Neuronal activity modifies the chromatin accessibility landscape in the adult brain

The Role of Epigenetic Mechanisms in the Regulation of Gene Expression in the Nervous System

(2016) Justyna Cholewa-Waclaw et al.   JOURNAL OF NEUROSCIENCE

Core pathway mutations induce de-differentiation of murine astrocytes into glioblastoma stem cells that are sensitive to radiation but resistant to temozolomide

(2016) Ralf S. Schmid et al.   NEURO-ONCOLOGY

Epigenetic mechanisms of neuroplasticity and the implications for stroke recovery

(2015) Ryan J. Felling et al.   EXPERIMENTAL NEUROLOGY

Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease

(2015) Elizabeta Gjoneska et al.   NATURE

Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum

(2015) Christopher L Frank et al.   NATURE NEUROSCIENCE

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

(2015) Alisa Mo et al.   NEURON

Epigenetic mechanisms of chronic pain

(2015) Giannina Descalzi et al.   TRENDS IN NEUROSCIENCES

Discovery of Transcription Factors and Regulatory Regions Driving In Vivo Tumor Development by ATAC-seq and FAIRE-seq Open Chromatin Profiling

(2015) Kristofer Davie et al.   PLoS Genetics

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

(2014) Li Shen et al.   BMC GENOMICS

Synaptic, transcriptional and chromatin genes disrupted in autism

(2014) Silvia De Rubeis et al.   NATURE

Genome-wide identification and characterization of functional neuronal activity–dependent enhancers

(2014) Athar N Malik et al.   NATURE NEUROSCIENCE

Decoding neural transcriptomes and epigenomes via high-throughput sequencing

(2014) Jaehoon Shin et al.   NATURE NEUROSCIENCE

Motif-based analysis of large nucleotide data sets using MEME-ChIP

(2014) Wenxiu Ma et al.   Nature Protocols

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

(2014) J. Vierstra et al.   SCIENCE

GAT: a simulation framework for testing the association of genomic intervals

(2013) A. Heger et al.   BIOINFORMATICS

Secreted Frizzled-Related Protein 3 Regulates Activity-Dependent Adult Hippocampal Neurogenesis

(2013) Mi-Hyeon Jang et al.   Cell Stem Cell

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain

(2013) Junjie U Guo et al.   NATURE NEUROSCIENCE

Epigenetics and persistent memory: implications for reconsolidation and silent extinction beyond the zero

(2013) K Matthew Lattal et al.   NATURE NEUROSCIENCE

The Emerging Field of Neuroepigenetics

(2013) J. David Sweatt   NEURON

DNA Modifications and Neurological Disorders

(2013) Yi-Lan Weng et al.   Neurotherapeutics

diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates

(2013) Li Shen et al.   PLoS One

Spatial Firing Correlates of Physiologically Distinct Cell Types of the Rat Dentate Gyrus

(2012) J. P. Neunuebel et al.   JOURNAL OF NEUROSCIENCE

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA

(2012) Jeremy M Simon et al.   Nature Protocols

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

Hydroxylation of 5-Methylcytosine by TET1 Promotes Active DNA Demethylation in the Adult Brain

(2011) Junjie U. Guo et al.   CELL

Emerging roles of TET proteins and 5-hydroxymethylcytosines in active DNA demethylation and beyond

(2011) Junjie U. Guo et al.   CELL CYCLE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Neuronal activity modifies the DNA methylation landscape in the adult brain

(2011) Junjie U Guo et al.   NATURE NEUROSCIENCE

ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity

(2011) Matthew D. Young et al.   NUCLEIC ACIDS RESEARCH

Epigenetic Regulation of Gene Expression in Physiological and Pathological Brain Processes

(2011) Johannes Gräff et al.   PHYSIOLOGICAL REVIEWS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Epigenetic regulation of the neural transcriptome: the meaning of the marks

(2010) Michael J Meaney et al.   NATURE NEUROSCIENCE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Serum Response Factor and a Putative Novel Transcription Factor Regulate Expression of the Immediate-Early Gene Arc/Arg3.1 in Neurons

(2009) S. A. Pintchovski et al.   JOURNAL OF NEUROSCIENCE

Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)

(2009) Paul G. Giresi et al.   METHODS

Neuronal Activity-Induced Gadd45b Promotes Epigenetic DNA Demethylation and Adult Neurogenesis

(2009) D. K. Ma et al.   SCIENCE

Decoding the Epigenetic Language of Neuronal Plasticity

(2008) Emiliana Borrelli et al.   NEURON

Synaptic activity-responsive element in the Arc/Arg3.1 promoter essential for synapse-to-nucleus signaling in activated neurons

(2008) T. Kawashima et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY