Environmental enrichment increases transcriptional and epigenetic differentiation between mouse dorsal and ventral dentate gyrus

[1]  Per B. Brockhoff,et al.  lmerTest Package: Tests in Linear Mixed Effects Models , 2017 .

[2]  Justin P Sandoval,et al.  Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex , 2017, Science.

[3]  E. Nestler,et al.  Understanding the epigenetic basis of sex differences in depression , 2017, Journal of neuroscience research.

[4]  A. Bird,et al.  The Role of Epigenetic Mechanisms in the Regulation of Gene Expression in the Nervous System , 2016, The Journal of Neuroscience.

[5]  G. Ming,et al.  Epigenetic mechanisms in neurogenesis , 2016, Nature Reviews Neuroscience.

[6]  Cynthia C. Hession,et al.  Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons , 2016, Science.

[7]  Nelson Spruston,et al.  Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neurons , 2016, eLife.

[8]  Conor Fitzpatrick,et al.  Nuclear RNA-seq of single neurons reveals molecular signatures of activation , 2016, Nature communications.

[9]  Mark S. Cembrowski,et al.  Author response: Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neurons , 2016 .

[10]  Mark S. Cembrowski,et al.  Spatial Gene-Expression Gradients Underlie Prominent Heterogeneity of CA1 Pyramidal Neurons , 2016, Neuron.

[11]  P. Smialowski,et al.  NeuroD1 reprograms chromatin and transcription factor landscapes to induce the neuronal program , 2016, The EMBO journal.

[12]  C. Ponting,et al.  Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity , 2015, Nature Methods.

[13]  Zachary S. Lorsch,et al.  Sex Differences in Nucleus Accumbens Transcriptome Profiles Associated with Susceptibility versus Resilience to Subchronic Variable Stress , 2015, The Journal of Neuroscience.

[14]  M. Meaney,et al.  Epigenetics/Programming in the HPA Axis. , 2015, Comprehensive Physiology.

[15]  D. Lie,et al.  Transcription-Factor-Dependent Control of Adult Hippocampal Neurogenesis. , 2015, Cold Spring Harbor perspectives in biology.

[16]  M. Bulyk,et al.  Grhl2 is required in nonneural tissues for neural progenitor survival and forebrain development , 2015, Genesis.

[17]  F. Gage,et al.  Environmental enrichment and neurogenesis: from mice to humans , 2015, Current Opinion in Behavioral Sciences.

[18]  J. Hébert,et al.  FGF Signaling Is Necessary for Neurogenesis in Young Mice and Sufficient to Reverse Its Decline in Old Mice , 2015, The Journal of Neuroscience.

[19]  Terrence J. Sejnowski,et al.  Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain , 2015, Neuron.

[20]  Jason P. Lerch,et al.  Environmental enrichment is associated with rapid volumetric brain changes in adult mice , 2015, NeuroImage.

[21]  Linda Koch.  Genomics: The best-laid plans of mice and men , 2014, Nature Reviews Genetics.

[22]  T. Maniatis,et al.  An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex , 2014, The Journal of Neuroscience.

[23]  M. Mallar Chakravarty,et al.  Pydpiper: a flexible toolkit for constructing novel registration pipelines , 2014, Front. Neuroinform..

[24]  K. Conneely,et al.  A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data , 2014, Nucleic acids research.

[25]  Guoping Fan,et al.  Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain , 2013, Nature Neuroscience.

[26]  J. David Sweatt,et al.  DNA methylation regulates associative reward learning , 2013, Nature Neuroscience.

[27]  Matthew D. Schultz,et al.  Global Epigenomic Reconfiguration During Mammalian Brain Development , 2013, Science.

[28]  Zachary D. Smith,et al.  DNA methylation: roles in mammalian development , 2013, Nature Reviews Genetics.

[29]  J. Sweatt,et al.  Epigenetic regulation of memory formation and maintenance. , 2013, Learning & memory.

[30]  Hao Wu,et al.  A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data , 2012, Biostatistics.

[31]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[32]  J. Girault,et al.  Characterization of dopamine D1 and D2 receptor‐expressing neurons in the mouse hippocampus , 2012, Hippocampus.

[33]  Bing Ren,et al.  Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine , 2012, Nature Protocols.

[34]  G. Hon,et al.  Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome , 2012, Cell.

[35]  Lindsay S. Cahill,et al.  Preparation of fixed mouse brains for MRI , 2012, NeuroImage.

[36]  Davis J. McCarthy,et al.  Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation , 2012, Nucleic acids research.

[37]  R. Bartesaghi,et al.  Impact of environmental enrichment on neurogenesis in the dentate gyrus during the early postnatal period , 2011, Brain Research.

[38]  Lindsay S. Cahill,et al.  Multiple-mouse Neuroanatomical Magnetic Resonance Imaging , 2011, Journal of visualized experiments : JoVE.

[39]  T. Ushijima,et al.  Hippocampal epigenetic modification at the brain‐derived neurotrophic factor gene induced by an enriched environment , 2011, Hippocampus.

[40]  R Mark Henkelman,et al.  MRI phenotyping of genetically altered mice. , 2011, Methods in molecular biology.

[41]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[42]  J. Frisén,et al.  Impaired Hippocampal Neurogenesis and Vascular Formation in Ephrin‐A5‐Deficient Mice , 2010, Stem cells.

[43]  K. Rockland,et al.  Expression of COUP-TFII Nuclear Receptor in Restricted GABAergic Neuronal Populations in the Adult Rat Hippocampus , 2010, The Journal of Neuroscience.

[44]  Hong-wei Dong,et al.  Are the Dorsal and Ventral Hippocampus Functionally Distinct Structures? , 2010, Neuron.

[45]  Michael J Meaney,et al.  Epigenetics and the environmental regulation of the genome and its function. , 2010, Annual review of psychology.

[46]  Lee E. Edsall,et al.  Human DNA methylomes at base resolution show widespread epigenomic differences , 2009, Nature.

[47]  K. Nave,et al.  Neurod1 is essential for the survival and maturation of adult-born neurons , 2009, Nature Neuroscience.

[48]  Gene W. Yeo,et al.  Wnt-mediated activation of NeuroD1 and retro-elements during adult neurogenesis , 2009, Nature Neuroscience.

[49]  David R. Liu,et al.  Conversion of 5-Methylcytosine to 5- Hydroxymethylcytosine in Mammalian DNA by the MLL Partner TET1 , 2009 .

[50]  N. Heintz,et al.  The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain , 2009, Science.

[51]  F. Mora,et al.  Environmental enrichment, prefrontal cortex, stress, and aging of the brain , 2009, Journal of Neural Transmission.

[52]  Jason S. Snyder,et al.  Anatomical gradients of adult neurogenesis and activity: Young neurons in the ventral dentate gyrus are activated by water maze training , 2009, Hippocampus.

[53]  G. Ming,et al.  Neuronal Activity–Induced Gadd45b Promotes Epigenetic DNA Demethylation and Adult Neurogenesis , 2009, Science.

[54]  Jeffrey D. Zaremba,et al.  Transcription factor MEF2C influences neural stem/progenitor cell differentiation and maturation in vivo , 2008, Proceedings of the National Academy of Sciences.

[55]  Brian B. Avants,et al.  Symmetric diffeomorphic image registration with cross-correlation: Evaluating automated labeling of elderly and neurodegenerative brain , 2008, Medical Image Anal..

[56]  R. Mark Henkelman,et al.  Automated deformation analysis in the YAC128 Huntington disease mouse model , 2008, NeuroImage.

[57]  Chiara Braschi,et al.  Brain‐derived neurotrophic factor (BDNF) is required for the enhancement of hippocampal neurogenesis following environmental enrichment , 2006, The European journal of neuroscience.

[58]  N. Lemon,et al.  Dopamine D1/D5 Receptors Gate the Acquisition of Novel Information through Hippocampal Long-Term Potentiation and Long-Term Depression , 2006, The Journal of Neuroscience.

[59]  M. Héry,et al.  Agomelatine, a New Antidepressant, Induces Regional Changes in Hippocampal Neurogenesis , 2006, Biological Psychiatry.

[60]  A. Artola,et al.  Long‐lasting modulation of the induction of LTD and LTP in rat hippocampal CA1 by behavioural stress and environmental enrichment , 2006, The European journal of neuroscience.

[61]  G. Mckhann.  VEGF Links Hippocampal Activity with Neurogenesis, Learning, and Memory. , 2005, Neurosurgery.

[62]  F. Gage,et al.  Neural consequences of enviromental enrichment , 2000, Nature Reviews Neuroscience.

[63]  P. Gruss,et al.  Pax3 and Pax7 are expressed in commissural neurons and restrict ventral neuronal identity in the spinal cord , 1998, Mechanisms of Development.

[64]  George Paxinos,et al.  The Mouse Brain in Stereotaxic Coordinates , 2001 .

[65]  F. Gage,et al.  More hippocampal neurons in adult mice living in an enriched environment , 1997, Nature.

[66]  D. Collins,et al.  Automatic 3D Intersubject Registration of MR Volumetric Data in Standardized Talairach Space , 1994, Journal of computer assisted tomography.

[67]  M. Miller,et al.  Bromodeoxyuridine immunohistochemical determination of the lengths of the cell cycle and the DNA-synthetic phase for an anatomically defined population , 1989, Journal of neurocytology.