A potential regulatory role for intronic microrna-338-3p for its host gene encoding apoptosis-associated Tyrosine Kinase

PLoS ONE

Volumn 7, Issue 2, 2012, Pages

  Kos, Aron ^a   Olde Loohuis, Nikkie F M ^a   Wieczorek, Martha L ^a   Glennon, Jeffrey C ^a   Martens, Gerard J M ^a   Kolk, Sharon M ^a   Aschrafi, Armaz ^a  

^a RADBOUD UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

APOPTOSIS ASSOCIATED TYROSINE KINASE; MESSENGER RNA; MICRORNA; MICRORNA 338 3P; MICRORNA 338 5P; REGULATOR PROTEIN; RNA; UNCLASSIFIED DRUG; AATK PROTEIN, RAT; APOPTOSIS REGULATORY PROTEIN; MIRN338 MICRORNA, RAT; PROTEIN TYROSINE KINASE;

3' UNTRANSLATED REGION; ANIMAL CELL; APOPTOSIS; APOPTOSIS ASSOCIATED TYROSINE KINASE GENE; ARTICLE; BINDING SITE; CELL DIFFERENTIATION; CELL MATURATION; CONTROLLED STUDY; DOWN REGULATION; GENE CONTROL; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE TARGETING; GENETIC CODE; GENETIC TRANSFECTION; HIPPOCAMPUS; IN VITRO STUDY; INTRON; NERVE CELL DEGENERATION; NEUROBLASTOMA CELL; NEUROMODULATION; NONHUMAN; RAT; REGULATOR GENE; SEQUENCE ANALYSIS; ANIMAL; BIOLOGICAL MODEL; BIOLOGY; CYTOLOGY; ENZYMOLOGY; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MOLECULAR GENETICS; NERVE CELL; NUCLEOTIDE SEQUENCE;

3' UNTRANSLATED REGIONS; ANIMALS; APOPTOSIS; APOPTOSIS REGULATORY PROTEINS; BASE SEQUENCE; CELL DIFFERENTIATION; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HIPPOCAMPUS; INTRONS; MICRORNAS; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE DATA; NEURONS; PROTEIN-TYROSINE KINASES; RATS;

EID: 84857164613     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0031022     Document Type: Article

References (37)

1. Ambros V, (2004) The functions of animal microRNAs. Nature 431: 350-355.
2. Fiore R, Siegel G, Schratt G, (2008) MicroRNA function in neuronal development, plasticity and disease. Biochim Biophys Acta 1779: 471-478.
3. Ivanovska I, Cleary MA, (2008) Combinatorial microRNAs: working together to make a difference. Cell Cycle 7: 3137-3142.
4. Willemsen MH, Valles A, Kirkels LA, Mastebroek M, Olde Loohuis N, et al. (2011) Chromosome 1p21.3 microdeletions comprising DPYD and MIR137 are associated with intellectual disability. J Med Genet 48: 810-818.
5. Mathonnet G, Fabian MR, Svitkin YV, Parsyan A, Huck L, et al. (2007) MicroRNA inhibition of translation initiation in vitro by targeting the cap-binding complex eIF4F. Science 317: 1764-1767.
6. Kim VN, (2005) MicroRNA biogenesis: coordinated cropping and dicing. Nat Rev Mol Cell Biol 6: 376-385.
7. Lutter D, Marr C, Krumsiek J, Lang EW, Theis FJ, (2010) Intronic microRNAs support their host genes by mediating synergistic and antagonistic regulatory effects. BMC Genomics 11: 224.
8. Corcoran DL, Pandit KV, Gordon B, Bhattacharjee A, Kaminski N, et al. (2009) Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data. PLoS One 4: e5279.
9. Barik S, (2008) An intronic microRNA silences genes that are functionally antagonistic to its host gene. Nucleic Acids Res 36: 5232-5241.
10. Gaozza E, Baker SJ, Vora RK, Reddy EP, (1997) AATYK: a novel tyrosine kinase induced during growth arrest and apoptosis of myeloid cells. Oncogene 15: 3127-3135.
11. Hughes JP, Ward DR, Facci L, Richardson JC, Skaper SD, (2010) Apoptosis-associated tyrosine kinase and neuronal cell death. Neurochem Res 35: 588-597.
12. Tomomura M, Fernandez-Gonzales A, Yano R, Yuzaki M, (2001) Characterization of the apoptosis-associated tyrosine kinase (AATYK) expressed in the CNS. Oncogene 20: 1022-1032.
13. Olde Loohuis NF, Kos A, Martens GJ, Van Bokhoven H, Nadif Kasri N, et al. (2011) MicroRNA networks direct neuronal development and plasticity. Cell Mol Life Sci.
14. Wu H, Ye C, Ramirez D, Manjunath N, (2009) Alternative processing of primary microRNA transcripts by Drosha generates 5′ end variation of mature microRNA. PLoS One 4: e7566.
15. Wienholds E, Kloosterman WP, Miska E, Alvarez-Saavedra E, Berezikov E, et al. (2005) MicroRNA expression in zebrafish embryonic development. Science 309: 310-311.
16. Zhao X, He X, Han X, Yu Y, Ye F, et al. (2010) MicroRNA-mediated control of oligodendrocyte differentiation. Neuron 65: 612-626.
17. Aschrafi A, Natera-Naranjo O, Gioio AE, Kaplan BB, (2010) Regulation of axonal trafficking of cytochrome c oxidase IV mRNA. Mol Cell Neurosci 43: 422-430.
18. Natera-Naranjo O, Aschrafi A, Gioio AE, Kaplan BB, (2010) Identification and quantitative analyses of microRNAs located in the distal axons of sympathetic neurons. RNA 16: 1516-1529.
19. Raghunath M, Patti R, Bannerman P, Lee CM, Baker S, et al. (2000) A novel kinase, AATYK induces and promotes neuronal differentiation in a human neuroblastoma (SH-SY5Y) cell line. Brain Res Mol Brain Res 77: 151-162.
20. Kim J, Krichevsky A, Grad Y, Hayes GD, Kosik KS, et al. (2004) Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc Natl Acad Sci U S A 101: 360-365.
21. Friedman RC, Farh KK, Burge CB, Bartel DP, (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19: 92-105.
22. Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, et al. (2005) Combinatorial microRNA target predictions. Nat Genet 37: 495-500.
23. Mukherji S, Ebert MS, Zheng GX, Tsang JS, Sharp PA, et al. (2011) MicroRNAs can generate thresholds in target gene expression. Nat Genet 43: 854-859.
24. Tomomura M, Hasegawa Y, Hashikawa T, Tomomura A, Yuzaki M, et al. (2003) Differential expression and function of apoptosis-associated tyrosine kinase (AATYK) in the developing mouse brain. Brain Res Mol Brain Res 112: 103-112.
25. Ragusa M, Majorana A, Banelli B, Barbagallo D, Statello L, et al. (2010) MIR152, MIR200B, and MIR338, human positional and functional neuroblastoma candidates, are involved in neuroblast differentiation and apoptosis. J Mol Med (Berl) 88: 1041-1053.
26. Gennarino VA, Sardiello M, Avellino R, Meola N, Maselli V, et al. (2009) MicroRNA target prediction by expression analysis of host genes. Genome Res 19: 481-490.
27. Baskerville S, Bartel DP, (2005) Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 11: 241-247.
28. Rodriguez A, Griffiths-Jones S, Ashurst JL, Bradley A, (2004) Identification of mammalian microRNA host genes and transcription units. Genome Res 14: 1902-1910.
29. Blower PE, Verducci JS, Lin S, Zhou J, Chung JH, et al. (2007) MicroRNA expression profiles for the NCI-60 cancer cell panel. Mol Cancer Ther 6: 1483-1491.
30. Wang YP, Li KB, (2009) Correlation of expression profiles between microRNAs and mRNA targets using NCI-60 data. BMC Genomics 10: 218.
31. Callis TE, Pandya K, Seok HY, Tang RH, Tatsuguchi M, et al. (2009) MicroRNA-208a is a regulator of cardiac hypertrophy and conduction in mice. J Clin Invest 119: 2772-2786.
32. Zhu Y, Kalbfleisch T, Brennan MD, Li Y, (2009) A MicroRNA gene is hosted in an intron of a schizophrenia-susceptibility gene. Schizophr Res 109: 86-89.
33. Lewis BP, Burge CB, Bartel DP, (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120: 15-20.
34. 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.
35. Schmittgen TD, Livak KJ, (2008) Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc 3: 1101-1108.
36. Aschrafi A, Schwechter AD, Mameza MG, Natera-Naranjo O, Gioio AE, et al. (2008) MicroRNA-338 regulates local cytochrome c oxidase IV mRNA levels and oxidative phosphorylation in the axons of sympathetic neurons. J Neurosci 28: 12581-12590.
37. Smart F, Aschrafi A, Atkins A, Owens GC, Pilotte J, et al. (2007) Two isoforms of the cold-inducible mRNA-binding protein RBM3 localize to dendrites and promote translation. J Neurochem 101: 1367-1379.