Emerging Roles for 3′ UTRs in Neurons

Monosomes actively translate synaptic mRNAs in neuronal processes

(2020) Anne Biever et al.   SCIENCE

Partial loss of CFIm25 causes learning deficits and aberrant neuronal alternative polyadenylation

(2020) Callison E Alcott et al.   eLife

Cell-type-specific quantification of protein synthesis in vivo

(2019) Lorena Hidalgo San Jose et al.   Nature Protocols

Choice of Alternative Polyadenylation Sites, Mediated by the RNA-Binding Protein Elavl3, Plays a Role in Differentiation of Inhibitory Neuronal Progenitors

(2019) Elena Grassi et al.   Frontiers in Cellular Neuroscience

Phosphoregulated FMRP phase separation models activity-dependent translation through bidirectional control of mRNA granule formation

(2019) Brian Tsang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of NGF Signaling by an Axonal Untranslated mRNA

(2019) Hamish Crerar et al.   NEURON

Comprehensive catalog of dendritically localized mRNA isoforms from sub-cellular sequencing of single mouse neurons

(2019) Sarah A. Middleton et al.   BMC BIOLOGY

Gain of Additional BIRC3 Protein Functions through 3ʹ-UTR-Mediated Protein Complex Formation

(2019) Shih-Han Lee et al.   MOLECULAR CELL

SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues

(2019) Jocelyn Y. Kishi et al.   NATURE METHODS

Live cell imaging reveals 3′-UTR dependent mRNA sorting to synapses

(2019) Karl E. Bauer et al.   Nature Communications

Elav-Mediated Exon Skipping and Alternative Polyadenylation of the Dscam1 Gene Are Required for Axon Outgrowth

(2019) Zhiping Zhang et al.   Cell Reports

RNA Granules Hitchhike on Lysosomes for Long-Distance Transport, Using Annexin A11 as a Molecular Tether

(2019) Ya-Cheng Liao et al.   CELL

Visualizing RNA dynamics in live cells with bright and stable fluorescent RNAs

(2019) Xianjun Chen et al.   NATURE BIOTECHNOLOGY

Inhibition of Axon Regeneration by Liquid-like TIAR-2 Granules

(2019) Matthew G. Andrusiak et al.   NEURON

The role of mRNA m6A methylation in the nervous system

(2019) Jiashuo Li et al.   Cell and Bioscience

Genomic Decoding of Neuronal Depolarization by Stimulus-Specific NPAS4 Heterodimers

(2019) G. Stefano Brigidi et al.   CELL

Role of MicroRNAs in Parkinson’s Disease

(2019) Suh Yee Goh et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Relationship of Sequence and Phase Separation in Protein Low-Complexity Regions

(2018) Erik W. Martin et al.   BIOCHEMISTRY

APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data

(2018) Congting Ye et al.   BIOINFORMATICS

Emerging roles for microRNA in the regulation of Drosophila circadian clock

(2018) Yongbo Xue et al.   BMC NEUROSCIENCE

Prion-like low-complexity sequences: Key regulators of protein solubility and phase behavior

(2018) Titus Franzmann et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The m6A-epitranscriptomic signature in neurobiology:from neurodevelopment to brain plasticity

(2018) Jocelyn Widagdo et al.   JOURNAL OF NEUROCHEMISTRY

m6A RNA Methylation Controls Neural Development and Is Involved in Human Diseases

(2018) Kunzhao Du et al.   MOLECULAR NEUROBIOLOGY

Alternative 3′ UTRs Modify the Localization, Regulatory Potential, Stability, and Plasticity of mRNAs in Neuronal Compartments

(2018) Georgi Tushev et al.   NEURON

Rapid, experience-dependent translation of neurogranin enables memory encoding

(2018) Kendrick J. Jones et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Locally translated mTOR controls axonal local translation in nerve injury

(2018) Marco Terenzio et al.   SCIENCE

Activity-Dependent Pre-miR-134 Dendritic Localization Is Required for Hippocampal Neuron Dendritogenesis

(2018) Federico Zampa et al.   Frontiers in Molecular Neuroscience

Alpha-synuclein mRNA isoform formation and translation affected by polymorphism in the human SNCA 3ʹUTR

(2018) Elizabeth S. Barrie et al.   Molecular Genetics & Genomic Medicine

Improving nanopore read accuracy with the R2C2 method enables the sequencing of highly multiplexed full-length single-cell cDNA

(2018) Roger Volden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Multiplexed Assay for Exon Recognition Reveals that an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Splicing Disruptions

(2018) Rocky Cheung et al.   MOLECULAR CELL

m6A facilitates hippocampus-dependent learning and memory through YTHDF1

(2018) Hailing Shi et al.   NATURE

Temporospatial guidance of activity-dependent gene expression by microRNA: mechanisms and functional implications for neural plasticity

(2018) Dylan Kiltschewskij et al.   NUCLEIC ACIDS RESEARCH

Alternative 3′ UTRs direct localization of functionally diverse protein isoforms in neuronal compartments

(2018) Camilla Ciolli Mattioli et al.   NUCLEIC ACIDS RESEARCH

Widespread Accumulation of Ribosome-Associated Isolated 3′ UTRs in Neuronal Cell Populations of the Aging Brain

(2018) Peter H. Sudmant et al.   Cell Reports

Active presynaptic ribosomes in the mammalian brain, and altered transmitter release after protein synthesis inhibition

(2018) Matthew S Scarnati et al.   eLife

Microfluidic isoform sequencing shows widespread splicing coordination in the human transcriptome

(2017) Hagen Tilgner et al.   GENOME RESEARCH

microRNAs in Parkinson’s Disease: From Pathogenesis to Novel Diagnostic and Therapeutic Approaches

(2017) Loredana Leggio et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

RNA phase transitions in repeat expansion disorders

(2017) Ankur Jain et al.   NATURE

SNCA 3′UTR genetic variants in patients with Parkinson’s disease and REM sleep behavior disorder

(2017) M. Toffoli et al.   NEUROLOGICAL SCIENCES

Discovering the 3′ UTR-mediated regulation of alpha-synuclein

(2017) Domenica Marchese et al.   NUCLEIC ACIDS RESEARCH

Transcription elongation rate has a tissue-specific impact on alternative cleavage and polyadenylation in Drosophila melanogaster

(2017) Xiaochuan Liu et al.   RNA

RNA editing with CRISPR-Cas13

(2017) David B. T. Cox et al.   SCIENCE

Post-transcriptional 3´-UTR cleavage of mRNA transcripts generates thousands of stable uncapped autonomous RNA fragments

(2017) Yuval Malka et al.   Nature Communications

Alterations in mRNA 3′ UTR Isoform Abundance Accompany Gene Expression Changes in Human Huntington’s Disease Brains

(2017) Lindsay Romo et al.   Cell Reports

ZBP1 phosphorylation at serine 181 regulates its dendritic transport and the development of dendritic trees of hippocampal neurons

(2017) Anna S. Urbanska et al.   Scientific Reports

Genome-Wide Analysis of RNA Secondary Structure

(2016) Philip C. Bevilacqua et al.   Annual Review of Genetics

Programmable RNA Tracking in Live Cells with CRISPR/Cas9

(2016) David A. Nelles et al.   CELL

Distal Alternative Last Exons Localize mRNAs to Neural Projections

(2016) J. Matthew Taliaferro et al.   MOLECULAR CELL

Genome-wide, integrative analysis implicates microRNA dysregulation in autism spectrum disorder

(2016) Ye E Wu et al.   NATURE NEUROSCIENCE

Nascent Proteome Remodeling following Homeostatic Scaling at Hippocampal Synapses

(2016) Christoph T. Schanzenbächer et al.   NEURON

Translation dynamics of single mRNAs in live cells and neurons

(2016) B. Wu et al.   SCIENCE

Real-time quantification of single RNA translation dynamics in living cells

(2016) T. Morisaki et al.   SCIENCE

Hypo- and Hyper-Assembly Diseases of RNA–Protein Complexes

(2016) Siddharth Shukla et al.   TRENDS IN MOLECULAR MEDICINE

Position-specific binding of FUS to nascent RNA regulates mRNA length

(2015) Akio Masuda et al.   GENES & DEVELOPMENT

A majority of m6A residues are in the last exons, allowing the potential for 3′ UTR regulation

(2015) Shengdong Ke et al.   GENES & DEVELOPMENT

Coordination of RNA Polymerase II Pausing and 3’ end processing factor recruitment with alternative polyadenylation

(2015) Becky Fusby et al.   MOLECULAR AND CELLULAR BIOLOGY

ELAV Links Paused Pol II to Alternative Polyadenylation in the Drosophila Nervous System

(2015) Katarzyna Oktaba et al.   MOLECULAR CELL

Alternative 3′ UTRs act as scaffolds to regulate membrane protein localization

(2015) Binyamin D. Berkovits et al.   NATURE

Direct visualization of newly synthesized target proteins in situ

(2015) Susanne tom Dieck et al.   NATURE METHODS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

A coding-independent function of an alternative Ube3a transcript during neuronal development

(2015) Jeremy Valluy et al.   NATURE NEUROSCIENCE

Determining the role of microRNAs in psychiatric disorders

(2015) Orna Issler et al.   NATURE REVIEWS NEUROSCIENCE

Widespread Differential Expression of Coding Region and 3′ UTR Sequences in Neurons and Other Tissues

(2015) Arif Kocabas et al.   NEURON

ALS/FTD Mutation-Induced Phase Transition of FUS Liquid Droplets and Reversible Hydrogels into Irreversible Hydrogels Impairs RNP Granule Function

(2015) Tetsuro Murakami et al.   NEURON

An RNA biosensor for imaging the first round of translation from single cells to living animals

(2015) J. M. Halstead et al.   SCIENCE

Liquid-Liquid Phase Separation in Biology

(2014) Anthony A. Hyman et al.   Annual Review of Cell and Developmental Biology

A change-point model for identifying 3′UTR switching by next-generation RNA sequencing

(2014) Wei Wang et al.   BIOINFORMATICS

The role of microRNAs in regulating neuronal connectivity

(2014) Hui Chiu et al.   Frontiers in Cellular Neuroscience

An ALS-associated mutation in the FUS 3′-UTR disrupts a microRNA–FUS regulatory circuitry

(2014) Stefano Dini Modigliani et al.   Nature Communications

Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3′-UTR landscape across seven tumour types

(2014) Zheng Xia et al.   Nature Communications

Mining the 3′UTR of Autism-implicated Genes for SNPs Perturbing MicroRNA Regulation

(2014) Varadharajan Vaishnavi et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Local translation in neuronal processes-in vivotests of a “heretical hypothesis”

(2013) Rotem B. Perry et al.   Developmental Neurobiology

Subcellular transcriptomics-Dissection of the mRNA composition in the axonal compartment of sensory neurons

(2013) Adi Minis et al.   Developmental Neurobiology

Polyadenylation site-specific differences in the activity of the neuronal βCstF-64 protein in PC-12 cells

(2013) Ganesh S. Shankarling et al.   GENE

Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression

(2013) S. Lianoglou et al.   GENES & DEVELOPMENT

Widespread and extensive lengthening of 3' UTRs in the mammalian brain

(2013) P. Miura et al.   GENOME RESEARCH

A HuD-ZBP1 ribonucleoprotein complex localizes GAP-43 mRNA into axons through its 3′ untranslated region AU-rich regulatory element

(2013) Soonmoon Yoo et al.   JOURNAL OF NEUROCHEMISTRY

Axonal Localization of Neuritin/CPG15 mRNA in Neuronal Populations through Distinct 5' and 3' UTR Elements

(2013) T. T. Merianda et al.   JOURNAL OF NEUROSCIENCE

KSRP Modulation of GAP-43 mRNA Stability Restricts Axonal Outgrowth in Embryonic Hippocampal Neurons

(2013) Clark W. Bird et al.   PLoS One

Overlapping and distinct functions of CstF64 and CstF64  in mammalian mRNA 3' processing

(2013) C. Yao et al.   RNA

miR-206 regulates brain-derived neurotrophic factor in Alzheimer disease model

(2012) Soon-Tae Lee et al.   ANNALS OF NEUROLOGY

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Cell-free Formation of RNA Granules: Low Complexity Sequence Domains Form Dynamic Fibers within Hydrogels

(2012) Masato Kato et al.   CELL

Getting RNA and Protein in Phase

(2012) Stephanie C. Weber et al.   CELL

Cell-free Formation of RNA Granules: Bound RNAs Identify Features and Components of Cellular Assemblies

(2012) Tina W. Han et al.   CELL

Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons

(2012) Kate D. Meyer et al.   CELL

Principles and roles of mRNA localization in animal development

(2012) C. Medioni et al.   DEVELOPMENT

miR-124-regulated RhoG reduces neuronal process complexity via ELMO/Dock180/Rac1 and Cdc42 signalling

(2012) Kristin Franke et al.   EMBO JOURNAL

Spatial arrangement of an RNA zipcode identifies mRNAs under post-transcriptional control

(2012) V. L. Patel et al.   GENES & DEVELOPMENT

ELAV mediates 3' UTR extension in the Drosophila nervous system

(2012) V. Hilgers et al.   GENES & DEVELOPMENT

Regulation of Zipcode Binding Protein 1 Transport Dynamics in Axons by Myosin Va

(2012) V. C. Nalavadi et al.   JOURNAL OF NEUROSCIENCE

Activity-Dependent Local Translation of Matrix Metalloproteinase-9

(2012) M. Dziembowska et al.   JOURNAL OF NEUROSCIENCE

MicroRNAs in learning, memory, and neurological diseases

(2012) W. Wang et al.   LEARNING & MEMORY

Analysis of alternative cleavage and polyadenylation by 3′ region extraction and deep sequencing

(2012) Mainul Hoque et al.   NATURE METHODS

microRNA-9 regulates axon extension and branching by targeting Map1b in mouse cortical neurons

(2012) Federico Dajas-Bailador et al.   NATURE NEUROSCIENCE

Subcellular Knockout of Importin β1 Perturbs Axonal Retrograde Signaling

(2012) Rotem Ben-Tov Perry et al.   NEURON

Why Have Tobacco Control Policies Stalled? Using Genetic Moderation to Examine Policy Impacts

(2012) Jason M. Fletcher   PLoS One

Identification of a cis-acting element that localizes mRNA to synapses

(2012) E. J. Meer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MicroRNAs in neuronal function and dysfunction

(2012) Heh-In Im et al.   TRENDS IN NEUROSCIENCES

Global Patterns of Tissue-Specific Alternative Polyadenylation in Drosophila

(2012) Peter Smibert et al.   Cell Reports

Genome-wide Analysis of Pre-mRNA 3′ End Processing Reveals a Decisive Role of Human Cleavage Factor I in the Regulation of 3′ UTR Length

(2012) Georges Martin et al.   Cell Reports

Molecular motors: directing traffic during RNA localization

(2011) James A. Gagnon et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Beyond Stereospecificity: Liquids and Mesoscale Organization of Cytoplasm

(2011) Anthony A. Hyman et al.   DEVELOPMENTAL CELL

RNA polymerase II kinetics inpolopolyadenylation signal selection

(2011) Pedro A B Pinto et al.   EMBO JOURNAL

G–quadruplex RNA structure as a signal for neurite mRNA targeting

(2011) Murugan Subramanian et al.   EMBO REPORTS

RNAscope

(2011) Fay Wang et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Axonal Localization of Transgene mRNA in Mature PNS and CNS Neurons

(2011) D. E. Willis et al.   JOURNAL OF NEUROSCIENCE

Alzheimer-specific variants in the 3'UTR of Amyloid precursor protein affect microRNA function

(2011) Charlotte Delay et al.   Molecular Neurodegeneration

miR-124 acts through CoREST to control onset of Sema3A sensitivity in navigating retinal growth cones

(2011) Marie-Laure Baudet et al.   NATURE NEUROSCIENCE

Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq

(2011) P. J. Shepard et al.   RNA

Conserved 3′-Untranslated Region Sequences Direct Subcellular Localization of Chaperone Protein mRNAs in Neurons

(2010) Deepika Vuppalanchi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Subcellular Profiling Reveals Distinct and Developmentally Regulated Repertoire of Growth Cone mRNAs

(2010) K. H. Zivraj et al.   JOURNAL OF NEUROSCIENCE

In situ detection and genotyping of individual mRNA molecules

(2010) Chatarina Larsson et al.   NATURE METHODS

In situ visualization and dynamics of newly synthesized proteins in rat hippocampal neurons

(2010) Daniela C Dieterich et al.   NATURE NEUROSCIENCE

An NGF-responsive element targets myo-inositol monophosphatase-1 mRNA to sympathetic neuron axons

(2010) Catia Andreassi et al.   NATURE NEUROSCIENCE

Expression of distinct RNAs from 3′ untranslated regions

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

microRNA-132 regulates dendritic growth and arborization of newborn neurons in the adult hippocampus

(2010) S. T. Magill et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptome analysis of embryonic and adult sensory axons reveals changes in mRNA repertoire localization

(2010) L. F. Gumy et al.   RNA

Pre-mRNA 3′-end processing complex assembly and function

(2010) Serena Chan et al.   Wiley Interdisciplinary Reviews-RNA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Specification of Neuronal Polarity Regulated by Local Translation of CRMP2 and Tau via the mTOR-p70S6K Pathway

(2009) Tsuyoshi Morita et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Axonal mRNA in Uninjured and Regenerating Cortical Mammalian Axons

(2009) A. M. Taylor et al.   JOURNAL OF NEUROSCIENCE

Prenatal exposure to maternal cigarette smoking interacts with a polymorphism in the α6 nicotinic acetylcholine receptor gene to influence drug use and striatum volume in adolescence

(2009) S Lotfipour et al.   MOLECULAR PSYCHIATRY

A single nucleotide polymorphism in the 3′UTR of the SNCA gene encoding alpha-synuclein is a new potential susceptibility locus for Parkinson disease

(2009) Sotiria Sotiriou et al.   NEUROSCIENCE LETTERS

Subcellular mRNA Localization in Animal Cells and Why It Matters

(2009) C. E. Holt et al.   SCIENCE

To localize or not to localize: mRNA fate is in 3′UTR ends

(2009) Catia Andreassi et al.   TRENDS IN CELL BIOLOGY

Alterations of the microRNA network cause neurodegenerative disease

(2009) Sébastien S. Hébert et al.   TRENDS IN NEUROSCIENCES

Distinct Role of Long 3′ UTR BDNF mRNA in Spine Morphology and Synaptic Plasticity in Hippocampal Neurons

(2008) Juan Ji An et al.   CELL

MicroRNA-298 and MicroRNA-328 Regulate Expression of Mouse β-Amyloid Precursor Protein-converting Enzyme 1

(2008) Vincent Boissonneault et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

(2008) Donny D. Licatalosi et al.   NATURE

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS

Localized Regulation of Axonal RanGTPase Controls Retrograde Injury Signaling in Peripheral Nerve

(2008) Dmitry Yudin et al.   NEURON