Emerging roles of non-coding RNAs in brain evolution, development, plasticity and disease

Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome

(2012) Zhiyu Peng et al.   NATURE BIOTECHNOLOGY

Coding vs non-coding: Translatability of short ORFs found in putative non-coding transcripts

(2011) Yuji Kageyama et al.   BIOCHIMIE

The can and can’t dos of p53 RNA

(2011) Marco M. Candeias   BIOCHIMIE

Steroid receptor RNA activator bi-faceted genetic system: Heads or Tails?

(2011) Charlton Cooper et al.   BIOCHIMIE

Molecular imaging of a cancer-targeting theragnostics probe using a nucleolin aptamer- and microRNA-221 molecular beacon-conjugated nanoparticle

(2011) Jin Kyeoung Kim et al.   BIOMATERIALS

The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA

(2011) Philipp Kapranov et al.   BMC BIOLOGY

A genome-wide survey for SNPs altering microRNA seed sites identifies functional candidates in GWAS

(2011) Kris Richardson et al.   BMC GENOMICS

Evolution, biogenesis and function of promoter-associated RNAs

(2011) Ryan J. Taft et al.   CELL CYCLE

Direct Reprogramming of Adult Human Fibroblasts to Functional Neurons under Defined Conditions

(2011) Rajesh Ambasudhan et al.   Cell Stem Cell

Highly Efficient miRNA-Mediated Reprogramming of Mouse and Human Somatic Cells to Pluripotency

(2011) Frederick Anokye-Danso et al.   Cell Stem Cell

Reprogramming of Mouse and Human Cells to Pluripotency Using Mature MicroRNAs

(2011) Norikatsu Miyoshi et al.   Cell Stem Cell

miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA

(2011) Thomas B Hansen et al.   EMBO JOURNAL

Molecular imaging of microRNAs

(2011) Fu Wang et al.   EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING

The search for endogenous siRNAs in the mammalian brain

(2011) Neil R. Smalheiser   EXPERIMENTAL NEUROLOGY

New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes

(2011) B. J. Parker et al.   GENOME RESEARCH

Dynamic interaction of Y RNAs with chromatin and initiation proteins during human DNA replication

(2011) A. T. Zhang et al.   JOURNAL OF CELL SCIENCE

Deletion of Astroglial Dicer Causes Non-Cell-Autonomous Neuronal Dysfunction and Degeneration

(2011) J. Tao et al.   JOURNAL OF NEUROSCIENCE

FXR1P But Not FMRP Regulates the Levels of Mammalian Brain-Specific microRNA-9 and microRNA-124

(2011) X.-L. Xu et al.   JOURNAL OF NEUROSCIENCE

MicroRNA-9 Regulates Neurogenesis in Mouse Telencephalon by Targeting Multiple Transcription Factors

(2011) M. Shibata et al.   JOURNAL OF NEUROSCIENCE

Dual Nature of Translational Control by Regulatory BC RNAs

(2011) T. Eom et al.   MOLECULAR AND CELLULAR BIOLOGY

A system for imaging the regulatory noncoding Xist RNA in living mouse embryonic stem cells

(2011) Karen Ng et al.   MOLECULAR BIOLOGY OF THE CELL

Reversible Inhibition of PSD-95 mRNA Translation by miR-125a, FMRP Phosphorylation, and mGluR Signaling

(2011) Ravi S. Muddashetty et al.   MOLECULAR CELL

Molecular Mechanisms of Long Noncoding RNAs

(2011) Kevin C. Wang et al.   MOLECULAR CELL

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

DICER1 deficit induces Alu RNA toxicity in age-related macular degeneration

(2011) Hiroki Kaneko et al.   NATURE

Somatic retrotransposition alters the genetic landscape of the human brain

(2011) J. Kenneth Baillie et al.   NATURE

MicroRNA-mediated conversion of human fibroblasts to neurons

(2011) Andrew S. Yoo et al.   NATURE

Targeted RNA sequencing reveals the deep complexity of the human transcriptome

(2011) Tim R Mercer et al.   NATURE BIOTECHNOLOGY

miR-34 miRNAs provide a barrier for somatic cell reprogramming

(2011) Yong Jin Choi et al.   NATURE CELL BIOLOGY

Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters

(2011) Tiffany Hung et al.   NATURE GENETICS

Transcription by RNA polymerase III: more complex than we thought

(2011) Robert J. White   NATURE REVIEWS GENETICS

Gene silencing in X-chromosome inactivation: advances in understanding facultative heterochromatin formation

(2011) Anton Wutz   NATURE REVIEWS GENETICS

Non-coding RNAs in human disease

(2011) Manel Esteller   NATURE REVIEWS GENETICS

Monoallelic deletion of the microRNA biogenesis gene Dgcr8 produces deficits in the development of excitatory synaptic transmission in the prefrontal cortex

(2011) Claude M Schofield et al.   Neural Development

The long noncoding RNA Six3OS acts in trans to regulate retinal development by modulating Six3 activity

(2011) Nicole A Rapicavoli et al.   Neural Development

A Transcriptomic Atlas of Mouse Neocortical Layers

(2011) T. Grant Belgard et al.   NEURON

CTCF Regulates Ataxin-7 Expression through Promotion of a Convergently Transcribed, Antisense Noncoding RNA

(2011) Bryce L. Sopher et al.   NEURON

Widespread expression of piRNA-like molecules in somatic tissues

(2011) Zheng Yan et al.   NUCLEIC ACIDS RESEARCH

RNA-Seq of Human Neurons Derived from iPS Cells Reveals Candidate Long Non-Coding RNAs Involved in Neurogenesis and Neuropsychiatric Disorders

(2011) Mingyan Lin et al.   PLoS One

Expression of Transposable Elements in Neural Tissues during Xenopus Development

(2011) Fernando Faunes et al.   PLoS One

Convergence of miRNA Expression Profiling, α-Synuclein Interacton and GWAS in Parkinson's Disease

(2011) Madalena Martins et al.   PLoS One

The Ataxin-2 protein is required for microRNA function and synapse-specific long-term olfactory habituation

(2011) C. McCann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MicroRNA regulation of homeostatic synaptic plasticity

(2011) J. E. Cohen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deep-sequencing of human Argonaute-associated small RNAs provides insight into miRNA sorting and reveals Argonaute association with RNA fragments of diverse origin

(2011) Alexander Maxwell Burroughs et al.   RNA Biology

Long noncoding RNAs are generated from the mitochondrial genome and regulated by nuclear-encoded proteins

(2011) O. Rackham et al.   RNA

A Drosophila genetic screen yields allelic series of core microRNA biogenesis factors and reveals post-developmental roles for microRNAs

(2011) P. Smibert et al.   RNA

Identification of piRNAs in the central nervous system

(2011) E. J. Lee et al.   RNA

The zipcode-binding protein ZBP1 influences the subcellular location of the Ro 60-kDa autoantigen and the noncoding Y3 RNA

(2011) S. Sim et al.   RNA

Variants on Chromosome 9p21.3 Correlated With ANRIL Expression Contribute to Stroke Risk and Recurrence in a Large Prospective Stroke Population

(2011) Weili Zhang et al.   STROKE

The relationship between transcription initiation RNAs and CCCTC-binding factor (CTCF) localization

(2011) Ryan J Taft et al.   Epigenetics & Chromatin

Tumour microvesicles contain retrotransposon elements and amplified oncogene sequences

(2011) Leonora Balaj et al.   Nature Communications

Nuclear localization of the mitochondrial ncRNAs in normal and cancer cells

(2011) Eduardo Landerer et al.   CELLULAR ONCOLOGY

MicroRNA-Driven Developmental Remodeling in the Brain Distinguishes Humans from Other Primates

(2011) Mehmet Somel et al.   PLOS BIOLOGY

Tsx Produces a Long Noncoding RNA and Has General Functions in the Germline, Stem Cells, and Brain

(2011) Montserrat C. Anguera et al.   PLoS Genetics

MicroRNA Expression and Regulation in Human, Chimpanzee, and Macaque Brains

(2011) Hai Yang Hu et al.   PLoS Genetics

Transfer RNA-derived fragments: origins, processing, and functions

(2011) Andrew Sobala et al.   Wiley Interdisciplinary Reviews-RNA

Functions and Regulation of RNA Editing by ADAR Deaminases

(2010) Kazuko Nishikura   Annual Review of Biochemistry

The long noncoding RNA RNCR2 directs mouse retinal cell specification.

(2010) Nicole A Rapicavoli et al.   BMC DEVELOPMENTAL BIOLOGY

Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation

(2010) Tim R Mercer et al.   BMC NEUROSCIENCE

Long non-coding RNAs in nervous system function and disease

(2010) Irfan A. Qureshi et al.   BRAIN RESEARCH

Long Noncoding RNAs with Enhancer-like Function in Human Cells

(2010) Ulf Andersson Ørom et al.   CELL

A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response

(2010) Maite Huarte et al.   CELL

REST and CoREST are transcriptional and epigenetic regulators of seminal neural fate decisions

(2010) Irfan A. Qureshi et al.   CELL CYCLE

MicroRNA-9 Coordinates Proliferation and Migration of Human Embryonic Stem Cell-Derived Neural Progenitors

(2010) Celine Delaloy et al.   Cell Stem Cell

Emergence of Chemical Biology Approaches to the RNAi/miRNA Pathway

(2010) Yujing Li et al.   CHEMISTRY & BIOLOGY

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

(2010) Delphine Bernard et al.   EMBO JOURNAL

Differential regulation of mature and precursor microRNA expression by NMDA and metabotropic glutamate receptor activation during LTP in the adult dentate gyrusin vivo

(2010) Karin Wibrand et al.   EUROPEAN JOURNAL OF NEUROSCIENCE

ANRIL, a long, noncoding RNA, is an unexpected major hotspot in GWAS

(2010) Eric Pasmant et al.   FASEB JOURNAL

MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain

(2010) M. Somel et al.   GENOME RESEARCH

Bidirectional transcription stimulates expansion and contraction of expanded (CTG)•(CAG) repeats

(2010) Masayuki Nakamori et al.   HUMAN MOLECULAR GENETICS

MicroRNA Loss Enhances Learning and Memory in Mice

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

New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism

(2010) Philipp Kapranov et al.   NATURE

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs

(2010) Yuntao S. Mao et al.   NATURE CELL BIOLOGY

Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans

(2010) Ryan J Taft et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2010) Jason C. Dugas et al.   NEURON

MicroRNA-Mediated Control of Oligodendrocyte Differentiation

(2010) Xianghui Zhao et al.   NEURON

A myriad of miRNA variants in control and Huntington’s disease brain regions detected by massively parallel sequencing

(2010) Eulàlia Martí et al.   NUCLEIC ACIDS RESEARCH

Genome-wide evidence for an essential role of the human Staf/ZNF143 transcription factor in bidirectional transcription

(2010) Yannick-Noël Anno et al.   NUCLEIC ACIDS RESEARCH

Expression of distinct RNAs from 3′ untranslated regions

(2010) Tim R. Mercer et al.   NUCLEIC ACIDS RESEARCH

The evolution and expression of the snaR family of small non-coding RNAs

(2010) Andrew M. Parrott et al.   NUCLEIC ACIDS RESEARCH

Adenosine-to-inosine RNA editing shapes transcriptome diversity in primates

(2010) N. Paz-Yaacov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Telomeric repeat-containing RNA structure in living cells

(2010) Y. Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Translation regulation of mRNAs by the fragile X family of proteins through the microRNA pathway

(2010) Anne Cheever et al.   RNA Biology

Fragile X protein family member FXR1P is regulated by microRNAs

(2010) A. Cheever et al.   RNA

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

Identification of novel ribonucleo-protein complexes from the brain-specific snoRNA MBII-52

(2010) Y. Soeno et al.   RNA

Identification and quantitative analyses of microRNAs located in the distal axons of sympathetic neurons

(2010) O. Natera-Naranjo et al.   RNA

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

Intergenic and Repeat Transcription in Human, Chimpanzee and Macaque Brains Measured by RNA-Seq

(2010) Augix Guohua Xu et al.   PLoS Computational Biology

Chromosome 9p21 SNPs Associated with Multiple Disease Phenotypes Correlate with ANRIL Expression

(2010) Michael S. Cunnington et al.   PLoS Genetics

Mitochondrial tRNA mutations and disease

(2010) John W. Yarham et al.   Wiley Interdisciplinary Reviews-RNA

Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes

(2010) Rebecca A Chodroff et al.   GENOME BIOLOGY

Evidence for natural antisense transcript-mediated inhibition of microRNA function

(2010) Mohammad Ali Faghihi et al.   GENOME BIOLOGY

The ribonome: a dominant force in co-ordinating gene expression

(2009) Kyle D. Mansfield et al.   BIOLOGY OF THE CELL

Environmental influence on L1 retrotransposons in the adult hippocampus

(2009) Alysson R. Muotri et al.   HIPPOCAMPUS

Epstein–Barr Virus-Induced Expression of a Novel Human Vault RNA

(2009) Constanze Nandy et al.   JOURNAL OF MOLECULAR BIOLOGY

The Bifunctional microRNA miR-9/miR-9* Regulates REST and CoREST and Is Downregulated in Huntington's Disease

(2009) A. N. Packer et al.   JOURNAL OF NEUROSCIENCE

BC1 Regulation of Metabotropic Glutamate Receptor-Mediated Neuronal Excitability

(2009) J. Zhong et al.   JOURNAL OF NEUROSCIENCE

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

L1 retrotransposition in human neural progenitor cells

(2009) Nicole G. Coufal et al.   NATURE

Tiny RNAs associated with transcription start sites in animals

(2009) Ryan J Taft et al.   NATURE GENETICS

Balanced gene regulation by an embryonic brain ncRNA is critical for adult hippocampal GABA circuitry

(2009) Allison M Bond et al.   NATURE NEUROSCIENCE

A feedback regulatory loop involving microRNA-9 and nuclear receptor TLX in neural stem cell fate determination

(2009) Chunnian Zhao et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

What are the roles of microRNAs at the mammalian synapse?

(2009) Anetta Konecna et al.   NEUROSCIENCE LETTERS

Expression Profile of MicroRNAs in Young Stroke Patients

(2009) Kay Sin Tan et al.   PLoS One

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

Small RNAs derived from snoRNAs

(2009) R. J. Taft et al.   RNA

Complex architecture and regulated expression of the Sox2ot locus during vertebrate development

(2009) P. P. Amaral et al.   RNA

Dicer independent small RNAs associate with telomeric heterochromatin

(2009) F. Cao et al.   RNA

Smart Magnetic Fluorescent Nanoparticle Imaging Probes to Monitor MicroRNAs

(2009) Do Won Hwang et al.   Small

Genomic and Transcriptional Co-Localization of Protein-Coding and Long Non-Coding RNA Pairs in the Developing Brain

(2009) Jasmina Ponjavic et al.   PLoS Genetics

RNA Gain-of-Function in Spinocerebellar Ataxia Type 8

(2009) Randy S. Daughters et al.   PLoS Genetics

Variation in the miRNA-433 Binding Site of FGF20 Confers Risk for Parkinson Disease by Overexpression of α-Synuclein

(2008) Gaofeng Wang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

miR-124 and miR-137 inhibit proliferation of glioblastoma multiforme cells and induce differentiation of brain tumor stem cells

(2008) Joachim Silber et al.   BMC Medicine

A new class of retroviral and satellite encoded small RNAs emanates from mammalian centromeres

(2008) Dawn M. Carone et al.   CHROMOSOMA

Regulation of microRNA Expression by Induction of Bidirectional Synaptic Plasticity

(2008) Chang Sin Park et al.   JOURNAL OF MOLECULAR NEUROSCIENCE

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

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

MicroRNA-9 Modulates Cajal-Retzius Cell Differentiation by Suppressing Foxg1 Expression in Mouse Medial Pallium

(2008) M. Shibata et al.   JOURNAL OF NEUROSCIENCE

A Human snoRNA with MicroRNA-Like Functions

(2008) Christine Ender et al.   MOLECULAR CELL

The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs

(2008) Katsutomo Okamura et al.   NATURE

Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription

(2008) Xiangting Wang et al.   NATURE

Glioblastoma microvesicles transport RNA and proteins that promote tumour growth and provide diagnostic biomarkers

(2008) Johan Skog et al.   NATURE CELL BIOLOGY

MicroRNA-9 directs late organizer activity of the midbrain-hindbrain boundary

(2008) Christoph Leucht et al.   NATURE NEUROSCIENCE

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

MicroRNAs and the advent of vertebrate morphological complexity

(2008) A. M. Heimberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE

MicroRNA Expression in the Blood and Brain of Rats Subjected to Transient Focal Ischemia by Middle Cerebral Artery Occlusion

(2008) Kandiah Jeyaseelan et al.   STROKE