Early-Life Gene Expression in Neurons Modulates Lasting Epigenetic States

Cell - Tập 171 - Trang 1151-1164.e16 - 2017
Hume Stroud1, Susan C. Su1, Sinisa Hrvatin1, Alexander W. Greben1, William Renthal1, Lisa D. Boxer1, M. Aurel Nagy1, Daniel R. Hochbaum1, Benyam Kinde1, Harrison W. Gabel1, Michael E. Greenberg1
1Department of Neurobiology, Harvard Medical School, Boston, MA 02115 USA

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