Chromatin-mediated alternative splicing regulates cocaine-reward behavior

Joint profiling of histone modifications and transcriptome in single cells from mouse brain

(2021) Chenxu Zhu et al.   NATURE METHODS

The methyltransferase SETD2 couples transcription and splicing by engaging mRNA processing factors through its SHI domain

(2021) Saikat Bhattacharya et al.   Nature Communications

Cell-type and fetal-sex-specific targets of prenatal alcohol exposure in developing mouse cerebral cortex

(2021) Nihal A. Salem et al.   iScience

Stratified analyses of genome wide association study data reveal haplotypes for a candidate gene on chromosome 2 (KIAA1211L) is associated with opioid use in patients of Arabian descent

(2020) Hiba Alblooshi et al.   BMC Psychiatry

Autism-Misregulated eIF4G Microexons Control Synaptic Translation and Higher Order Cognitive Functions

(2020) Thomas Gonatopoulos-Pournatzis et al.   MOLECULAR CELL

Integrated proteogenomic approach identifying a protein signature of COPD and a new splice variant of SORBS1

(2020) Corry-Anke Brandsma et al.   THORAX

Nr4a1 suppresses cocaine-induced behavior via epigenetic regulation of homeostatic target genes

(2020) Marco D. Carpenter et al.   Nature Communications

Specific histone modifications associate with alternative exon selection during mammalian development

(2020) Qiwen Hu et al.   NUCLEIC ACIDS RESEARCH

Extensive splicing changes in an ALS/FTD transgenic mouse model overexpressing cytoplasmic fused in sarcoma

(2020) Daisuke Ito et al.   Scientific Reports

Cell-specific exon methylation and CTCF binding in neurons regulate calcium ion channel splicing and function

(2020) Eduardo Javier López Soto et al.   eLife

High throughput error corrected Nanopore single cell transcriptome sequencing

(2020) Kevin Lebrigand et al.   Nature Communications

Altered levels of CSF proteins in patients with FTD, presymptomatic mutation carriers and non-carriers

(2020) Julia Remnestål et al.   Translational Neurodegeneration

Concentration-dependent splicing is enabled by Rbfox motifs of intermediate affinity

(2020) Bridget E. Begg et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

CUX2, BRAP and ALDH2 are associated with metabolic traits in people with excessive alcohol consumption

(2020) I-Chun Chen et al.   Scientific Reports

A multi-ethnic meta-analysis identifies novel genes, including ACSL5, associated with amyotrophic lateral sclerosis

(2020) Ryoichi Nakamura et al.   Communications Biology

Differential NOVA2-Mediated Splicing in Excitatory and Inhibitory Neurons Regulates Cortical Development and Cerebellar Function

(2019) Yuhki Saito et al.   NEURON

Neurexin 3 transmembrane and soluble isoform expression and splicing haplotype are associated with neuron inflammasome and Alzheimer’s disease

(2019) Akitoyo Hishimoto et al.   Alzheimers Research & Therapy

An RNA Switch of a Large Exon of Ninein Is Regulated by the Neural Stem Cell Specific-RNA Binding Protein, Qki5

(2019) Yoshika Hayakawa-Yano et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

LncRNA Riken-201 and Riken-203 modulates neural development by regulating the Sox6 through sequestering miRNAs

(2019) Lei Zhang et al.   CELL PROLIFERATION

Reversal of Peripheral Neuropathic Pain by the Small-Molecule Natural Product Physalin F via Block of CaV2.3 (R-Type) and CaV2.2 (N-Type) Voltage-Gated Calcium Channels

(2019) Zhiming Shan et al.   ACS Chemical Neuroscience

Expression of AHI1 Rescues Amyloidogenic Pathology in Alzheimer’s Disease Model Cells

(2019) Lai-Lei Ting et al.   MOLECULAR NEUROBIOLOGY

Alternative Splicing of Presynaptic Neurexins Differentially Controls Postsynaptic NMDA and AMPA Receptor Responses

(2019) Jinye Dai et al.   NEURON

Dynamic CRMP2 Regulation of CaV2.2 in the Prefrontal Cortex Contributes to the Reinstatement of Cocaine Seeking

(2019) William C. Buchta et al.   MOLECULAR NEUROBIOLOGY

H3K36 Methylation and the Chromodomain Protein Eaf3 Are Required for Proper Cotranscriptional Spliceosome Assembly

(2019) Calvin S. Leung et al.   Cell Reports

Alternative splicing of neuronal genes: new mechanisms and new therapies

(2019) Diane Lipscombe et al.   CURRENT OPINION IN NEUROBIOLOGY

Stress resilience is promoted by a Zfp189-driven transcriptional network in prefrontal cortex

(2019) Zachary S. Lorsch et al.   NATURE NEUROSCIENCE

SETD5 Regulates Chromatin Methylation State and Preserves Global Transcriptional Fidelity during Brain Development and Neuronal Wiring

(2019) Alessandro Sessa et al.   NEURON

Mechanisms of Neuronal Alternative Splicing and Strategies for Therapeutic Interventions

(2019) Eduardo Javier Lopez Soto et al.   JOURNAL OF NEUROSCIENCE

Shisa7 is a GABAA receptor auxiliary subunit controlling benzodiazepine actions

(2019) Wenyan Han et al.   SCIENCE

Cell type-specific transcriptional programs in mouse prefrontal cortex during adolescence and addiction

(2019) Aritra Bhattacherjee et al.   Nature Communications

Cacna1b alternative splicing impacts excitatory neurotransmission and is linked to behavioral responses to aversive stimuli

(2019) Alexandra Bunda et al.   Molecular Brain

Phosphorylation of Npas4 by MAPK Regulates Reward-Related Gene Expression and Behaviors

(2019) Yasuhiro Funahashi et al.   Cell Reports

Cocaine Self-administration Alters Transcriptome-wide Responses in the Brain’s Reward Circuitry

(2018) Deena M. Walker et al.   BIOLOGICAL PSYCHIATRY

A Golgi Lipid Signaling Pathway Controls Apical Golgi Distribution and Cell Polarity during Neurogenesis

(2018) Zhigang Xie et al.   DEVELOPMENTAL CELL

Tyrosine hydroxylase down-regulation after loss of Abelson helper integration site 1 (AHI1) promotes depression via the circadian clock pathway in mice

(2018) Dongkai Guo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Single Sample Sequencing (S3EQ) of epigenome and transcriptome in nucleus accumbens

(2018) S.J. Xu et al.   JOURNAL OF NEUROSCIENCE METHODS

EpiProfile 2.0: A Computational Platform for Processing Epi-Proteomics Mass Spectrometry Data

(2018) Zuo-Fei Yuan et al.   JOURNAL OF PROTEOME RESEARCH

Targeted in situ genome-wide profiling with high efficiency for low cell numbers

(2018) Peter J Skene et al.   Nature Protocols

Changes in neuronal immunofluorescence in the C- versus N-terminal domains of hnRNP H following D1 dopamine receptor activation

(2018) Qiu T. Ruan et al.   NEUROSCIENCE LETTERS

SRSF10-mediated IL1RAP alternative splicing regulates cervical cancer oncogenesis via mIL1RAP-NF-κB-CD47 axis

(2018) Fei Liu et al.   ONCOGENE

Loss of Sfpq Causes Long-Gene Transcriptopathy in the Brain

(2018) Akihide Takeuchi et al.   Cell Reports

The RNA-binding protein ROD1/PTBP3 cotranscriptionally defines AID-loading sites to mediate antibody class switch in mammalian genomes

(2018) Juan Chen et al.   CELL RESEARCH

SEC31A mutation affects ER homeostasis, causing neurological syndrome

(2018) Daniel Halperin et al.   JOURNAL OF MEDICAL GENETICS

Genome-wide CRISPR-Cas9 Interrogation of Splicing Networks Reveals a Mechanism for Recognition of Autism-Misregulated Neuronal Microexons

(2018) Thomas Gonatopoulos-Pournatzis et al.   MOLECULAR CELL

RBM25 is a global splicing factor promoting inclusion of alternatively spliced exons and is itself regulated by lysine mono-methylation

(2017) Scott M. Carlson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Histone methyltransferase SETD2 modulates alternative splicing to inhibit intestinal tumorigenesis

(2017) Huairui Yuan et al.   JOURNAL OF CLINICAL INVESTIGATION

Chromatin-state discovery and genome annotation with ChromHMM

(2017) Jason Ernst et al.   Nature Protocols

Regulation of heat shock transcription factors and their roles in physiology and disease

(2017) Rocio Gomez-Pastor et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Deep learning of the splicing (epi)genetic code reveals a novel candidate mechanism linking histone modifications to ESC fate decision

(2017) Yungang Xu et al.   NUCLEIC ACIDS RESEARCH

The localization of pre mRNA splicing factor PRPF38B is a novel prognostic biomarker that may predict survival benefit of trastuzumab in patients with breast cancer overexpressing HER2

(2017) Tarek M.A. Abdel-Fatah et al.   Oncotarget

Histone posttranslational modifications predict specific alternative exon subtypes in mammalian brain

(2017) Qiwen Hu et al.   PLoS Computational Biology

Histone gene replacement reveals a post-transcriptional role for H3K36 in maintaining metazoan transcriptome fidelity

(2017) Michael P Meers et al.   eLife

An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

(2017) Peter J Skene et al.   eLife

Disrupted iron regulation in the brain and periphery in cocaine addiction

(2017) K D Ersche et al.   Translational Psychiatry

Cell-Type-Specific Alternative Splicing Governs Cell Fate in the Developing Cerebral Cortex

(2016) Xiaochang Zhang et al.   CELL

RNA-binding proteins, neural development and the addictions

(2016) C. D. Bryant et al.   GENES BRAIN AND BEHAVIOR

Targeted Epigenetic Remodeling of the Cdk5 Gene in Nucleus Accumbens Regulates Cocaine- and Stress-Evoked Behavior

(2016) E. A. Heller et al.   JOURNAL OF NEUROSCIENCE

Impaired Dendritic Development and Memory in Sorbs2 Knock-Out Mice

(2016) Q. Zhang et al.   JOURNAL OF NEUROSCIENCE

Genome-wide changes in lncRNA, splicing and regional gene expression patterns in autism

(2016) Neelroop N. Parikshak et al.   NATURE

Time to connect: bringing social context into addiction neuroscience

(2016) Markus Heilig et al.   NATURE REVIEWS NEUROSCIENCE

Cytoplasmic Rbfox1 Regulates the Expression of Synaptic and Autism-Related Genes

(2016) Ji-Ann Lee et al.   NEURON

Herpes simplex virus ICP27 regulates alternative pre-mRNA polyadenylation and splicing in a sequence-dependent manner

(2016) Shuang Tang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Histone H3K36 methylation regulates pre-mRNA splicing inSaccharomyces cerevisiae

(2016) Matthew R. Sorenson et al.   RNA Biology

The RNA-binding landscape of RBM10 and its role in alternative splicing regulation in models of mouse early development

(2016) Julie Rodor et al.   RNA Biology

Agonists and Antagonists of TGF-β Family Ligands

(2016) Chenbei Chang   Cold Spring Harbor Perspectives in Biology

PTBP1 and PTBP2 Serve Both Specific and Redundant Functions in Neuronal Pre-mRNA Splicing

(2016) John K. Vuong et al.   Cell Reports

Methamphetamine blunts Ca2+ currents and excitatory synaptic transmission through D1/5 receptor-mediated mechanisms in the mouse medial prefrontal cortex

(2015) Betina González et al.   ADDICTION BIOLOGY

RNA sequencing of transcriptomes in human brain regions: protein-coding and non-coding RNAs, isoforms and alleles

(2015) Amy Webb et al.   BMC GENOMICS

Temporal patterns of gene expression during calyx of held development

(2015) Douglas R. Kolson et al.   Developmental Neurobiology

The sequenced rat brain transcriptome - its use in identifying networks predisposing alcohol consumption

(2015) Laura M. Saba et al.   FEBS Journal

Clinically relevant genetic biomarkers from the brain in alcoholism with representation on high resolution chromosome ideograms

(2015) Ann M. Manzardo et al.   GENE

Role of DNA Methylation in the Nucleus Accumbens in Incubation of Cocaine Craving

(2015) R. Massart et al.   JOURNAL OF NEUROSCIENCE

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

(2015) Alisa Mo et al.   NEURON

Regulation of mammalian transcription and splicing by Nuclear RNAi

(2015) Roya Kalantari et al.   NUCLEIC ACIDS RESEARCH

TDP-43 repression of nonconserved cryptic exons is compromised in ALS-FTD

(2015) J. P. Ling et al.   SCIENCE

SP-R210 (Myo18A) Isoforms as Intrinsic Modulators of Macrophage Priming and Activation

(2015) Linlin Yang et al.   PLoS One

A Heroin Addiction Severity-Associated Intronic Single Nucleotide Polymorphism Modulates Alternative Pre-mRNA Splicing of the   Opioid Receptor Gene OPRM1 via hnRNPH Interactions

(2014) J. Xu et al.   JOURNAL OF NEUROSCIENCE

Long-term parental methamphetamine exposure of mice influences behavior and hippocampal DNA methylation of the offspring

(2014) Y Itzhak et al.   MOLECULAR PSYCHIATRY

Locus-specific epigenetic remodeling controls addiction- and depression-related behaviors

(2014) Elizabeth A Heller et al.   NATURE NEUROSCIENCE

Understanding the addiction cycle: A complex biology with distinct contributions of genotype vs. sex at each stage

(2014) C.J. Wilhelm et al.   NEUROSCIENCE

Targeting SR Proteins Improves SMN Expression in Spinal Muscular Atrophy Cells

(2014) Claribel D. Wee et al.   PLoS One

rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

(2014) Shihao Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens

(2014) Jian Feng et al.   GENOME BIOLOGY

Identification of Alternative Splicing Events Regulated by the Oncogenic Factor SRSF1 in Lung Cancer

(2013) F. J. de Miguel et al.   CANCER RESEARCH

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

p63 and Brg1 control developmentally regulated higher-order chromatin remodelling at the epidermal differentiation complex locus in epidermal progenitor cells

(2013) A. N. Mardaryev et al.   DEVELOPMENT

FUS-mediated alternative splicing in the nervous system: consequences for ALS and FTLD

(2013) Denise Orozco et al.   JOURNAL OF MOLECULAR MEDICINE-JMM

The C-terminal domain of Brd2 is important for chromatin interaction and regulation of transcription and alternative splicing

(2013) Jarmila Hnilicová et al.   MOLECULAR BIOLOGY OF THE CELL

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

Changes in gene expression within the extended amygdala following binge-like alcohol drinking by adolescent alcohol-preferring (P) rats

(2013) William J. McBride et al.   PHARMACOLOGY BIOCHEMISTRY AND BEHAVIOR

ALS-linked TDP-43 mutations produce aberrant RNA splicing and adult-onset motor neuron disease without aggregation or loss of nuclear TDP-43

(2013) E. S. Arnold et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Epigenetic features are significantly associated with alternative splicing

(2012) Yuanpeng Zhou et al.   BMC GENOMICS

RBFOX1 regulates both splicing and transcriptional networks in human neuronal development

(2012) Brent L. Fogel et al.   HUMAN MOLECULAR GENETICS

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

(2012) Caryn S. Ross-Innes et al.   NATURE

Epigenetic inheritance of a cocaine-resistance phenotype

(2012) Fair M Vassoler et al.   NATURE NEUROSCIENCE

Coordinated dysregulation of mRNAs and microRNAs in the rat medial prefrontal cortex following a history of alcohol dependence

(2012) J D Tapocik et al.   PHARMACOGENOMICS JOURNAL

LSM Proteins Provide Accurate Splicing and Decay of Selected Transcripts to Ensure Normal Arabidopsis Development

(2012) C. Perea-Resa et al.   PLANT CELL

Dysfunctional gene splicing as a potential contributor to neuropsychiatric disorders

(2011) Stephen J. Glatt et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART B-NEUROPSYCHIATRIC GENETICS

Polymorphisms in ABLIM1 are Associated with Personality Traits and Alcohol Dependence

(2011) Ke-Sheng Wang et al.   JOURNAL OF MOLECULAR NEUROSCIENCE

Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36

(2011) Sérgio Fernandes de Almeida et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Gender-stratified gene and gene–treatment interactions in smoking cessation

(2011) W Lee et al.   PHARMACOGENOMICS JOURNAL

Histone Deacetylase Activity Modulates Alternative Splicing

(2011) Jarmila Hnilicová et al.   PLoS One

Differential patterns of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, nucleosome density and H3K36me3 marking in fission yeast

(2011) Brian T Wilhelm et al.   GENOME BIOLOGY

Cocaine-induced neuroadaptations in glutamate transmission

(2010) Heath D. Schmidt et al.   Annals of the New York Academy of Sciences

Gene expression changes in the medial prefrontal cortex and nucleus accumbens following abstinence from cocaine self-administration

(2010) Willard M Freeman et al.   BMC NEUROSCIENCE

Cocaine-Induced Chromatin Remodeling Increases Brain-Derived Neurotrophic Factor Transcription in the Rat Medial Prefrontal Cortex, Which Alters the Reinforcing Efficacy of Cocaine

(2010) G. Sadri-Vakili et al.   JOURNAL OF NEUROSCIENCE

Adam22 Is a Major Neuronal Receptor for Lgi4-Mediated Schwann Cell Signaling

(2010) E. Ozkaynak et al.   JOURNAL OF NEUROSCIENCE

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

Regulation of Alternative Splicing by Histone Modifications

(2010) R. F. Luco et al.   SCIENCE

Identification of tyrosine kinase, HCK, and tumor suppressor, BIN1, as potential mediators ofAHI-1oncogene in primary and transformed CTCL cells

(2009) Erin Kennah et al.   BLOOD

Heterogeneous Nuclear Ribonucleoprotein L Is a Subunit of Human KMT3a/Set2 Complex Required for H3 Lys-36 Trimethylation Activityin Vivo

(2009) Wen Yuan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Unknown

(2009) Tomas Drgon et al.   MOLECULAR MEDICINE

Differential chromatin marking of introns and expressed exons by H3K36me3

(2009) Paulina Kolasinska-Zwierz et al.   NATURE GENETICS

The regulation of neuronal gene expression by alcohol

(2009) Leonardo Pignataro et al.   PHARMACOLOGY & THERAPEUTICS

Tissue- and Cell-Specific Alternative Splicing of NFIC

(2008) Ejvis Lamani et al.   CELLS TISSUES ORGANS

Integrative proteomic analysis of the nucleus accumbens in rhesus monkeys following cocaine self-administration

(2008) N S Tannu et al.   MOLECULAR PSYCHIATRY