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DNA Modifications in the Brain. Neuroepigenetic Regulation of Gene Expression


PREFACEHistory and Modern View on DNA Modifications in the BrainDNA METHYLATION AND ITS INFLUENCE ON DNA STRUCTURE AND INTERACTION WITH PROTEINSREPLICATIVE DNA METHYLATION AND THE INHERITANCE OF THE DNA METHYLATION PATTERNDNA METHYLTRANSFERASESDNA DEMETHYLATIONSPECIFICITY OF DNA METHYLATIONFUNCTIONAL ROLES OF DNA METHYLATIONSpecies, tissue, and age specificityGene expressionLearning and memoryEarly life stress behaviorCONCLUSIONACKNOWLEDGMENTREFERENCESApproaches to Detecting DNA Base Modification in the BrainMETHODS FOR DETECTION OF DNA MODIFICATIONS IN THE GENOMEChromatography and mass spectrometrySouthern blotBISULFITE SEQUENCING FOR THE DETECTION OF 5mCANALYSIS OF BISULFITE-TREATED DNA WITHOUT SEQUENCINGEXTENDING BISULFITE SEQUENCING: BEYOND 5mCRESTRICTION ENZYMES FOR DNA MODIFICATIONSDNA IMMUNOPRECIPITATIONOTHER CHEMICAL APPROACHESSUMMARYDETECTION OF DNA MODIFICATIONS IN THE BRAINCANDIDATE GENE APPROACHMICROARRAY SCREENINGGENOME-WIDE SEQUENCING APPROACHESCONCLUSIONS AND FUTURE DIRECTIONSREFERENCESActive DNA Demethylation in NeurodevelopmentFUNDAMENTAL BRAIN DEVELOPMENTINTERPLAY OF DNA METHYLATION AND DEMETHYLATIONDNA methyltransferaseTen-eleven translocation cytosine dioxygenaseThymine DNA glycosylaseMAPPING AND QUANTIFICATION OF THE DERIVATIVES OF 5mCDISCUSSIONREFERENCESTET and 5hmC in Neurodevelopment and the Adult BrainGLOBAL 5hmC AND TET EXPRESSION THROUGHOUT THE ADULT BRAINGENOMIC DISTRIBUTION OF 5hmCROLE OF 5hmC IN BRAIN DEVELOPMENThmC CHANGES ASSOCIATED WITH NEURONAL DIFFERENTIATIONROLE OF 5hmC IN AGING AND NEURODEGENERATIONROLE OF TET ENZYMES IN BRAIN FUNCTIONCONCLUSIONREFERENCESBeyond mCG: DNA Methylation in Noncanonical Sequence ContextINTRODUCTION: BEYOND CG METHYLATIONVARIABLE NON-CG METHYLATION ACROSS CELL TYPESNON-CG METHYLATION AND BRAIN CELL DIVERSITYNON-CG METHYLATION IN X CHROMOSOME INACTIVATIONPOSSIBLE FUNCTIONS OF NON-CG METHYLATIONOUTLOOK AND FUTURE DIRECTIONSACKNOWLEDGMENTSREFERENCESDNA Modifications and MemoryDNA MODIFICATIONS AND NEURONAL MEMORYDNA MODIFICATION AND BEHAVIORAL MEMORYSpatial and fear memory systemsReward-related memory systemsDNA methylation in brain diseases involving cognitive deficitsFUTURE DIRECTIONSHow is DNA methylation regulated at specific genes?How does DNA methylation regulate cell-wide or synapse-specific plasticity to control memory?How do other DNA modifications contribute to memory formation?CONCLUSIONSACKNOWLEDGMENTSREFERENCESMeasuring CpG Methylation by SMRT SequencingDNA METHYLOME OF DISEASE-ASSOCIATED REPEATSTRADITIONAL METHODS FOR OBSERVING DNA METHYLOMESMRT SEQUENCING TO DETECT DNA MODIFICATIONSPREDICTION OF THE REGIONAL METHYLATION STATE FROM KINETIC DATAGENOME-WIDE METHYLATION PATTERN OF REPETITIVE ELEMENTS IN THE HUMAN GENOMEANALYSIS OF AN ACTIVE TRANSPOSABLE ELEMENTDISCUSSIONREFERENCESEpigenetic Modifications of DNA and Drug AddictionADDICTION AND REWARD PATHWAYDNA METHYLATION AND ITS CATALYZING DNMT ENZYMES IN ADDICTIONStudies of cocaine and other psychostimulantsStudies of ethanolMETHYL-CYTOSINE OXIDATION AND ITS TET CATALYZING ENZYMES IN ADDICTIONGENOME-WIDE MAPPING OF DNA MODIFICATIONS IN ADDICTIONCHALLENGES AND FUTURE DIRECTIONSACKNOWLEDGMENTSREFERENCESWhat Does the Future Hold for the Study of Nucleic Acid Modifications in the Brain?EXPANDING THE REALM OF POSSIBILITY: DNA MODIFICATIONS ON ALL FOUR BASESDNA MODIFICATIONS DRIVE DNA STRUCTURE AND FUNCTIONDNA MODIFICATIONS INFLUENCE DNA EDITINGTAKING NEUROEPIGENETICS TO THE NEXT LEVEL: EPITRANSCRIPTOMICS COMES OF AGEOUTSTANDING QUESTIONS AND EMERGING TECHNOLOGIESSUMMARY AND CONCLUSIONSREFERENCES
 
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