CoChat
Sign Up
Cited by 41

The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.

miRNA Regulons Associated with Synaptic Function

Paschou, Maria, Paraskevopoulou, Maria D., Vlachos, Ioannis S., Koukouraki, Pelagia, Hatzigeorgiou, Artemis G., Doxakis, Epaminondas·2012·PLoS ONE
DOI 10.1371/journal.pone.0046189PMC PMC3468272
Open this paper in CoChat — free account

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1371/journal.pone.0046189

Cites

6 of 6 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • mRNAs of presynaptic genes, like SNCA, display significantly longer 3′UTRs than all other cellular transcripts, indicating they are biased toward post-transcriptional regulation.

    “Further, the mRNAs of presynaptic genes, like SNCA, display significantly longer 3′UTRs than all other cellular transcripts, indicating that they are biased toward post-transcriptional regulation of expression [17].”

    From RNA binding protein AUF1/HNRNPD regulates nuclear export, stability and translation of SNCA transcripts (2023) · cites this paper as [17]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 62

  1. [2]Hirokawa N, Niwa S, Tanaka Y (2010) Molecular motors in neurons: transport mechanisms and roles in brain function, development, and disease. Neuron 68: 610– 638. 21092854
  2. [3]Santos MS, Li H, Voglmaier SM (2009) Synaptic vesicle protein trafficking at the glutamate synapse. Neuroscience 158: 189– 203. 18472224 PMC2667334
  3. [4]Liu-Yesucevitz L, Bassell GJ, Gitler AD, Hart AC, Klann E, et al (2011) Local RNA translation at the synapse and in disease. J Neurosci 31: 16086– 16093. 22072660 PMC3241995
  4. [5]Swanger SA, Bassell GJ (2011) Making and breaking synapses through local mRNA regulation. Curr Opin Genet Dev 21: 414– 421. 21530231 PMC3149745
  5. [6]Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T (2001) Identification of novel genes coding for small expressed RNAs. Science 294: 853– 858. 11679670
  6. [7]Lau NC, Lim LP, Weinstein EG, Bartel DP (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294: 858– 862. 11679671
  7. [8]Lee RC, Ambros V (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294: 862– 864. 11679672
  8. [9]Bartel DP, Chen CZ (2004) Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nat Rev Genet 5: 396– 400. 15143321
  9. [10]Esau C, Davis S, Murray SF, Yu XX, Pandey SK, et al (2006) miR-122 regulation of lipid metabolism revealed by in vivo antisense targeting. Cell metabolism 3: 87– 98. 16459310
  10. [11]Krutzfeldt J, Rajewsky N, Braich R, Rajeev KG, Tuschl T, et al (2005) Silencing of microRNAs in vivo with ‘antagomirs’. Nature 438: 685– 689. 16258535
  11. [12]Kozomara A, Griffiths-Jones S (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39: D152– 157. 21037258 PMC3013655
  12. [13]Wienholds E, Plasterk RH (2005) MicroRNA function in animal development. FEBS Lett 579: 5911– 5922. 16111679
  13. [14]Lai EC (2005) miRNAs: whys and wherefores of miRNA-mediated regulation. Curr Biol 15: R458– 460. 15964265
  14. [15]Lugli G, Torvik VI, Larson J, Smalheiser NR (2008) Expression of microRNAs and their precursors in synaptic fractions of adult mouse forebrain. J Neurochem 106: 650– 661. 18410515 PMC3711666
  15. [16]Lugli G, Larson J, Martone ME, Jones Y, Smalheiser NR (2005) Dicer and eIF2c are enriched at postsynaptic densities in adult mouse brain and are modified by neuronal activity in a calpain-dependent manner. J Neurochem 94: 896– 905. 16092937
  16. [17]Krol J, Busskamp V, Markiewicz I, Stadler MB, Ribi S, et al (2010) Characterizing light-regulated retinal microRNAs reveals rapid turnover as a common property of neuronal microRNAs. Cell 141: 618– 631. 20478254
  17. [19]Hahn CG, Banerjee A, Macdonald ML, Cho DS, Kamins J, et al (2009) The post-synaptic density of human postmortem brain tissues: an experimental study paradigm for neuropsychiatric illnesses. PLoS One 4: e5251. 19370153 PMC2666803
  18. [21]Yoshimura Y, Yamauchi Y, Shinkawa T, Taoka M, Donai H, et al (2004) Molecular constituents of the postsynaptic density fraction revealed by proteomic analysis using multidimensional liquid chromatography-tandem mass spectrometry. J Neurochem 88: 759– 768. 14720225
  19. [22]Ziv NE, Garner CC (2004) Cellular and molecular mechanisms of presynaptic assembly. Nat Rev Neurosci 5: 385– 399. 15100721
  20. [23]Matsumoto M, Setou M, Inokuchi K (2007) Transcriptome analysis reveals the population of dendritic RNAs and their redistribution by neural activity. Neurosci Res 57: 411– 423. 17207874
  21. [24]Bruses JL (2010) Identification of gene transcripts expressed by postsynaptic neurons during synapse formation encoding cell surface proteins with presumptive synaptogenic activity. Synapse 64: 47– 60. 19728367 PMC2783745
  22. [26]Stryker E, Johnson KG (2007) LAR, liprin alpha and the regulation of active zone morphogenesis. J Cell Sci 120: 3723– 3728. 17959628
  23. [27]Vessey JP, Karra D (2007) More than just synaptic building blocks: scaffolding proteins of the post-synaptic density regulate dendritic patterning. J Neurochem 102: 324– 332. 17596209
  24. [28]Spangler SA, Hoogenraad CC (2007) Liprin-alpha proteins: scaffold molecules for synapse maturation. Biochem Soc Trans 35: 1278– 1282. 17956329
  25. [29]Rebhan M, Chalifa-Caspi V, Prilusky J, Lancet D (1997) GeneCards: integrating information about genes, proteins and diseases. Trends Genet 13: 163. 9097728
  26. [30]Kinsella RJ, Kahari A, Haider S, Zamora J, Proctor G, et al (2011) Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database (Oxford) 2011: bar030. 21785142 PMC3170168
  27. [31]Garcia DM, Baek D, Shin C, Bell GW, Grimson A, et al (2011) Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat Struct Mol Biol 18: 1139– 1146. 21909094 PMC3190056
  28. [32]Reczko M, Maragkakis M, Alexiou P, Grosse I, Hatzigeorgiou AG (2012) Functional microRNA targets in protein coding sequences. Bioinformatics 28: 771– 776. 22285563
  29. [33]Vlachos IS, Kostoulas N, Vergoulis T, Georgakilas G, Reczko M, et al (2012) DIANA miRPath v.2.0: investigating the combinatorial effect of microRNAs in pathways. Nucleic Acids Res 40: W498– W504. 22649059 PMC3394305
  30. [34]Alexiou P, Maragkakis M, Papadopoulos GL, Reczko M, Hatzigeorgiou AG (2009) Lost in translation: an assessment and perspective for computational microRNA target identification. Bioinformatics 25: 3049– 3055. 19789267
  31. [35]Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, et al (2009) ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 25: 1091– 1093. 19237447 PMC2666812
  32. [36]Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25– 29. 10802651 PMC3037419
  33. [37]Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, et al (2010) Cytoscape Web: an interactive web-based network browser. Bioinformatics 26: 2347– 2348. 20656902 PMC2935447
  34. [39]Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, et al (2007) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 27: 91– 105. 17612493 PMC3800283
  35. [40]Gu S, Jin L, Zhang F, Sarnow P, Kay MA (2009) Biological basis for restriction of microRNA targets to the 3′ untranslated region in mammalian mRNAs. Nat Struct Mol Biol 16: 144– 150. 19182800 PMC2713750
  36. [41]Sandberg R, Neilson JR, Sarma A, Sharp PA, Burge CB (2008) Proliferating cells express mRNAs with shortened 3′ untranslated regions and fewer microRNA target sites. Science 320: 1643– 1647. 18566288 PMC2587246
  37. [42]Enright AJ, John B, Gaul U, Tuschl T, Sander C, et al (2003) MicroRNA targets in Drosophila. Genome Biol 5: R1. 14709173 PMC395733
  38. [43]Hsu R, Schofield CM, Dela Cruz CG, Jones-Davis DM, Blelloch R, et al (2012) Loss of microRNAs in pyramidal neurons leads to specific changes in inhibitory synaptic transmission in the prefrontal cortex. Mol Cell Neurosci 50: 283– 292. 22728723 PMC3613865
  39. [44]Davis TH, Cuellar TL, Koch SM, Barker AJ, Harfe BD, et al (2008) Conditional loss of Dicer disrupts cellular and tissue morphogenesis in the cortex and hippocampus. J Neurosci 28: 4322– 4330. 18434510 PMC3844796
  40. [45]Li Q, Bian S, Hong J, Kawase-Koga Y, Zhu E, et al (2011) Timing specific requirement of microRNA function is essential for embryonic and postnatal hippocampal development. PLoS One 6: e26000. 21991391 PMC3186801
  41. [46]An JJ, Gharami K, Liao GY, Woo NH, Lau AG, et al (2008) Distinct role of long 3′ UTR BDNF mRNA in spine morphology and synaptic plasticity in hippocampal neurons. Cell 134: 175– 187. 18614020 PMC2527207
  42. [47]Ji Z, Lee JY, Pan Z, Jiang B, Tian B (2009) Progressive lengthening of 3′ untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development. Proc Natl Acad Sci U S A 106: 7028– 7033. 19372383 PMC2669788
  43. [48]Bergauer T, Krueger U, Lader E, Pilk S, Wolter I, et al (2009) Analysis of putative miRNA binding sites and mRNA 3′ ends as targets for siRNA-mediated gene knockdown. Oligonucleotides 19: 41– 52. 19196098
  44. [49]Majoros WH, Ohler U (2007) Spatial preferences of microRNA targets in 3′ untranslated regions. BMC Genomics 8: 152. 17555584 PMC1904200
  45. [50]Beveridge NJ, Cairns MJ (2012) MicroRNA dysregulation in schizophrenia. Neurobiology of disease 46: 263– 271. 22207190
  46. [52]Inukai S, de Lencastre A, Turner M, Slack F (2012) Novel MicroRNAs Differentially Expressed during Aging in the Mouse Brain. PLoS One 7: e40028. 22844398 PMC3402511
  47. [53]Gunaratne PH, Lin YC, Benham AL, Drnevich J, Coarfa C, et al (2011) Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrain. BMC Genomics 12: 277. 21627805 PMC3118218
  48. [54]Agostini M, Tucci P, Steinert JR, Shalom-Feuerstein R, Rouleau M, et al (2011) microRNA-34a regulates neurite outgrowth, spinal morphology, and function. Proc Natl Acad Sci U S A 108 (52) 21099– 21104. 22160706 PMC3248521
  49. [55]Agostini M, Tucci P, Killick R, Candi E, Sayan BS, et al (2011) Neuronal differentiation by TAp73 is mediated by microRNA-34a regulation of synaptic protein targets. Proc Natl Acad Sci U S A 108 (52) 21093– 21098. 22160687 PMC3248477
  50. [56]Wang WX, Huang Q, Hu Y, Stromberg AJ, Nelson PT (2011) Patterns of microRNA expression in normal and early Alzheimer's disease human temporal cortex: white matter versus gray matter. Acta Neuropathol 121: 193– 205. 20936480 PMC3073518
  51. [57]Kim AH, Reimers M, Maher B, Williamson V, McMichael O, et al (2010) MicroRNA expression profiling in the prefrontal cortex of individuals affected with schizophrenia and bipolar disorders. Schizophr Res 124: 183– 191. 20675101 PMC4373420
  52. [58]Sano T, Reynolds JP, Jimenez-Mateos EM, Matsushima S, Taki W, et al (2012) MicroRNA-34a upregulation during seizure-induced neuronal death. Cell death & disease 3: e287. 22436728 PMC3317348
  53. [59]Zovoilis A, Agbemenyah HY, Agis-Balboa RC, Stilling RM, Edbauer D, et al (2011) microRNA-34c is a novel target to treat dementias. EMBO J 30: 4299– 4308. 21946562 PMC3199394
  54. [60]Haramati S, Navon I, Issler O, Ezra-Nevo G, Gil S, et al (2011) MicroRNA as repressors of stress-induced anxiety: the case of amygdalar miR-34. J Neurosci 31: 14191– 14203. 21976504 PMC6623664
  55. [61]Magill ST, Cambronne XA, Luikart BW, Lioy DT, Leighton BH, et al (2010) microRNA-132 regulates dendritic growth and arborization of newborn neurons in the adult hippocampus. Proc Natl Acad Sci U S A 107: 20382– 20387. 21059906 PMC2996687
  56. [62]Pathania M, Torres-Reveron J, Yan L, Kimura T, Lin TV, et al (2012) miR-132 Enhances Dendritic Morphogenesis, Spine Density, Synaptic Integration, and Survival of Newborn Olfactory Bulb Neurons. PLoS One 7: e38174. 22693596 PMC3364964
  57. [63]Tognini P, Putignano E, Coatti A, Pizzorusso T (2011) Experience-dependent expression of miR-132 regulates ocular dominance plasticity. Nat Neurosci 14: 1237– 1239. 21892154 PMC3183093
  58. [64]Cheng HY, Papp JW, Varlamova O, Dziema H, Russell B, et al (2007) microRNA modulation of circadian-clock period and entrainment. Neuron 54: 813– 829. 17553428 PMC2590749
  59. [65]Lee K, Kim JH, Kwon OB, An K, Ryu J, et al (2012) An activity-regulated microRNA, miR-188, controls dendritic plasticity and synaptic transmission by downregulating neuropilin-2. J Neurosci 32: 5678– 5687. 22514329 PMC5010781
  60. [66]Zhou S, Yu B, Qian T, Yao D, Wang Y, et al (2011) Early changes of microRNAs expression in the dorsal root ganglia following rat sciatic nerve transection. Neuroscience letters 494: 89– 93. 21371527
  61. [68]Siegel G, Obernosterer G, Fiore R, Oehmen M, Bicker S, et al (2009) A functional screen implicates microRNA-138-dependent regulation of the depalmitoylation enzyme APT1 in dendritic spine morphogenesis. Nature cell biology 11: 705– 716. 19465924 PMC3595613
  62. [69]Jimenez-Mateos EM, Engel T, Merino-Serrais P, McKiernan RC, Tanaka K, et al (2012) Silencing microRNA-134 produces neuroprotective and prolonged seizure-suppressive effects. Nature medicine 18 (7) 1087– 1094. PMC3438344 22683779

Cited by

Sorted by citations

Metadata

Authors
Paschou, M., Paraskevopoulou, M. D., Vlachos, I. S., Koukouraki, P., Hatzigeorgiou, A. G., & Doxakis, E.
Venue
PLoS ONE
Publisher
Public Library of Science (PLoS)
Published
2012-10-08
Volume
7
Issue
10
Pages
e46189
ISSN
1932-6203
DOI
10.1371/journal.pone.0046189
PMC
PMC3468272
Cited by
41
References
6
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (unspecified)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review