam RC, Masuno M, Tommerup N, van Ommen GJ, Goodman RH, Peters DJ (1995) Rubinstein-Taybi syndrome caused by mutations in the transcriptional co-activator CBP. Nature 376:348–351

    Article  PubMed  CAS  Google Scholar 

  • Philibert RA, Gunter TD, Beach SR, Brody GH, Madan A (2008) MAOA methylation is associated with nicotine and alcohol dependence in women. Am J Med Genet B Neuropsychiatr Genet 147B:565–570

    Article  PubMed  CAS  Google Scholar 

  • Philibert RA, Beach SR, Gunter TD, Brody GH, Madan A, Gerrard M (2010) The effect of smoking on MAOA promoter methylation in DNA prepared from lymphoblasts and whole blood. Am J Med Genet B Neuropsychiatr Genet 153B:619–628

    PubMed  CAS  Google Scholar 

  • Pidsley R, Mill J (2011) Epigenetic studies of psychosis: current findings, methodological approaches, and implications for postmortem research. Biol Psychiatry 69:146–156

    Article  PubMed  Google Scholar 

  • Pietrzykowski AZ (2010) The role of microRNAs in drug addiction: a big lesson from tiny molecules. Int Rev Neurobiol 91:1–24

    Article  PubMed  CAS  Google Scholar 

  • Pietrzykowski AZ, Friesen RM, Martin GE, Puig SI, Nowak CL, Wynne PM, Siegelmann HT, Treistman SN (2008) Posttranscriptional regulation of BK channel splice variant stability by miR-9 underlies neuroadaptation to alcohol. Neuron 59:274–287

    Article  PubMed  CAS  Google Scholar 

  • Pirotte D, Wislet-Gendebien S, Cloes JM, Rogister B (2010) Neuregulin-1 modulates the differentiation of neural stem cells in vitro through an interaction with the Swi/Snf complex. Mol Cell Neurosci 43:72–80

    Article  PubMed  CAS  Google Scholar 

  • Rakyan VK, Down TA, Balding DJ, Beck S (2011) Epigenome-wide association studies for common human diseases. Nat Rev Genet 12:529–541

    Article  PubMed  CAS  Google Scholar 

  • Rapicavoli NA, Poth EM, Blackshaw S (2010) The long noncoding RNA RNCR2 directs mouse retinal cell specification. BMC Dev Biol 10:49

    Article  PubMed  CAS  Google Scholar 

  • Rehm J, Mathers C, Popova S, Thavorncharoensap M, Teerawattananon Y, Patra J (2009) Global burden of disease and injury and economic cost attributable to alcohol use and alcohol-use disorders. Lancet 373:2223–2233

    Article  PubMed  Google Scholar 

  • Reid AE, Hooker J, Shumay E, Logan J, Shea C, Kim SW, Collins S, Xu Y, Volkow N, Fowler JS (2009) Evaluation of 6-([(18)F]fluoroacetamido)-1-hexanoicanilide for PET imaging of histone deacetylase in the baboon brain. Nucl Med Biol 36:247–258

    Article  PubMed  CAS  Google Scholar 

  • Renthal W, Nestler EJ (2009a) Chromatin regulation in drug addiction and depression. Dialogues Clin Neurosci 11:257–268

    PubMed  Google Scholar 

  • Renthal W, Nestler EJ (2009b) Histone acetylation in drug addiction. Semin Cell Dev Biol 20:387–394

    Article  PubMed  CAS  Google Scholar 

  • Renthal W, Maze I, Krishnan V, Covington HE III, Xiao G, Kumar A, Russo SJ, Graham A, Tsankova N, Kippin TE, Kerstetter KA, Neve RL, Haggarty SJ, McKinsey TA, Bassel-Duby R, Olson EN, Nestler EJ (2007) Histone deacetylase 5 epigenetically controls behavioral adaptations to chronic emotional stimuli. Neuron 56:517–529

    Article  PubMed  CAS  Google Scholar 

  • Renthal W, Carle TL, Maze I, Covington HE III, Truong HT, Alibhai I, Kumar A, Montgomery RL, Olson EN, Nestler EJ (2008) Delta FosB mediates epigenetic desensitization of the c-fos gene after chronic amphetamine exposure. J Neurosci 28:7344–7349

    Article  PubMed  CAS  Google Scholar 

  • Renthal W, Kumar A, Xiao G, Wilkinson M, Covington HE III, Maze I, Sikder D, Robison AJ, Laplant Q, Dietz DM, Russo SJ, Vialou V, Chakravarty S, Kodadek TJ, Stack A, Kabbaj M, Nestler EJ (2009) Genome-wide analysis of chromatin regulation by cocaine reveals a role for sirtuins. Neuron 62:335–348

    Article  PubMed  CAS  Google Scholar 

  • Romieu P, Host L, Gobaille S, Sandner G, Aunis D, Zwiller J (2008) Histone deacetylase inhibitors decrease cocaine but not sucrose self-administration in rats. J Neurosci 28:9342–9348

    Article  PubMed  CAS  Google Scholar 

  • Roth TL, Lubin FD, Funk AJ, Sweatt JD (2009) Lasting epigenetic influence of early-life adversity on the BDNF gene. Biol Psychiatry 65:760–769

    Article  PubMed  CAS  Google Scholar 

  • Saba R, Schratt GM (2010) MicroRNAs in neuronal development, function and dysfunction. Brain Res 1338:3–13

    Article  PubMed  CAS  Google Scholar 

  • Sadri-Vakili G, Kumaresan V, Schmidt HD, Famous KR, Chawla P, Vassoler FM, Overland RP, Xia E, Bass CE, Terwilliger EF, Pierce RC, Cha JH (2010) Cocaine-induced chromatin remodeling increases brain-derived neurotrophic factor transcription in the rat medial prefrontal cortex, which alters the reinforcing efficacy of cocaine. J Neurosci 30:11735–11744

    Article  PubMed  CAS  Google Scholar 

  • Sanchez R, Zhou MM (2011) The PHD finger: a versatile epigenome reader. Trends Biochem Sci 36:364–372

    PubMed  CAS  Google Scholar 

  • Sanchis-Segura C, Lopez-Atalaya JP, Barco A (2009) Selective boosting of transcriptional and behavioral responses to drugs of abuse by histone deacetylase inhibition. Neuropsychopharmacology 34:2642–2654

    Article  PubMed  CAS  Google Scholar 

  • Satta R, Maloku E, Zhubi A, Pibiri F, Hajos M, Costa E, Guidotti A (2008) Nicotine decreases DNA methyltransferase 1 expression and glutamic acid decarboxylase 67 promoter methylation in GABAergic interneurons. Proc Natl Acad Sci U S A 105:16356–16361

    Article  PubMed  CAS  Google Scholar 

  • Schaefer A, O’Carroll D, Tan CL, Hillman D, Sugimori M, Llinas R, Greengard P (2007) Cerebellar neurodegeneration in the absence of microRNAs. J Exp Med 204:1553–1558

    Article  PubMed  CAS  Google Scholar 

  • Schaefer A, Sampath SC, Intrator A, Min A, Gertler TS, Surmeier DJ, Tarakhovsky A, Greengard P (2009) Control of cognition and adaptive behavior by the GLP/G9a epigenetic suppressor complex. Neuron 64:678–691

    Article  PubMed  CAS  Google Scholar 

  • Schaefer A, Im HI, Veno MT, Fowler CD, Min A, Intrator A, Kjems J, Kenny PJ, O’Carroll D, Greengard P (2010) Argonaute 2 in dopamine 2 receptor-expressing neurons regulates cocaine addiction. J Exp Med 207:1843–1851

    Article  PubMed  CAS  Google Scholar 

  • Schotta G, Lachner M, Sarma K, Ebert A, Sengupta R, Reuter G, Reinberg D, Jenuwein T (2004) A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin. Genes Dev 18:1251–1262

    Article  PubMed  CAS  Google Scholar 

  • Schratt G (2009) microRNAs at the synapse. Nat Rev Neurosci 10:842–849

    Article  PubMed  CAS  Google Scholar 

  • Schratt GM, Tuebing F, Nigh EA, Kane CG, Sabatini ME, Kiebler M, Greenberg ME (2006) A brain-specific microRNA regulates dendritic spine development. Nature 439:283–289

    Article  PubMed  CAS  Google Scholar 

  • Schroeder FA, Penta KL, Matevossian A, Jones SR, Konradi C, Tapper AR, Akbarian S (2008) Drug-induced activation of dopamine D(1) receptor signaling and inhibition of class I/II histone deacetylase induce chromatin remodeling in reward circuitry and modulate cocaine-related behaviors. Neuropsychopharmacology 33:2981–2992

    Article  PubMed  CAS  Google Scholar 

  • Sharma S, Kelly TK, Jones PA (2010) Epigenetics in cancer. Carcinogenesis 31:27–36

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Skene PJ, Illingworth RS, Webb S, Kerr AR, James KD, Turner DJ, Andrews R, Bird AP (2010) Neuronal MeCP2 is expressed at near histone-octamer levels and globally alters the chromatin state. Mol Cell 37:457–468

    Article  PubMed  CAS  Google Scholar 

  • Skinner MK, Anway MD, Savenkova MI, Gore AC, Crews D (2008) Transgenerational epigenetic programming of the brain transcriptome and anxiety behavior. PLoS One 3:e3745

    Article  PubMed  CAS  Google Scholar 

  • Skinner MK, Manikkam M, Guerrero-Bosagna C (2010) Epigenetic transgenerational actions of environmental factors in disease etiology. Trends Endocrinol Metab 21:214–222

    Article  PubMed  CAS  Google Scholar 

  • Stipanovich A, Valjent E, Matamales M, Nishi A, Ahn JH, Maroteaux M, Bertran-Gonzalez J, Brami-Cherrier K, Enslen H, Corbille AG, Filhol O, Nairn AC, Greengard P, Herve D, Girault JA (2008) A phosphatase cascade by which rewarding stimuli control nucleosomal response. Nature 453:879–884

    Article  PubMed  CAS  Google Scholar 

  • St Laurent G 3rd, Faghihi MA, Wahlestedt C (2009) Non-coding RNA transcripts: sensors of neuronal stress, modulators of synaptic plasticity, and agents of change in the onset of Alzheimer's disease. Neurosci Lett 466(2):81–88, Dec 4

    Article  PubMed  CAS  Google Scholar 

  • Strauch K, Baur MP (2005) Parent-of-origin, imprinting, mitochondrial, and X-linked effects in traits related to alcohol dependence: presentation Group 18 of Genetic Analysis Workshop 14. Genet Epidemiol 29(Suppl 1):S125–S132

    Article  PubMed  Google Scholar 

  • Stroud H, Feng S, Morey KS, Pradhan S, Jacobsen SE (2011) 5-hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells. Genome Biol 12:R54

    Article  PubMed  CAS  Google Scholar 

  • Sulzer D (2011) How addictive drugs disrupt presynaptic dopamine neurotransmission. Neuron 69:628–649

    Article  PubMed  CAS  Google Scholar 

  • Sun J, Wang L, Jiang B, Hui B, Lv Z, Ma L (2008) The effects of sodium butyrate, an inhibitor of histone deacetylase, on the cocaine- and sucrose-maintained self-administration in rats. Neurosci Lett 441:72–76

    Article  PubMed  CAS  Google Scholar 

  • Sung HE, Richter L, Vaughan R, Johnson PB, Thom B (2005) Nonmedical use of prescription opioids among teenagers in the United States: trends and correlates. J Adolesc Health 37:44–51

    Article  PubMed  Google Scholar 

  • Svenningsson P, Nairn AC, Greengard P (2005) DARPP-32 mediates the actions of multiple drugs of abuse. AAPS J 7:E353–E360

    Article  PubMed  CAS  Google Scholar 

  • Szulwach KE, Li X, Li Y, Song CX, Han JW, Kim S, Namburi S, Hermetz K, Kim JJ, Rudd MK, Yoon YS, Ren B, He C, Jin P (2011) Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells. PLoS Genet 7:e1002154

    Article  PubMed  CAS  Google Scholar 

  • Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, Agarwal S, Iyer LM, Liu DR, Aravind L, Rao A (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324:930–935

    Article  PubMed  CAS  Google Scholar 

  • Talbert PB, Henikoff S (2010) Histone variants–ancient wrap artists of the epigenome. Nat Rev Mol Cell Biol 11:264–275

    Article  PubMed  CAS  Google Scholar 

  • Taqi MM, Bazov I, Watanabe H, Sheedy D, Harper C, Alkass K, Druid H, Wentzel P, Nyberg F, Yakovleva T, Bakalkin G (2011) Prodynorphin CpG-SNPs associated with alcohol dependence: elevated methylation in the brain of human alcoholics. Addict Biol 6:499–509

    Article  Google Scholar 

  • Thiagalingam S, Cheng KH, Lee HJ, Mineva N, Thiagalingam A, Ponte JF (2003) Histone deacetylases: unique players in shaping the epigenetic histone code. Ann N Y Acad Sci 983:84–100

    Article  PubMed  CAS  Google Scholar 

  • Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY (2010) Long noncoding RNA as modular scaffold of histone modification complexes. Science 329:689–693

    Article  PubMed  CAS  Google Scholar 

  • 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 9:519–525

    Article  PubMed  CAS  Google Scholar 

  • Tsankova N, Renthal W, Kumar A, Nestler EJ (2007) Epigenetic regulation in psychiatric disorders. Nat Rev Neurosci 8:355–367

    Article  PubMed  CAS  Google Scholar 

  • Turek-Plewa J, Jagodzinski PP (2005) The role of mammalian DNA methyltransferases in the regulation of gene expression. Cell Mol Biol Lett 10:631–647

    PubMed  CAS  Google Scholar 

  • Uhl GR, Drgon T, Johnson C, Fatusin OO, Liu QR, Contoreggi C, Li CY, Buck K, Crabbe J (2008) “Higher order” addiction molecular genetics: convergent data from genome-wide association in humans and mice. Biochem Pharmacol 75:98–111

    Article  PubMed  CAS  Google Scholar 

  • Van den Oever MC, Spijker S, Smit AB, De Vries TJ (2010) Prefrontal cortex plasticity mechanisms in drug seeking and relapse. Neurosci Biobehav Rev 35:276–284

    Article  PubMed  Google Scholar 

  • Vanyushin BF (2006) DNA methylation in plants. Curr Top Microbiol Immunol 301:67–122

    Article  PubMed  CAS  Google Scholar 

  • Vaquero A, Sternglanz R, Reinberg D (2007) NAD + −dependent deacetylation of H4 lysine 16 by class III HDACs. Oncogene 26:5505–5520

    Article  PubMed  CAS  Google Scholar 

  • Vucetic Z, Kimmel J, Totoki K, Hollenbeck E, Reyes TM (2010) Maternal high-fat diet alters methylation and gene expression of dopamine and opioid-related genes. Endocrinology 151:4756–4764

    Article  PubMed  CAS  Google Scholar 

  • Vucetic Z, Kimmel J, Reyes TM (2011) Chronic high-fat diet drives postnatal epigenetic regulation of mu-opioid receptor in the brain. Neuropsychopharmacology 36:1199–1206

    Article  PubMed  CAS  Google Scholar 

  • Wang Y, Krishnan HR, Ghezzi A, Yin JC, Atkinson NS (2007) Drug-induced epigenetic changes produce drug tolerance. PLoS Biol 5:e265

    Article  PubMed  CAS  Google Scholar 

  • Wang L, Lv Z, Hu Z, Sheng J, Hui B, Sun J, Ma L (2010a) Chronic cocaine-induced H3 acetylation and transcriptional activation of CaMKIIalpha in the nucleus accumbens is critical for motivation for drug reinforcement. Neuropsychopharmacology 35:913–928

    Article  PubMed  CAS  Google Scholar 

  • Wang R, Zhang Y, Qing H, Liu M, Yang P (2010b) The extinction of morphine-induced conditioned place preference by histone deacetylase inhibition. Neurosci Lett 483:137–142

    Article  PubMed  CAS  Google Scholar 

  • Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA, Wysocka J, Lei M, Dekker J, Helms JA, Chang HY (2011) A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472:120–124

    Article  PubMed  CAS  Google Scholar 

  • Waterland RA, Michels KB (2007) Epigenetic epidemiology of the developmental origins hypothesis. Annu Rev Nutr 27:363–388

    Article  PubMed  CAS  Google Scholar 

  • Weaver IC, Cervoni N, Champagne FA, D’Alessio AC, Sharma S, Seckl JR, Dymov S, Szyf M, Meaney MJ (2004) Epigenetic programming by maternal behavior. Nat Neurosci 7:847–854

    Article  PubMed  CAS  Google Scholar 

  • Weiss IC, Franklin TB, Vizi S, Mansuy IM (2011) Inheritable effect of unpredictable maternal separation on behavioral responses in mice. Front Behav Neurosci 5:3

    Article  PubMed  Google Scholar 

  • Weller M, Stupp R, Reifenberger G, Brandes AA, van den Bent MJ, Wick W, Hegi ME (2010) MGMT promoter methylation in malignant gliomas: ready for personalized medicine? Nat Rev Neurol 6:39–51

    Article  PubMed  CAS  Google Scholar 

  • Wen B, Wu H, Shinkai Y, Irizarry RA, Feinberg AP (2009) Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells. Nat Genet 41:246–250

    Article  PubMed  CAS  Google Scholar 

  • Wilkinson MB, Xiao G, Kumar A, Laplant Q, Renthal W, Sikder D, Kodadek TJ, Nestler EJ (2009) Imipramine treatment and resiliency exhibit similar chromatin regulation in the mouse nucleus accumbens in depression models. J Neurosci 29:7820–7832

    Article  PubMed  CAS  Google Scholar 

  • Wong CC, Mill J, Fernandes C (2011) Drugs and addiction: an introduction to epigenetics. Addiction 106:480–489

    Article  PubMed  Google Scholar 

  • Wossidlo M, Nakamura T, Lepikhov K, Marques CJ, Zakhartchenko V, Boiani M, Arand J, Nakano T, Reik W, Walter J (2011) 5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming. Nat Commun 2:241

    Article  PubMed  CAS  Google Scholar 

  • Wu SC, Zhang Y (2010) Active DNA demethylation: many roads lead to Rome. Nat Rev Mol Cell Biol 11:607–620

    Article  PubMed  CAS  Google Scholar 

  • Wu H, Zhang Y (2011) Tet1 and 5-hydroxymethylation: a genome-wide view in mouse embryonic stem cells. Cell Cycle 10:2428–2436

    Article  PubMed  CAS  Google Scholar 

  • Yamada T, Fischle W, Sugiyama T, Allis CD, Grewal SI (2005) The nucleation and maintenance of heterochromatin by a histone deacetylase in fission yeast. Mol Cell 20:173–185

    Article  PubMed  CAS  Google Scholar 

  • Yasui DH, Peddada S, Bieda MC, Vallero RO, Hogart A, Nagarajan RP, Thatcher KN, Farnham PJ, LaSalle JM (2007) Integrated epigenomic analyses of neuronal MeCP2 reveal a role for long-range interaction with active genes. Proc Natl Acad Sci U S A 104:19416–19421

    Article  PubMed  CAS  Google Scholar 

  • Yoo AS, Crabtree GR (2009) ATP-dependent chromatin remodeling in neural development. Curr Opin Neurobiol 19:120–126

    Article  PubMed  CAS  Google Scholar 

  • Yoo AS, Staahl BT, Chen L, Crabtree GR (2009) MicroRNA-mediated switching of chromatin-remodelling complexes in neural development. Nature 460:642–646

    PubMed  CAS  Google Scholar 

  • Young JI, Hong EP, Castle JC, Crespo-Barreto J, Bowman AB, Rose MF, Kang D, Richman R, Johnson JM, Berget S, Zoghbi HY (2005) Regulation of RNA splicing by the methylation-dependent transcriptional repressor methyl-CpG binding protein 2. Proc Natl Acad Sci U S A 102:17551–17558

    Article  PubMed  CAS  Google Scholar 

  • Youngson NA, Whitelaw E (2008) Transgenerational epigenetic effects. Annu Rev Genomics Hum Genet 9:233–257

    Article  PubMed  CAS  Google Scholar 

  • Yu M, Hon GC, Szulwac KE, Song C-X, Zhang L, Kim A, Li X, Dai Q, Shin Y, Park B, Min J-H, Jen P, Ren B, He C (2012) Base-resolution analysis of 5-Hydroxymethylcytosine in the mammalian genome. Cell 149(6):1368–1380

    Article  PubMed  CAS  Google Scholar 

  • Zambrano E, Martinez-Samayoa PM, Bautista CJ, Deas M, Guillen L, Rodriguez-Gonzalez GL, Guzman C, Larrea F, Nathanielsz PW (2005) Sex differences in transgenerational alterations of growth and metabolism in progeny (F2) of female offspring (F1) of rats fed a low protein diet during pregnancy and lactation. J Physiol 566:225–236

    Article  PubMed  CAS  Google Scholar 

  • Zhang TY, Meaney MJ (2010) Epigenetics and the environmental regulation of the genome and its function. Annu Rev Psychol 61:439–466

    Article  PubMed  Google Scholar 

  • Zhang Z, Pugh BF (2011) High-resolution genome-wide mapping of the primary structure of chromatin. Cell 144:175–186

    Article  PubMed  CAS  Google Scholar 

  • Zhao J, Ohsumi TK, Kung JT, Ogawa Y, Grau DJ, Sarma K, Song JJ, Kingston RE, Borowsky M, Lee JT (2010) Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol Cell 40:939–953

    Article  PubMed  CAS  Google Scholar 

  • Zhou Z, Hong EJ, Cohen S, Zhao WN, Ho HY, Schmidt L, Chen WG, Lin Y, Savner E, Griffith EC, Hu L, Steen JA, Weitz CJ, Greenberg ME (2006) Brain-specific phosphorylation of MeCP2 regulates activity-dependent Bdnf transcription, dendritic growth, and spine maturation. Neuron 52:255–269

    Article  PubMed  CAS  Google Scholar 

  • Zhou Z, Yuan Q, Mash DC, Goldman D (2011) Substance-specific and shared transcription and epigenetic changes in the human hippocampus chronically exposed to cocaine and alcohol. Proc Natl Acad Sci U S A 108:6626–6631

    Article  PubMed  CAS  Google Scholar 

  • Zhubi A, Veldic M, Puri NV, Kadriu B, Caruncho H, Loza I, Sershen H, Lajtha A, Smith RC, Guidotti A, Davis JM, Costa E (2009) An upregulation of DNA-methyltransferase 1 and 3a expressed in telencephalic GABAergic neurons of schizophrenia patients is also detected in peripheral blood lymphocytes. Schizophr Res 111:115–122

    Article  PubMed  CAS  Google Scholar 

  • Zocchi L, Sassone-Corsi P (2010) Joining the dots: from chromatin remodeling to neuronal plasticity. Curr Opin Neurobiol 20:432–440

    Article  PubMed  CAS  Google Scholar 

  • Zuber J, Shi J, Wang E, Rappaport AR, Herrmann H, Sison EA, Magoon D, Qi J, Blatt K, Wunderlich M, Taylor MJ, Johns C, Chicas A, Mulloy JC, Kogan SC, Brown P, Valent P, Bradner JE, Lowe SW, Vakoc CR (2011) RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia. Nature 478:524–528

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

I would like to acknowledge suggestions and input from Nigel Atkinson, Elizabeth Byrnes, Paul Kenny, Courtney Miller, Eric Nestler, Lisa Onken, Jonathan Pollock, Joni Rutter, Anne Schaefer, Susan Volman, Anne West, David White, and Marcelo Wood, as well as excellent assistance on the manuscript by Dena Procaccini. The author is solely responsible for any errors that may be found in this chapter.

Author information

Authors and Affiliations

  1. National Institute on Drug Abuse, 6001 Executive Boulevard, Bethesda, Maryland, 20892-9561, USA

    John S. Satterlee

Authors
  1. John S. Satterlee
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to John S. Satterlee .

Editor information

Editors and Affiliations

  1. School of Medicine and Public Health, McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, University Avenue 1400, Madison, 53706, Wisconsin, USA

    Randy L. Jirtle

  2. National Institute of Environmental Hea, NIEHS, National Institutes of Health, Research Triangle Park, 27709, North Carolina, USA

    Frederick L. Tyson

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Satterlee, J.S. (2013). Epigenomic and Noncoding RNA Regulation in Addictive Processes. In: Jirtle, R., Tyson, F. (eds) Environmental Epigenomics in Health and Disease. Epigenetics and Human Health. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-36827-1_7

Download citation

Publish with us

Policies and ethics

Search

Navigation