Regulatory RNAs and control of epigenetic mechanisms: expectations for cognition and cognitive dysfunction

Computational identification of epigenetically regulated lncRNAs and their associated genes based on integrating genomic data

(2015) Tingting Zhao et al.   FEBS LETTERS

Noncoding RNAs and neurobehavioral mechanisms in psychiatric disease

(2015) J Kocerha et al.   MOLECULAR PSYCHIATRY

Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways

(2015)   NATURE NEUROSCIENCE

Double-stranded RNA made inC. elegansneurons can enter the germline and cause transgenerational gene silencing

(2015) Sindhuja Devanapally et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Breeding scheme and maternal small RNAs affect the efficiency of transgenerational inheritance of a paramutation in mice

(2015) Shuiqiao Yuan et al.   Scientific Reports

Transcriptional regulation mechanism mediated by miRNA–DNA•DNA triplex structure stabilized by Argonaute

(2014) Julia D. Toscano-Garibay et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

LongTarget: a tool to predict lncRNA DNA-binding motifs and binding sites via Hoogsteen base-pairing analysis

(2014) Sha He et al.   BIOINFORMATICS

Molecular Mechanism of Action of Plant DRM De Novo DNA Methyltransferases

(2014) Xuehua Zhong et al.   CELL

piRNAs

(2014) Bo W. Han et al.   CURRENT BIOLOGY

Involvement of Telomerase Reverse Transcriptase in Heterochromatin Maintenance

(2014) Y. Maida et al.   MOLECULAR AND CELLULAR BIOLOGY

The Long Noncoding RNAs NEAT1 and MALAT1 Bind Active Chromatin Sites

(2014) Jason A. West et al.   MOLECULAR CELL

Integrating the roles of long and small non-coding RNA in brain function and disease

(2014) G Barry   MOLECULAR PSYCHIATRY

PIWI proteins and PIWI-interacting RNAs in the soma

(2014) Robert J. Ross et al.   NATURE

Methylomic profiling implicates cortical deregulation of ANK1 in Alzheimer's disease

(2014) Katie Lunnon et al.   NATURE NEUROSCIENCE

Implication of sperm RNAs in transgenerational inheritance of the effects of early trauma in mice

(2014) Katharina Gapp et al.   NATURE NEUROSCIENCE

Targeted sequencing for gene discovery and quantification using RNA CaptureSeq

(2014) Tim R Mercer et al.   Nature Protocols

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity

(2014) Marjori A. Matzke et al.   NATURE REVIEWS GENETICS

A census of human RNA-binding proteins

(2014) Stefanie Gerstberger et al.   NATURE REVIEWS GENETICS

The rise of regulatory RNA

(2014) Kevin V. Morris et al.   NATURE REVIEWS GENETICS

Epigenetic mechanisms of memory formation and reconsolidation

(2014) Timothy J. Jarome et al.   NEUROBIOLOGY OF LEARNING AND MEMORY

Epigenetic modifications in the nervous system and their impact upon cognitive impairments

(2014) Andrii Rudenko et al.   NEUROPHARMACOLOGY

NF-κB directly mediates epigenetic deregulation of common microRNAs in Epstein-Barr virus-mediated transformation of B-cells and in lymphomas

(2014) Roser Vento-Tormo et al.   NUCLEIC ACIDS RESEARCH

Expression of microRNAs and Other Small RNAs in Prefrontal Cortex in Schizophrenia, Bipolar Disorder and Depressed Subjects

(2014) Neil R. Smalheiser et al.   PLoS One

Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations

(2014) Glenn K. Fu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes

(2014) Nicholas T. Ingolia et al.   Cell Reports

To be or not to be a piRNA: genomic origin and processing of piRNAs

(2014) Adrien Le Thomas et al.   GENOME BIOLOGY

Competing endogenous RNAs (ceRNAs): new entrants to the intricacies of gene regulation

(2014) Reena V. Kartha et al.   Frontiers in Genetics

Nuclear lncRNAs as epigenetic regulators—Beyond skepticism

(2013) Shinichi Nakagawa et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Gene regulation by the act of long non-coding RNA transcription

(2013) Aleksandra E Kornienko et al.   BMC BIOLOGY

Roles of long noncoding RNAs in brain development, functional diversification and neurodegenerative diseases

(2013) Ping Wu et al.   BRAIN RESEARCH BULLETIN

Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins

(2013) Mitchell Guttman et al.   CELL

Ribosome profiling reveals resemblance between long non-coding RNAs and 5′ leaders of coding RNAs

(2013) Guo-Liang Chew et al.   DEVELOPMENT

Chromatin remodeling by the small RNA machinery in mammalian cells

(2013) Long-Cheng Li   Epigenetics

RNA-mediated gene activation

(2013) Alan L Jiao et al.   Epigenetics

An Emerging Role for Long Non-Coding RNA Dysregulation in Neurological Disorders

(2013) Chiara Fenoglio et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Guided by RNAs: X-Inactivation as a Model for lncRNA Function

(2013) John E. Froberg et al.   JOURNAL OF MOLECULAR BIOLOGY

The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing

(2013) G Barry et al.   MOLECULAR PSYCHIATRY

DNMT1-interacting RNAs block gene-specific DNA methylation

(2013) Annalisa Di Ruscio et al.   NATURE

Parental olfactory experience influences behavior and neural structure in subsequent generations

(2013) Brian G Dias et al.   NATURE NEUROSCIENCE

Gene regulation by antisense transcription

(2013) Vicent Pelechano et al.   NATURE REVIEWS GENETICS

Emerging epigenetic mechanisms of long non-coding RNAs

(2013) K. Schaukowitch et al.   NEUROSCIENCE

Deep sequencing of small RNAs identifies canonical and non-canonical miRNA and endogenous siRNAs in mammalian somatic tissues

(2013) Leandro Castellano et al.   NUCLEIC ACIDS RESEARCH

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Systematic Transcriptome Wide Analysis of lncRNA-miRNA Interactions

(2013) Saakshi Jalali et al.   PLoS One

Dysregulation of the long non-coding RNA transcriptome in a Rett syndrome mouse model

(2013) Paolo Petazzi et al.   RNA Biology

Finding the target sites of RNA-binding proteins

(2013) Xiao Li et al.   Wiley Interdisciplinary Reviews-RNA

MALAT-1, a non protein-coding RNA is upregulated in the cerebellum, hippocampus and brain stem of human alcoholics

(2012) Rosemarie Kryger et al.   ALCOHOL

The p53 mRNA-Mdm2 Interaction Controls Mdm2 Nuclear Trafficking and Is Required for p53 Activation following DNA Damage

(2012) Madhavsai Gajjar et al.   CANCER CELL

A Role for Neuronal piRNAs in the Epigenetic Control of Memory-Related Synaptic Plasticity

(2012) Priyamvada Rajasethupathy et al.   CELL

BACE1 in Alzheimer's disease

(2012) M. Sathya et al.   CLINICA CHIMICA ACTA

Naturally occurring endo-siRNA silences LINE-1 retrotransposons in human cells through DNA methylation

(2012) Long Chen et al.   Epigenetics

Activity-Dependent Human Brain Coding/Noncoding Gene Regulatory Networks

(2012) L. Lipovich et al.   GENETICS

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Aberrant Expression of Long Noncoding RNAs in Autistic Brain

(2012) Mark N. Ziats et al.   JOURNAL OF MOLECULAR NEUROSCIENCE

G9a/GLP Histone Lysine Dimethyltransferase Complex Activity in the Hippocampus and the Entorhinal Cortex Is Required for Gene Activation and Silencing during Memory Consolidation

(2012) S. Gupta-Agarwal et al.   JOURNAL OF NEUROSCIENCE

Cytoplasmic Assembly and Selective Nuclear Import of Arabidopsis ARGONAUTE4/siRNA Complexes

(2012) Ruiqiang Ye et al.   MOLECULAR CELL

Modular regulatory principles of large non-coding RNAs

(2012) Mitchell Guttman et al.   NATURE

Inhibition of natural antisense transcripts in vivo results in gene-specific transcriptional upregulation

(2012) Farzaneh Modarresi et al.   NATURE BIOTECHNOLOGY

The functions of microRNAs in pluripotency and reprogramming

(2012) Trevor R. Leonardo et al.   NATURE CELL BIOLOGY

Intronic RNAs mediate EZH2 regulation of epigenetic targets

(2012) Sònia Guil et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Histone Regulation in the CNS: Basic Principles of Epigenetic Plasticity

(2012) Ian Maze et al.   NEUROPSYCHOPHARMACOLOGY

The Dynamics of DNA Methylation in Schizophrenia and Related Psychiatric Disorders

(2012) Dennis R Grayson et al.   NEUROPSYCHOPHARMACOLOGY

MicroRNA-132 dysregulation in schizophrenia has implications for both neurodevelopment and adult brain function

(2012) B. H. Miller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Loss of the abundant nuclear non-coding RNAMALAT1is compatible with life and development

(2012) Moritz Eißmann et al.   RNA Biology

The lncRNA Malat1 Is Dispensable for Mouse Development but Its Transcription Plays a cis-Regulatory Role in the Adult

(2012) Bin Zhang et al.   Cell Reports

Epigenetic transgenerational inheritance of somatic transcriptomes and epigenetic control regions

(2012) Michael K Skinner et al.   GENOME BIOLOGY

Downregulation of miR-132 by promoter methylation contributes to pancreatic cancer development

(2011) Shuyu Zhang et al.   CARCINOGENESIS

The p53 mRNA-Mdm2 interaction

(2011) Nadia Naski et al.   CELL CYCLE

MicroRNAs in  -Cell Biology, Insulin Resistance, Diabetes and Its Complications

(2011) S. L. Fernandez-Valverde et al.   DIABETES

Small RNA-mediated regulation of iPS cell generation

(2011) Zhonghan Li et al.   EMBO JOURNAL

The search for endogenous siRNAs in the mammalian brain

(2011) Neil R. Smalheiser   EXPERIMENTAL NEUROLOGY

miRNAs and regulation of cell signaling

(2011) Atsuhiko Ichimura et al.   FEBS Journal

MicroRNAs and cardiovascular diseases

(2011) Koh Ono et al.   FEBS Journal

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

Targeted RNA sequencing reveals the deep complexity of the human transcriptome

(2011) Tim R Mercer et al.   NATURE BIOTECHNOLOGY

Genome-wide association study identifies five new schizophrenia loci

(2011)   NATURE GENETICS

Experience-dependent expression of miR-132 regulates ocular dominance plasticity

(2011) Paola Tognini et al.   NATURE NEUROSCIENCE

The role of histone acetylation in age-associated memory impairment and Alzheimer’s disease

(2011) Roman Manuel Stilling et al.   NEUROBIOLOGY OF LEARNING AND MEMORY

MicroRNA regulation of neural plasticity and memory

(2011) Timothy W. Bredy et al.   NEUROBIOLOGY OF LEARNING AND MEMORY

Growth factors stimulate expression of neuronal and glial miR-132

(2011) Tadahiro Numakawa et al.   NEUROSCIENCE LETTERS

Epigenetic Mechanisms

(2011) Farah D. Lubin et al.   NEUROSCIENTIST

Species-specific microRNA roles elucidated following astrocyte activation

(2011) Eyal Mor et al.   NUCLEIC ACIDS RESEARCH

Identification of piRNAs in the central nervous system

(2011) E. J. Lee et al.   RNA

miR-137 forms a regulatory loop with nuclear receptor TLX and LSD1 in neural stem cells

(2011) GuoQiang Sun et al.   Nature Communications

Epigenetic Memory in Mammals

(2011) Zoë Migicovsky et al.   Frontiers in Genetics

Upregulation of Dicer and MicroRNA Expression in the Dorsolateral Prefrontal Cortex Brodmann Area 46 in Schizophrenia

(2010) Danielle M. Santarelli et al.   BIOLOGICAL PSYCHIATRY

Altered MicroRNA Expression Profiles in Postmortem Brain Samples from Individuals with Schizophrenia and Bipolar Disorder

(2010) Michael P. Moreau et al.   BIOLOGICAL PSYCHIATRY

A Novel microRNA and transcription factor mediated regulatory network in schizophrenia

(2010) An-Yuan Guo et al.   BMC Systems Biology

Paternally Induced Transgenerational Environmental Reprogramming of Metabolic Gene Expression in Mammals

(2010) Benjamin R. Carone et al.   CELL

Epigenetic regulation in neural stem cell differentiation

(2010) Berry Juliandi et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression

(2010) Delphine Bernard et al.   EMBO JOURNAL

Long antisense non-coding RNAs function to direct epigenetic complexes that regulate transcription in human cells

(2010) Kevin V. Morris   Epigenetics

Shaping the oligodendrocyte identity by epigenetic control

(2010) Yang Yu et al.   Epigenetics

Analysis of microRNA knockouts in mice

(2010) C. Y. Park et al.   HUMAN MOLECULAR GENETICS

Genetic ablation of Dicer in adult forebrain neurons results in abnormal tau hyperphosphorylation and neurodegeneration

(2010) Sébastien S. Hébert et al.   HUMAN MOLECULAR GENETICS

Cross talk between microRNA and epigenetic regulation in adult neurogenesis

(2010) Keith E. Szulwach et al.   JOURNAL OF CELL BIOLOGY

RNAase-III enzyme Dicer maintains signaling pathways for differentiation and survival in mouse cortical neural stem cells

(2010) Y. Kawase-Koga et al.   JOURNAL OF CELL SCIENCE

MicroRNA Loss Enhances Learning and Memory in Mice

(2010) W. Konopka et al.   JOURNAL OF NEUROSCIENCE

Silencing of Integrated Human Papillomavirus-16 Oncogenes by Small Interfering RNA-Mediated Heterochromatization

(2010) J. K. Palanichamy et al.   MOLECULAR CANCER THERAPEUTICS

An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation

(2010) Zhihuan Gao et al.   NATURE

Dicer1 and miR-219 Are Required for Normal Oligodendrocyte Differentiation and Myelination

(2010) Jason C. Dugas et al.   NEURON

miRBase: integrating microRNA annotation and deep-sequencing data

(2010) A. Kozomara et al.   NUCLEIC ACIDS RESEARCH

In-Depth Transcriptome Analysis Reveals Novel TARs and Prevalent Antisense Transcription in Human Cell Lines

(2010) Daniel Klevebring et al.   PLoS One

The MicroRNA and MessengerRNA Profile of the RNA-Induced Silencing Complex in Human Primary Astrocyte and Astrocytoma Cells

(2010) Joanna J. Moser et al.   PLoS One

Endogenous siRNAs and noncoding RNA-derived small RNAs are expressed in adult mouse hippocampus and are up-regulated in olfactory discrimination training

(2010) N. R. Smalheiser et al.   RNA

Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure

(2010) X. Li et al.   RNA

Molecular Signals of Epigenetic States

(2010) Roberto Bonasio et al.   SCIENCE

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

Wnt1-cre-mediated Conditional Loss of Dicer Results in Malformation of the Midbrain and Cerebellum and Failure of Neural Crest and Dopaminergic Differentiation in Mice

(2010) Tianwen Huang et al.   Journal of Molecular Cell Biology

Roles of RNAi in chromatin regulation and epigenetic inheritance

(2010) Hugh P Cam   Epigenomics

Evidence for natural antisense transcript-mediated inhibition of microRNA function

(2010) Mohammad Ali Faghihi et al.   GENOME BIOLOGY

A Broadly Conserved Pathway Generates 3′UTR-Directed Primary piRNAs

(2009) Nicolas Robine et al.   CURRENT BIOLOGY

NRPD4, a protein related to the RPB4 subunit of RNA polymerase II, is a component of RNA polymerases IV and V and is required for RNA-directed DNA methylation

(2009) X.-J. He et al.   GENES & DEVELOPMENT

Common themes in siRNA-mediated epigenetic silencing pathways

(2009) Andre Verdel et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Schizophrenia is associated with an increase in cortical microRNA biogenesis

(2009) N J Beveridge et al.   MOLECULAR PSYCHIATRY

Epigenetic dynamics of stem cells and cell lineage commitment: digging Waddington's canal

(2009) Myriam Hemberger et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

MicroRNA-219 modulates NMDA receptor-mediated neurobehavioral dysfunction

(2009) J. Kocerha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

(2009) Ahmad M. Khalil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Heterochromatin Protein 1 (HP1a) Positively Regulates Euchromatic Gene Expression through RNA Transcript Association and Interaction with hnRNPs in Drosophila

(2009) Lucia Piacentini et al.   PLoS Genetics

Noncoding Transcription by RNA Polymerase Pol IVb/Pol V Mediates Transcriptional Silencing of Overlapping and Adjacent Genes

(2008) Andrzej T. Wierzbicki et al.   CELL

miRNAs are essential for survival and differentiation of newborn neurons but not for expansion of neural progenitors during early neurogenesis in the mouse embryonic neocortex

(2008) D. De Pietri Tonelli et al.   DEVELOPMENT

DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes

(2008) S. Kuramochi-Miyagawa et al.   GENES & DEVELOPMENT

Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs

(2008) J. E. Babiarz et al.   GENES & DEVELOPMENT

Most mammalian mRNAs are conserved targets of microRNAs

(2008) R. C. Friedman et al.   GENOME RESEARCH

A set of differentially expressed miRNAs, including miR-30a-5p, act as post-transcriptional inhibitors of BDNF in prefrontal cortex

(2008) Nikolaos Mellios et al.   HUMAN MOLECULAR GENETICS

Conditional Loss of Dicer Disrupts Cellular and Tissue Morphogenesis in the Cortex and Hippocampus

(2008) T. H. Davis et al.   JOURNAL OF NEUROSCIENCE

A piRNA Pathway Primed by Individual Transposons Is Linked to De Novo DNA Methylation in Mice

(2008) Alexei A. Aravin et al.   MOLECULAR CELL

Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes

(2008) Toshiaki Watanabe et al.   NATURE

Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes

(2008) Oliver H. Tam et al.   NATURE

p53 mRNA controls p53 activity by managing Mdm2 functions

(2008) Marco M. Candeias et al.   NATURE CELL BIOLOGY

Nanog and Oct4 associate with unique transcriptional repression complexes in embryonic stem cells

(2008) Jiancong Liang et al.   NATURE CELL BIOLOGY

Altered brain microRNA biogenesis contributes to phenotypic deficits in a 22q11-deletion mouse model

(2008) Kimberly L Stark et al.   NATURE GENETICS

Specific expression of long noncoding RNAs in the mouse brain

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