Emerging Roles of Long Non-Coding RNAs as Drivers of Brain Evolution

The Impact of Studying Brain Plasticity

(2019) Pedro Mateos-Aparicio et al.   Frontiers in Cellular Neuroscience

Neocortical Expansion Due to Increased Proliferation of Basal Progenitors Is Linked to Changes in Their Morphology

(2019) Nereo Kalebic et al.   Cell Stem Cell

New insights into the development of the human cerebral cortex

(2019) Zoltán Molnár et al.   JOURNAL OF ANATOMY

The small peptide world in long noncoding RNAs

(2018) Seo-Won Choi et al.   BRIEFINGS IN BIOINFORMATICS

Splicing regulation by long noncoding RNAs

(2018) Natali Romero-Barrios et al.   NUCLEIC ACIDS RESEARCH

Mechanisms of Long Non-Coding RNAs in the Assembly and Plasticity of Neural Circuitry

(2017) Andi Wang et al.   Frontiers in Neural Circuits

CpG and Non-CpG Methylation in Epigenetic Gene Regulation and Brain Function

(2017) et al.   Genes

Long Noncoding RNA MALAT1 Promotes Hepatocellular Carcinoma Development by SRSF1 Upregulation and mTOR Activation

(2016) Pushkar Malakar et al.   CANCER RESEARCH

The Molecular Basis of Human Brain Evolution

(2016) Wolfgang Enard   CURRENT BIOLOGY

Long noncoding RNAs: Central to nervous system development

(2016) Ronald P. Hart et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL NEUROSCIENCE

LncRNA MALAT1 promotes development of mantle cell lymphoma by associating with EZH2

(2016) Xin Wang et al.   Journal of Translational Medicine

Hedgehog signaling promotes basal progenitor expansion and the growth and folding of the neocortex

(2016) Lei Wang et al.   NATURE NEUROSCIENCE

Long Non-coding RNAs in the Cytoplasm

(2016) Farooq Rashid et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Mammalian Brains Are Made of These: A Dataset of the Numbers and Densities of Neuronal and Nonneuronal Cells in the Brain of Glires, Primates, Scandentia, Eulipotyphlans, Afrotherians and Artiodactyls, and Their Relationship with Body Mass

(2015) Suzana Herculano-Houzel et al.   BRAIN BEHAVIOR AND EVOLUTION

The Long Noncoding RNA Pnky Regulates Neuronal Differentiation of Embryonic and Postnatal Neural Stem Cells

(2015) Alexander D. Ramos et al.   Cell Stem Cell

Long non-coding RNA MEG3 functions as a competing endogenous RNA to regulate gastric cancer progression

(2015) Weizhao Peng et al.   JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH

The PU.1-Regulated Long Noncoding RNA Lnc-MC Controls Human Monocyte/Macrophage Differentiation through Interaction with MicroRNA-199a-5p

(2015) Ming-Tai Chen et al.   MOLECULAR AND CELLULAR BIOLOGY

The Outer Subventricular Zone and Primate-Specific Cortical Complexification

(2015) Colette Dehay et al.   NEURON

Mechanisms of Long Non-coding RNAs in Mammalian Nervous System Development, Plasticity, Disease, and Evolution

(2015) James A. Briggs et al.   NEURON

DeCoN: Genome-wide Analysis of In Vivo Transcriptional Dynamics during Pyramidal Neuron Fate Selection in Neocortex

(2015) Bradley J. Molyneaux et al.   NEURON

Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved

(2015) Anne Nitsche et al.   RNA

Sustained Pax6 Expression Generates Primate-like Basal Radial Glia in Developing Mouse Neocortex

(2015) Fong Kuan Wong et al.   PLOS BIOLOGY

Dynamic expression of long noncoding RNAs and repeat elements in synaptic plasticity

(2015) Jesper L. V. Maag et al.   Frontiers in Neuroscience

Long non-coding RNA MALAT1 promotes tumour growth and metastasis in colorectal cancer through binding to SFPQ and releasing oncogene PTBP2 from SFPQ/PTBP2 complex

(2014) Q Ji et al.   BRITISH JOURNAL OF CANCER

Thalamic afferents influence cortical progenitors via ephrin A5-EphA4 interactions

(2014) K. Gerstmann et al.   DEVELOPMENT

Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates

(2014) J. Hatakeyama et al.   DEVELOPMENT

Long Noncoding RNA Modulates Alternative Splicing Regulators in Arabidopsis

(2014) Florian Bardou et al.   DEVELOPMENTAL CELL

The long non-coding RNA Paupar regulates the expression of both local and distal genes

(2014) K. W. Vance et al.   EMBO JOURNAL

The H19 long noncoding RNA gives rise to microRNAs miR-675-3p and miR-675-5p to promote skeletal muscle differentiation and regeneration

(2014) B. K. Dey et al.   GENES & DEVELOPMENT

Noncoding Transcription by Alternative RNA Polymerases Dynamically Regulates an Auxin-Driven Chromatin Loop

(2014) Federico Ariel et al.   MOLECULAR CELL

Interactions between JARID2 and Noncoding RNAs Regulate PRC2 Recruitment to Chromatin

(2014) Syuzo Kaneko et al.   MOLECULAR CELL

An Evolutionarily Conserved Long Noncoding RNA TUNA Controls Pluripotency and Neural Lineage Commitment

(2014) Nianwei Lin et al.   MOLECULAR CELL

A dimeric state for PRC2

(2014) Chen Davidovich et al.   NUCLEIC ACIDS RESEARCH

Spatio-temporal extension in site of origin for cortical calretinin neurons in primates

(2014) Ana Hladnik et al.   Frontiers in Neuroanatomy

An Adaptive Threshold in Mammalian Neocortical Evolution

(2014) Eric Lewitus et al.   PLOS BIOLOGY

The long non-coding RNA Dali is an epigenetic regulator of neural differentiation

(2014) Vladislava Chalei et al.   eLife

Long Non-Coding RNA NEAT1 Associates with SRp40 to Temporally Regulate PPARγ2 Splicing during Adipogenesis in 3T3-L1 Cells

(2014) Denise Cooper et al.   Genes

Trnp1 Regulates Expansion and Folding of the Mammalian Cerebral Cortex by Control of Radial Glial Fate

(2013) Ronny Stahl et al.   CELL

Long Noncoding RNAs: Cellular Address Codes in Development and Disease

(2013) Pedro J. Batista et al.   CELL

Identifying Recent Adaptations in Large-Scale Genomic Data

(2013) Sharon R. Grossman et al.   CELL

How unique is the human neocortex?

(2013) Z. Molnar et al.   DEVELOPMENT

Chromatin Regulation by BAF170 Controls Cerebral Cortical Size and Thickness

(2013) Tran Cong Tuoc et al.   DEVELOPMENTAL CELL

Regulation of cerebral cortex size and folding by expansion of basal progenitors

(2013) Miki Nonaka-Kinoshita et al.   EMBO JOURNAL

Transcriptome sequencing during mouse brain development identifies long non-coding RNAs functionally involved in neurogenic commitment

(2013) Julieta Aprea et al.   EMBO JOURNAL

Dynamic Interactions between Intermediate Neurogenic Progenitors and Radial Glia in Embryonic Mouse Neocortex: Potential Role in Dll1-Notch Signaling

(2013) B. R. Nelson et al.   JOURNAL OF NEUROSCIENCE

eRNAs Promote Transcription by Establishing Chromatin Accessibility at Defined Genomic Loci

(2013) Kambiz Mousavi et al.   MOLECULAR CELL

Remodeling of the Enhancer Landscape during Macrophage Activation Is Coupled to Enhancer Transcription

(2013) Minna U. Kaikkonen et al.   MOLECULAR CELL

Circular Intronic Long Noncoding RNAs

(2013) Yang Zhang et al.   MOLECULAR CELL

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

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription

(2013) Michael T. Y. Lam et al.   NATURE

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

Long non-coding RNAs: new players in cell differentiation and development

(2013) Alessandro Fatica et al.   NATURE REVIEWS GENETICS

Molecular logic of neocortical projection neuron specification, development and diversity

(2013) Luciano Custo Greig et al.   NATURE REVIEWS NEUROSCIENCE

Precursor Diversity and Complexity of Lineage Relationships in the Outer Subventricular Zone of the Primate

(2013) Marion Betizeau et al.   NEURON

TINCR, staufen1, and cellular differentiation

(2013) Markus Kretz   RNA Biology

Cortical High-Density Counterstream Architectures

(2013) N. T. Markov et al.   SCIENCE

Multiple knockout mouse models reveal lincRNAs are required for life and brain development

(2013) Martin Sauvageau et al.   eLife

Mechanisms of Gamma Oscillations

(2012) György Buzsáki et al.   Annual Review of Neuroscience

Origins of Human Cooperation and Morality

(2012) Michael Tomasello et al.   Annual Review of Psychology

A Long ncRNA Links Copy Number Variation to a Polycomb/Trithorax Epigenetic Switch in FSHD Muscular Dystrophy

(2012) Daphne S. Cabianca et al.   CELL

OSVZ progenitors in the human cortex: an updated perspective on neurodevelopmental disease

(2012) Bridget E LaMonica et al.   CURRENT OPINION IN NEUROBIOLOGY

Long non-coding RNAgadd7interacts with TDP-43 and regulatesCdk6mRNA decay

(2012) Xuefeng Liu et al.   EMBO JOURNAL

Activity-Dependent Human Brain Coding/Noncoding Gene Regulatory Networks

(2012) L. Lipovich et al.   GENETICS

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Biogenesis and Mechanism of Action of Small Non-Coding RNAs: Insights from the Point of View of Structural Biology

(2012) Marina C. Costa et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Posttranscriptional Gene Regulation by Long Noncoding RNA

(2012) Je-Hyun Yoon et al.   JOURNAL OF MOLECULAR BIOLOGY

LincRNA-p21 Suppresses Target mRNA Translation

(2012) Je-Hyun Yoon et al.   MOLECULAR CELL

Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat

(2012) Claudia Carrieri et al.   NATURE

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

(2012) Farzaneh Modarresi et al.   NATURE BIOTECHNOLOGY

The H19 lincRNA is a developmental reservoir of miR-675 that suppresses growth and Igf1r

(2012) Andrew Keniry et al.   NATURE CELL BIOLOGY

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

(2012) Irfan A. Qureshi et al.   NATURE REVIEWS NEUROSCIENCE

Intronic RNAs mediate EZH2 regulation of epigenetic targets

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

Fate-Restricted Neural Progenitors in the Mammalian Cerebral Cortex

(2012) S. J. Franco et al.   SCIENCE

Epigenetic Regulation by Long Noncoding RNAs

(2012) J. T. Lee   SCIENCE

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

Emerging Roles of Exosomes in Neuron–Glia Communication

(2012) Carsten Frühbeis et al.   Frontiers in Physiology

Development and Evolution of the Human Neocortex

(2011) Jan H. Lui et al.   CELL

Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution

(2011) Igor Ulitsky et al.   CELL

Coding-Independent Regulation of the Tumor Suppressor PTEN by Competing Endogenous mRNAs

(2011) Yvonne Tay et al.   CELL

In Vivo Identification of Tumor- Suppressive PTEN ceRNAs in an Oncogenic BRAF-Induced Mouse Model of Melanoma

(2011) Florian A. Karreth et al.   CELL

A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language?

(2011) Leonardo Salmena et al.   CELL

Brain Tumor Microvesicles: Insights into Intercellular Communication in the Nervous System

(2011) Kristan E. van der Vos et al.   CELLULAR AND MOLECULAR NEUROBIOLOGY

Compartmentalization of Cerebral Cortical Germinal Zones in a Lissencephalic Primate and Gyrencephalic Rodent

(2011) F. Garcia-Moreno et al.   CEREBRAL CORTEX

Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors

(2011) Shi-Yan Ng et al.   EMBO JOURNAL

Competition between a noncoding exon and introns: Gomafu contains tandem UACUAAC repeats and associates with splicing factor-1

(2011) Hitomi Tsuiji et al.   GENES TO CELLS

Segregation of feedforward and feedback projections in mouse visual cortex

(2011) Vladimir K. Berezovskii et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Oblique Radial Glial Divisions in the Developing Mouse Neocortex Induce Self-Renewing Progenitors outside the Germinal Zone That Resemble Primate Outer Subventricular Zone Progenitors

(2011) A. Shitamukai et al.   JOURNAL OF NEUROSCIENCE

Molecular Mechanisms of Long Noncoding RNAs

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

lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements

(2011) Chenguang Gong et al.   NATURE

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

(2011) Kerstin Lindblad-Toh et al.   NATURE

A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

(2011) Kevin C. Wang et al.   NATURE

The Polycomb complex PRC2 and its mark in life

(2011) Raphaël Margueron et al.   NATURE

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

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

(2011) Tiffany Hung et al.   NATURE GENETICS

A new subtype of progenitor cell in the mouse embryonic neocortex

(2011) Xiaoqun Wang et al.   NATURE NEUROSCIENCE

A Transcriptomic Atlas of Mouse Neocortical Layers

(2011) T. Grant Belgard et al.   NEURON

The Brain Basis of Language Processing: From Structure to Function

(2011) Angela D. Friederici   PHYSIOLOGICAL REVIEWS

Long noncoding RNAs and human disease

(2011) Orly Wapinski et al.   TRENDS IN CELL BIOLOGY

Neuronal Activity-Regulated Gene Transcription in Synapse Development and Cognitive Function

(2011) A. E. West et al.   Cold Spring Harbor Perspectives in Biology

The Role of the Human Prefrontal Cortex in Social Cognition and Moral Judgment

(2010) Chad E. Forbes et al.   Annual Review of Neuroscience

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 Noncoding RNAs with Enhancer-like Function in Human Cells

(2010) Ulf Andersson Ørom et al.   CELL

A Role for Intermediate Radial Glia in the Tangential Expansion of the Mammalian Cerebral Cortex

(2010) Isabel Reillo et al.   CEREBRAL CORTEX

Multiple origins of the cortical gamma rhythm

(2010) Miles A. Whittington et al.   Developmental Neurobiology

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

(2010) Delphine Bernard et al.   EMBO JOURNAL

The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation

(2010) Vidisha Tripathi et al.   MOLECULAR CELL

Genome-wide Identification of Polycomb-Associated RNAs by RIP-seq

(2010) Jing Zhao et al.   MOLECULAR CELL

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Neurogenic radial glia in the outer subventricular zone of human neocortex

(2010) David V. Hansen et al.   NATURE

OSVZ progenitors of human and ferret neocortex are epithelial-like and expand by integrin signaling

(2010) Simone A Fietz et al.   NATURE NEUROSCIENCE

Expression of distinct RNAs from 3′ untranslated regions

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

Long non-coding RNA ANRIL is required for the PRC2 recruitment to and silencing of p15 INK4B tumor suppressor gene

(2010) Y Kotake et al.   ONCOGENE

Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing

(2010) J. Q. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

Intermediate Neuronal Progenitors (Basal Progenitors) Produce Pyramidal–Projection Neurons for All Layers of Cerebral Cortex

(2009) Tom Kowalczyk et al.   CEREBRAL CORTEX

New meaning in the message: Noncoding RNAs and their role in retinal development

(2009) Nicole A. Rapicavoli et al.   DEVELOPMENTAL DYNAMICS

BC1 Regulation of Metabotropic Glutamate Receptor-Mediated Neuronal Excitability

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

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

(2009) Allison M Bond et al.   NATURE NEUROSCIENCE

Evolution of the neocortex: a perspective from developmental biology

(2009) Pasko Rakic   NATURE REVIEWS NEUROSCIENCE

Translational Control of Long-Lasting Synaptic Plasticity and Memory

(2009) Mauro Costa-Mattioli et al.   NEURON

Ratcheting up the ratchet: on the evolution of cumulative culture

(2009) C. Tennie et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Global discovery of primate-specific genes in the human genome

(2009) S.-K. Tay 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

Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells

(2009) J. Sheik Mohamed et al.   RNA

Significant features in the early prenatal development of the human brain

(2008) Ronan O’Rahilly et al.   ANNALS OF ANATOMY-ANATOMISCHER ANZEIGER

MicroRNA-encoding long non-coding RNAs

(2008) Shunmin He et al.   BMC GENOMICS

RNAs as extracellular signaling molecules

(2008) Marcel E Dinger et al.   JOURNAL OF MOLECULAR ENDOCRINOLOGY

Kcnq1ot1 Antisense Noncoding RNA Mediates Lineage-Specific Transcriptional Silencing through Chromatin-Level Regulation

(2008) Radha Raman Pandey et al.   MOLECULAR CELL

Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of β-secretase

(2008) Mohammad Ali Faghihi et al.   NATURE MEDICINE

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

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE

Does the chimpanzee have a theory of mind? 30 years later

(2008) Josep Call et al.   TRENDS IN COGNITIVE SCIENCES