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

Neurons localize mRNAs near synapses where their translation can be regulated by synaptic demand and activity. Differences in the 3' UTRs of mRNAs can change their localization, stability, and translational regulation. Using 3' end RNA sequencing of microdissected rat brain slices, we discovered a huge diversity in mRNA 3' UTRs, with many transcripts showing enrichment for a particular 3' UTR isoform in either somata or the neuropil. The 3' UTR isoforms of localized transcripts are significantly longer than the 3' UTRs of non-localized transcripts and often code for proteins associated with axons, dendrites, and synapses. Surprisingly, long 3' UTRs add not only new, but also duplicate regulatory elements. The neuropil-enriched 3' UTR isoforms have significantly longer half-lives than somata-enriched isoforms. Finally, the 3' UTR isoforms can be significantly altered by enhanced activity. Most of the 3' UTR plasticity is transcription dependent, but intriguing examples of changes that are consistent with altered stability, trafficking between compartments, or local "remodeling" remain.

[1]  U. Hobohm,et al.  Selection of representative protein data sets , 1992, Protein science : a publication of the Protein Society.

[2]  Chen Zhang,et al.  SynDB: a Synapse protein DataBase based on synapse ontology , 2006, Nucleic Acids Res..

[3]  S. Warren,et al.  Identification of consensus binding sites clarifies FMRP binding determinants , 2016, Nucleic acids research.

[4]  P. Sharp,et al.  Proliferating Cells Express mRNAs with Shortened 3' Untranslated Regions and Fewer MicroRNA Target Sites , 2008, Science.

[5]  M. Levine,et al.  Neural-specific elongation of 3′ UTRs during Drosophila development , 2011, Proceedings of the National Academy of Sciences.

[6]  R. Elkon,et al.  Alternative cleavage and polyadenylation: extent, regulation and function , 2013, Nature Reviews Genetics.

[7]  E. Schuman,et al.  Visualization of newly synthesized neuronal RNA in vitro and in vivo using click-chemistry , 2016, RNA biology.

[8]  B. Tian,et al.  Alternative polyadenylation of mRNA precursors , 2016, Nature Reviews Molecular Cell Biology.

[9]  Sebastian D. Mackowiak,et al.  The Landscape of C. elegans 3′UTRs , 2010, Science.

[10]  Johannes E. Schindelin,et al.  Fiji: an open-source platform for biological-image analysis , 2012, Nature Methods.

[11]  E. Quinlan,et al.  CPEB-Mediated Cytoplasmic Polyadenylation and the Regulation of Experience-Dependent Translation of α-CaMKII mRNA at Synapses , 1998, Neuron.

[12]  Eric T. Wang,et al.  Distal Alternative Last Exons Localize mRNAs to Neural Projections. , 2016, Molecular cell.

[13]  C. Holt,et al.  Cytoplasmic polyadenylation and cytoplasmic polyadenylation element-dependent mRNA regulation are involved in Xenopus retinal axon development , 2009, Neural Development.

[14]  E. Kandel,et al.  The 3'-untranslated region of CaMKII alpha is a cis-acting signal for the localization and translation of mRNA in dendrites. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[16]  J. Bourne,et al.  Local Zones of Endoplasmic Reticulum Complexity Confine Cargo in Neuronal Dendrites , 2012, Cell.

[17]  Giovanni Coppola,et al.  Transcriptome analysis of embryonic and adult sensory axons reveals changes in mRNA repertoire localization. , 2011, RNA.

[18]  Yi-shuian Huang,et al.  Facilitation of dendritic mRNA transport by CPEB. , 2003, Genes & development.

[19]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[20]  C. Garner,et al.  Identification of a cis‐acting dendritic targeting element in the mRNA encoding the alpha subunit of Ca2+/calmodulin‐dependent protein kinase II , 2001, The European journal of neuroscience.

[21]  J. Mandel,et al.  G–quadruplex RNA structure as a signal for neurite mRNA targeting , 2011, EMBO reports.

[22]  C. Burge,et al.  3′ UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts , 2013, Genome research.

[23]  E. Schuman,et al.  A Requirement for Local Protein Synthesis in Neurotrophin-Induced Hippocampal Synaptic Plasticity , 1996, Science.

[24]  Ana Kozomara,et al.  miRBase: annotating high confidence microRNAs using deep sequencing data , 2013, Nucleic Acids Res..

[25]  Terrence S. Furey,et al.  The UCSC Table Browser data retrieval tool , 2004, Nucleic Acids Res..

[26]  E. Lai,et al.  Widespread and extensive lengthening of 3′ UTRs in the mammalian brain , 2013, Genome research.

[27]  Haifei Xu,et al.  Distinct cellular toxicity of two mutant huntingtin mRNA variants due to translation regulation , 2017, PloS one.

[28]  M. Pellegrini,et al.  Rapid Changes in the Translatome during the Conversion of Growth Cones to Synaptic Terminals. , 2016, Cell reports.

[29]  D. Bartel,et al.  Predicting effective microRNA target sites in mammalian mRNAs , 2015, eLife.

[30]  Uwe Ohler,et al.  FMR1 targets distinct mRNA sequence elements to regulate protein expression , 2012, Nature.

[31]  Yongsheng Shi,et al.  Alternative polyadenylation: new insights from global analyses. , 2012, RNA.

[32]  C. Mayr,et al.  Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells , 2009, Cell.

[33]  Steven W. Flavell,et al.  Genome-Wide Analysis of MEF2 Transcriptional Program Reveals Synaptic Target Genes and Neuronal Activity-Dependent Polyadenylation Site Selection , 2008, Neuron.

[34]  Erin M. Schuman,et al.  Dynamic Visualization of Local Protein Synthesis in Hippocampal Neurons , 2001, Neuron.

[35]  Davis J. McCarthy,et al.  Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation , 2012, Nucleic acids research.

[36]  Minghui Jiang,et al.  uShuffle: A useful tool for shuffling biological sequences while preserving the k-let counts , 2008, BMC Bioinformatics.

[37]  Erin M. Schuman,et al.  The Local Transcriptome in the Synaptic Neuropil Revealed by Deep Sequencing and High-Resolution Imaging , 2012, Neuron.

[38]  Peter F. Stadler,et al.  ViennaRNA Package 2.0 , 2011, Algorithms for Molecular Biology.

[39]  E. Schuman,et al.  Direct visualization of newly synthesized target proteins in situ , 2015, Nature Methods.

[40]  C. Holt,et al.  The Central Dogma Decentralized: New Perspectives on RNA Function and Local Translation in Neurons , 2013, Neuron.

[41]  David Haussler,et al.  The UCSC Genome Browser database: 2017 update , 2016, Nucleic Acids Res..

[42]  S. Linnarsson,et al.  Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq , 2015, Science.

[43]  K. Harris,et al.  Ultrastructural Analysis of Hippocampal Neuropil from the Connectomics Perspective , 2010, Neuron.

[44]  J. Richter,et al.  Dendritic GluN2A Synthesis Mediates Activity-Induced NMDA Receptor Insertion , 2013, The Journal of Neuroscience.

[45]  Brendan J. Frey,et al.  A compendium of RNA-binding motifs for decoding gene regulation , 2013, Nature.

[46]  James B. Brown,et al.  Global patterns of tissue-specific alternative polyadenylation in Drosophila. , 2012, Cell reports.

[47]  Michael Piper,et al.  Subcellular Profiling Reveals Distinct and Developmentally Regulated Repertoire of Growth Cone mRNAs , 2010, The Journal of Neuroscience.

[48]  R. Zukin,et al.  Bidirectional control of mRNA translation and synaptic plasticity by the cytoplasmic polyadenylation complex. , 2012, Molecular cell.

[49]  E. Trotta,et al.  On the Normalization of the Minimum Free Energy of RNAs by Sequence Length , 2014, PloS one.

[50]  E. Schuman,et al.  Activity-dependent spatially localized miRNA maturation in neuronal dendrites , 2017, Science.

[51]  D. Bartel,et al.  Extensive alternative polyadenylation during zebrafish development , 2012, Genome research.

[52]  Bin Tian,et al.  A large-scale analysis of mRNA polyadenylation of human and mouse genes , 2005, Nucleic acids research.

[53]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[54]  N. Perrone-Bizzozero,et al.  Different motif requirements for the localization zipcode element of β-actin mRNA binding by HuD and ZBP1 , 2015, Nucleic acids research.

[55]  T. Babak,et al.  A quantitative atlas of polyadenylation in five mammals , 2012, Genome research.

[56]  Anton J. Enright,et al.  MicroRNA targets in Drosophila , 2003, Genome Biology.

[57]  Ernesto Picardi,et al.  UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs , 2009, Nucleic Acids Res..

[58]  M. Kiebler,et al.  Faculty Opinions recommendation of Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. , 2009 .

[59]  R. Carroll,et al.  Activity Bidirectionally Regulates AMPA Receptor mRNA Abundance in Dendrites of Hippocampal Neurons , 2006, The Journal of Neuroscience.

[60]  J. Richter,et al.  Cytoplasmic polyadenylation elements mediate masking and unmasking of cyclin B1 mRNA , 1999, The EMBO journal.

[61]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[62]  Erin M. Schuman,et al.  Proteostasis in complex dendrites , 2013, Nature Reviews Neuroscience.

[63]  E. Schuman,et al.  Unconventional secretory processing diversifies neuronal ion channel properties , 2016, eLife.

[64]  A. Nairn.  Faculty Opinions recommendation of Disruption of dendritic translation of CaMKIIalpha impairs stabilization of synaptic plasticity and memory consolidation. , 2003 .

[65]  M. Mayford,et al.  Disruption of Dendritic Translation of CaMKIIα Impairs Stabilization of Synaptic Plasticity and Memory Consolidation , 2002, Neuron.

[66]  Giovanni Coppola,et al.  Activity-Dependent Regulation of Alternative Cleavage and Polyadenylation During Hippocampal Long-Term Potentiation , 2017, Scientific Reports.

[67]  C. Holt,et al.  Dynamic Axonal Translation in Developing and Mature Visual Circuits , 2016, Cell.

[68]  B. Tian,et al.  Progressive lengthening of 3′ untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development , 2009, Proceedings of the National Academy of Sciences.

[69]  D. Blackwood,et al.  A common variant in the 3′UTR of the GRIK4 glutamate receptor gene affects transcript abundance and protects against bipolar disorder , 2008, Proceedings of the National Academy of Sciences.

[70]  Mikael Bodén,et al.  MEME Suite: tools for motif discovery and searching , 2009, Nucleic Acids Res..

[71]  Lindy E. Barrett,et al.  RNA splicing capability of live neuronal dendrites. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[72]  Sören Müller,et al.  APADB: a database for alternative polyadenylation and microRNA regulation events , 2014, Database J. Biol. Databases Curation.

[73]  Eric T. Wang,et al.  Transcriptome-wide Regulation of Pre-mRNA Splicing and mRNA Localization by Muscleblind Proteins , 2012, Cell.

[74]  Gary Ruvkun,et al.  Identification of many microRNAs that copurify with polyribosomes in mammalian neurons , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[75]  M. Tohyama,et al.  Two cis-acting elements in the 3′ untranslated region of α-CaMKII regulate its dendritic targeting , 2000, Nature Neuroscience.

[76]  K. Sobczak,et al.  MBNL proteins and their target RNAs, interaction and splicing regulation , 2014, Nucleic acids research.