Gene network and pathway analysis of mice with conditional ablation of dicer in post-mitotic neurons

PLoS ONE

Volumn 7, Issue 8, 2012, Pages

  Dorval, Véronique ^a,b   Smith, Pascal Y ^a,b   Delay, Charlotte ^a,b   Calvo, Ezequiel ^a,b   Planel, Emmanuel ^a,b   Zommer, Nadège ^c,d   Buée, Luc ^c,d   Hébert, Sébastien S ^a,b  

^a LAVAL UNIVERSITY   (Canada)

^b UNIVERSITÉ LAVAL   (Canada)

^c UNIV LILLE   (France)

^d INSERM   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DICER; DNA METHYLTRANSFERASE 3A; LIM KINASE 1; MICRORNA; MICRORNA 124;

3' UNTRANSLATED REGION; ADULT ANIMAL; ANIMAL TISSUE; ARTICLE; BRAIN NERVE CELL; CONTROLLED STUDY; DNMT3A GENE; DOWN REGULATION; FOREBRAIN; GENE; GENE EXPRESSION REGULATION; GENOME ANALYSIS; IN VIVO STUDY; LIMK1 GENE; MICROARRAY ANALYSIS; MITOSIS; MOUSE; NONHUMAN; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TNRC6C GENE; TRANSCRIPTOMICS; UPREGULATION;

AGING; ANIMALS; BRAIN; COMPUTATIONAL BIOLOGY; DEAD-BOX RNA HELICASES; GENE DELETION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE REGULATORY NETWORKS; MICE; MICE, KNOCKOUT; MICRORNAS; MITOSIS; NEURONS; ORGAN SPECIFICITY; REPRODUCIBILITY OF RESULTS; RIBONUCLEASE III; SIGNAL TRANSDUCTION;

EID: 84865442904     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0044060     Document Type: Article

References (51)

1. Lau P, Hudson LD, (2010) MicroRNAs in neural cell differentiation. Brain Res 1338: 14-19.
2. Liu C, Zhao X, (2009) MicroRNAs in adult and embryonic neurogenesis. Neuromolecular Med 11: 141-152.
3. Lee Y, Kim M, Han J, Yeom KH, Lee S, et al. (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J 23: 4051-4060.
4. Sontheimer EJ, (2005) Assembly and function of RNA silencing complexes. Nat Rev Mol Cell Biol 6: 127-138.
5. Ambros V, (2004) The functions of animal microRNAs. Nature 431: 350-355.
6. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB, (2003) Prediction of mammalian microRNA targets. Cell 115: 787-798.
7. John B, Enright AJ, Aravin A, Tuschl T, Sander C, et al. (2004) Human MicroRNA targets. PLoS Biol 2: e363.
8. Miska EA, Alvarez-Saavedra E, Townsend M, Yoshii A, Sestan N, et al. (2004) Microarray analysis of microRNA expression in the developing mammalian brain. Genome Biol 5: R68.
9. Sempere LF, Freemantle S, Pitha-Rowe I, Moss E, Dmitrovsky E, et al. (2004) Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation. Genome Biol 5: R13.
10. Barad O, Meiri E, Avniel A, Aharonov R, Barzilai A, et al. (2004) MicroRNA expression detected by oligonucleotide microarrays: system establishment and expression profiling in human tissues. Genome Res 14: 2486-2494.
11. Hohjoh H, Fukushima T, (2007) Marked change in microRNA expression during neuronal differentiation of human teratocarcinoma NTera2D1 and mouse embryonal carcinoma P19 cells. Biochem Biophys Res Commun 362: 360-367.
12. Kapsimali M, Kloosterman WP, de Bruijn E, Rosa F, Plasterk RH, et al. (2007) MicroRNAs show a wide diversity of expression profiles in the developing and mature central nervous system. Genome Biol 8: R173.
13. 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.
14. Hebert SS, Papadopoulou AS, Smith P, Galas MC, Planel E, et al. (2010) Genetic ablation of Dicer in adult forebrain neurons results in abnormal tau hyperphosphorylation and neurodegeneration. Hum Mol Genet 19: 3959-3969.
15. Hebert SS, De Strooper B, (2009) Alterations of the microRNA network cause neurodegenerative disease. Trends Neurosci 32: 199-206.
16. Cheng LC, Pastrana E, Tavazoie M, Doetsch F, (2009) miR-124 regulates adult neurogenesis in the subventricular zone stem cell niche. Nat Neurosci 12: 399-408.
17. Makeyev EV, Zhang J, Carrasco MA, Maniatis T, (2007) The MicroRNA miR-124 promotes neuronal differentiation by triggering brain-specific alternative pre-mRNA splicing. Mol Cell 27: 435-448.
18. Silber J, Lim DA, Petritsch C, Persson AI, Maunakea AK, et al. (2008) miR-124 and miR-137 inhibit proliferation of glioblastoma multiforme cells and induce differentiation of brain tumor stem cells. BMC Med 6: 14.
19. Visvanathan J, Lee S, Lee B, Lee JW, Lee SK, (2007) The microRNA miR-124 antagonizes the anti-neural REST/SCP1 pathway during embryonic CNS development. Genes Dev 21: 744-749.
20. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, et al. (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433: 769-773.
21. Kosik KS, (2006) The neuronal microRNA system. Nat Rev Neurosci 7: 911-920.
22. 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.
23. Schratt GM, Tuebing F, Nigh EA, Kane CG, Sabatini ME, et al. (2006) A brain-specific microRNA regulates dendritic spine development. Nature 439: 283-289.
24. Sevignani C, Calin GA, Siracusa LD, Croce CM, (2006) Mammalian microRNAs: a small world for fine-tuning gene expression. Mamm Genome 17: 189-202.
25. Huang da W, Sherman BT, Lempicki RA, (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.
26. Till S, Lejeune E, Thermann R, Bortfeld M, Hothorn M, et al. (2007) A conserved motif in Argonaute-interacting proteins mediates functional interactions through the Argonaute PIWI domain. Nat Struct Mol Biol 14: 897-903.
27. Tokumaru S, Suzuki M, Yamada H, Nagino M, Takahashi T, (2008) let-7 regulates Dicer expression and constitutes a negative feedback loop. Carcinogenesis 29: 2073-2077.
28. Cuellar TL, Davis TH, Nelson PT, Loeb GB, Harfe BD, et al. (2008) Dicer loss in striatal neurons produces behavioral and neuroanatomical phenotypes in the absence of neurodegeneration. Proc Natl Acad Sci U S A 105: 5614-5619.
29. Scott RW, Olson MF, (2007) LIM kinases: function, regulation and association with human disease. J Mol Med (Berl) 85: 555-568.
30. Fabbri M, Garzon R, Cimmino A, Liu Z, Zanesi N, et al. (2007) MicroRNA-29 family reverts aberrant methylation in lung cancer by targeting DNA methyltransferases 3A and 3B. Proc Natl Acad Sci U S A 104: 15805-15810.
31. Feng J, Zhou Y, Campbell SL, Le T, Li E, et al. (2010) Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons. Nat Neurosci 13: 423-430.
32. Chestnut BA, Chang Q, Price A, Lesuisse C, Wong M, et al. (2011) Epigenetic regulation of motor neuron cell death through DNA methylation. J Neurosci 31: 16619-16636.
33. Hebert SS, Papadopoulou AS, Smith P, Galas MC, Planel E, et al. (2010) Genetic ablation of Dicer in adult forebrain neurons results in abnormal tau hyperphosphorylation and neurodegeneration. Hum Mol Genet 19: 3959-3969.
34. Babiarz JE, Hsu R, Melton C, Thomas M, Ullian EM, et al. (2011) A role for noncanonical microRNAs in the mammalian brain revealed by phenotypic differences in Dgcr8 versus Dicer1 knockouts and small RNA sequencing. RNA 17: 1489-1501.
35. Liang Y, Ridzon D, Wong L, Chen C, (2007) Characterization of microRNA expression profiles in normal human tissues. BMC Genomics 8: 166.
36. Brodersen P, Voinnet O, (2009) Revisiting the principles of microRNA target recognition and mode of action. Nat Rev Mol Cell Biol 10: 141-148.
37. Hebert SS, Nelson PT, (2011) Studying microRNAs in the brain: Technical lessons learned from the first ten years. Exp Neurol 235: 397-401.
38. Shirdel EA, Xie W, Mak TW, Jurisica I, (2011) NAViGaTing the micronome - using multiple microRNA prediction databases to identify signalling pathway-associated microRNAs. PLoS ONE 6: e17429.
39. Keene JD, Komisarow JM, Friedersdorf MB, (2006) RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. Nat Protoc 1: 302-307.
40. Wang WX, Wilfred BR, Hu Y, Stromberg AJ, Nelson PT, (2010) Anti-Argonaute RIP-Chip shows that miRNA transfections alter global patterns of mRNA recruitment to microribonucleoprotein complexes. RNA 16: 394-404.
41. Edbauer D, Neilson JR, Foster KA, Wang CF, Seeburg DP, et al. (2010) Regulation of synaptic structure and function by FMRP-associated microRNAs miR-125b and miR-132. Neuron 65: 373-384.
42. 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.
43. Nudelman AS, DiRocco DP, Lambert TJ, Garelick MG, Le J, et al. (2010) Neuronal activity rapidly induces transcription of the CREB-regulated microRNA-132, in vivo. Hippocampus 20: 492-498.
44. Kole AJ, Swahari V, Hammond SM, Deshmukh M, (2011) miR-29b is activated during neuronal maturation and targets BH3-only genes to restrict apoptosis. Genes Dev 25: 125-130.
45. Manakov SA, Grant SG, Enright AJ, (2009) Reciprocal regulation of microRNA and mRNA profiles in neuronal development and synapse formation. BMC Genomics 10: 419.
46. Qureshi IA, Mehler MF, (2009) Regulation of non-coding RNA networks in the nervous system - what's the REST of the story? Neurosci Lett 466: 73-80.
47. Hebert SS, Serneels L, Tolia A, Craessaerts K, Derks C, et al. (2006) Regulated intramembrane proteolysis of amyloid precursor protein and regulation of expression of putative target genes. EMBO Rep 7: 739-745.
48. Smith P, Al Hashimi A, Girard J, Delay C, Hebert SS (2011) In vivo regulation of Amyloid precursor protein neuronal splicing by microRNAs. J Neurochem.
49. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264.
50. Smyth GK, (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3: Article3.
51. Benjamini Y, Drai D, Elmer G, Kafkafi N, Golani I, (2001) Controlling the false discovery rate in behavior genetics research. Behav Brain Res 125: 279-284.