Early-Life Gene Expression in Neurons Modulates Lasting Epigenetic States
Tài liệu tham khảo
Anders, 2015, HTSeq--a Python framework to work with high-throughput sequencing data, Bioinformatics, 31, 166, 10.1093/bioinformatics/btu638
Baubec, 2013, Methylation-dependent and -independent genomic targeting principles of the MBD protein family, Cell, 153, 480, 10.1016/j.cell.2013.03.011
Baubec, 2015, Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation, Nature, 520, 243, 10.1038/nature14176
Bird, 2002, DNA methylation patterns and epigenetic memory, Genes Dev., 16, 6, 10.1101/gad.947102
Bloodgood, 2013, The activity-dependent transcription factor NPAS4 regulates domain-specific inhibition, Nature, 503, 121, 10.1038/nature12743
Booth, 2012, Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution, Science, 336, 934, 10.1126/science.1220671
Chahrour, 2007, The story of Rett syndrome: from clinic to neurobiology, Neuron, 56, 422, 10.1016/j.neuron.2007.10.001
Chen, 2003, Derepression of BDNF transcription involves calcium-dependent phosphorylation of MeCP2, Science, 302, 885, 10.1126/science.1086446
Chen, 2015, MeCP2 binds to non-CG methylated DNA as neurons mature, influencing transcription and the timing of onset for Rett syndrome, Proc. Natl. Acad. Sci. USA, 112, 5509, 10.1073/pnas.1505909112
Feng, 2005, Dynamic expression of de novo DNA methyltransferases Dnmt3a and Dnmt3b in the central nervous system, J. Neurosci. Res., 79, 734, 10.1002/jnr.20404
Gabel, 2015, Disruption of DNA-methylation-dependent long gene repression in Rett syndrome, Nature, 522, 89, 10.1038/nature14319
Gibson, 2012, Mutations in EZH2 cause Weaver syndrome, Am. J. Hum. Genet., 90, 110, 10.1016/j.ajhg.2011.11.018
Gunnersen, 2007, Sez-6 proteins affect dendritic arborization patterns and excitability of cortical pyramidal neurons, Neuron, 56, 621, 10.1016/j.neuron.2007.09.018
Guo, 2014, Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain, Nat. Neurosci., 17, 215, 10.1038/nn.3607
Guo, 2015, Structural insight into autoinhibition and histone H3-induced activation of DNMT3A, Nature, 517, 640, 10.1038/nature13899
Guy, 2001, A mouse Mecp2-null mutation causes neurological symptoms that mimic Rett syndrome, Nat. Genet., 27, 322, 10.1038/85899
He, 2015, Non-CG Methylation in the Human Genome, Annu. Rev. Genomics Hum. Genet., 16, 55, 10.1146/annurev-genom-090413-025437
Hippenmeyer, 2005, A developmental switch in the response of DRG neurons to ETS transcription factor signaling, PLoS Biol., 3, e159, 10.1371/journal.pbio.0030159
Huang da, 2009, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources, Nat. Protoc., 4, 44, 10.1038/nprot.2008.211
Jaenisch, 2003, Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals, Nat. Genet., 33, 245, 10.1038/ng1089
Kaneda, 2004, Essential role for de novo DNA methyltransferase Dnmt3a in paternal and maternal imprinting, Nature, 429, 900, 10.1038/nature02633
Kim, 2013, TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions, Genome Biol., 14, R36, 10.1186/gb-2013-14-4-r36
Kinde, 2016, DNA methylation in the gene body influences MeCP2-mediated gene repression, Proc. Natl. Acad. Sci. USA, 113, 15114, 10.1073/pnas.1618737114
Klein, 2015, Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells, Cell, 161, 1187, 10.1016/j.cell.2015.04.044
Kriaucionis, 2009, The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain, Science, 324, 929, 10.1126/science.1169786
Lagger, 2017, MeCP2 recognizes cytosine methylated tri-nucleotide and di-nucleotide sequences to tune transcription in the mammalian brain, PLoS Genet., 13, e1006793, 10.1371/journal.pgen.1006793
Langmead, 2009, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biol., 10, R25, 10.1186/gb-2009-10-3-r25
Li, 2011, Histone tails regulate DNA methylation by allosterically activating de novo methyltransferase, Cell Res., 21, 1172, 10.1038/cr.2011.92
Lister, 2015, Turning over DNA methylation in the mind, Front. Neurosci., 9, 252, 10.3389/fnins.2015.00252
Lister, 2013, Global epigenomic reconfiguration during mammalian brain development, Science, 341, 1237905, 10.1126/science.1237905
Mamiya, 2008, Changes in attack behavior and activity in EphA5 knockout mice, Brain Res., 1205, 91, 10.1016/j.brainres.2008.02.047
Mardinly, 2016, Sensory experience regulates cortical inhibition by inducing IGF1 in VIP neurons, Nature, 531, 371, 10.1038/nature17187
Margueron, 2011, The Polycomb complex PRC2 and its mark in life, Nature, 469, 343, 10.1038/nature09784
Markram, 2004, Interneurons of the neocortical inhibitory system, Nat. Rev. Neurosci., 5, 793, 10.1038/nrn1519
Mo, 2015, Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain, Neuron, 86, 1369, 10.1016/j.neuron.2015.05.018
Nguyen, 2007, Ablation of de novo DNA methyltransferase Dnmt3a in the nervous system leads to neuromuscular defects and shortened lifespan, Dev. Dyn., 236, 1663, 10.1002/dvdy.21176
Nord, 2013, Rapid and pervasive changes in genome-wide enhancer usage during mammalian development, Cell, 155, 1521, 10.1016/j.cell.2013.11.033
Ooi, 2007, DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA, Nature, 448, 714, 10.1038/nature05987
Pastor, 2013, TETonic shift: biological roles of TET proteins in DNA demethylation and transcription, Nat. Rev. Mol. Cell Biol., 14, 341, 10.1038/nrm3589
Rose, 2014, Understanding the relationship between DNA methylation and histone lysine methylation, Biochim. Biophys. Acta, 1839, 1362, 10.1016/j.bbagrm.2014.02.007
Rube, 2016, Sequence features accurately predict genome-wide MeCP2 binding in vivo, Nat. Commun., 7, 11025, 10.1038/ncomms11025
Sanders, 2015, Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci, Neuron, 87, 1215, 10.1016/j.neuron.2015.09.016
Satija, 2015, Spatial reconstruction of single-cell gene expression data, Nat. Biotechnol., 33, 495, 10.1038/nbt.3192
Shen, 2008, EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency, Mol. Cell, 32, 491, 10.1016/j.molcel.2008.10.016
Skene, 2010, Neuronal MeCP2 is expressed at near histone-octamer levels and globally alters the chromatin state, Mol. Cell, 37, 457, 10.1016/j.molcel.2010.01.030
Song, 2012, Mapping recently identified nucleotide variants in the genome and transcriptome, Nat. Biotechnol., 30, 1107, 10.1038/nbt.2398
Sugino, 2014, Cell-type-specific repression by methyl-CpG-binding protein 2 is biased toward long genes, J. Neurosci., 34, 12877, 10.1523/JNEUROSCI.2674-14.2014
Sztainberg, 2016, Lessons learned from studying syndromic autism spectrum disorders, Nat. Neurosci., 19, 1408, 10.1038/nn.4420
Taniguchi, 2011, A resource of Cre driver lines for genetic targeting of GABAergic neurons in cerebral cortex, Neuron, 71, 995, 10.1016/j.neuron.2011.07.026
Tatton-Brown, 2014, Mutations in the DNA methyltransferase gene DNMT3A cause an overgrowth syndrome with intellectual disability, Nat. Genet., 46, 385, 10.1038/ng.2917
Trapnell, 2014, The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells, Nat. Biotechnol., 32, 381, 10.1038/nbt.2859
Tronche, 1999, Disruption of the glucocorticoid receptor gene in the nervous system results in reduced anxiety, Nat. Genet., 23, 99, 10.1038/12703
Vissers, 2016, Genetic studies in intellectual disability and related disorders, Nat. Rev. Genet., 17, 9, 10.1038/nrg3999
von Schimmelmann, 2016, Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration, Nat. Neurosci., 19, 1321, 10.1038/nn.4360
Wilkinson, 2001, Multiple roles of EPH receptors and ephrins in neural development, Nat. Rev. Neurosci., 2, 155, 10.1038/35058515
Xi, 2009, BSMAP: whole genome bisulfite sequence MAPping program, BMC Bioinformatics, 10, 232, 10.1186/1471-2105-10-232
Yu, 2007, Febrile seizures are associated with mutation of seizure-related (SEZ) 6, a brain-specific gene, J. Neurosci. Res., 85, 166, 10.1002/jnr.21103
Zang, 2009, A clustering approach for identification of enriched domains from histone modification ChIP-Seq data, Bioinformatics, 25, 1952, 10.1093/bioinformatics/btp340
Zhang, 2014, Ezh2 regulates adult hippocampal neurogenesis and memory, J. Neurosci., 34, 5184, 10.1523/JNEUROSCI.4129-13.2014
Zilionis, 2017, Single-cell barcoding and sequencing using droplet microfluidics, Nat. Protoc., 12, 44, 10.1038/nprot.2016.154