MicroRNAs (miRNAs) are important gene regulators that are abundantly expressed in both the developing and adult mammalian brain. These non-coding gene transcripts are involved in post-transcriptional regulatory processes by binding to specific target mRNAs. Approximately one third of known miRNA genes are located within intronic regions of protein coding and non-coding regions, and previous studies have suggested a role for intronic miRNAs as negative feedback regulators of their host genes. In the present study, we monitored the dynamic gene expression changes of the intronic miR-338-3p and miR-338-5p and their host gene Apoptosis-associated Tyrosine Kinase (AATK) during the maturation of rat hippocampal neurons. This revealed an uncorrelated expression pattern of mature miR-338 strands with their host gene. Sequence analysis of the 3′ untranslated region (UTR) of rat AATK mRNA revealed the presence of two putative binding sites for miR-338-3p. Thus, miR-338-3p may have the capacity to modulate AATK mRNA levels in neurons. Transfection of miR-338-3p mimics into rat B35 neuroblastoma cells resulted in a significant decrease of AATK mRNA levels, while the transfection of synthetic miR-338-5p mimics did not alter AATK levels. Our results point to a possible molecular mechanism by which miR-338-3p participates in the regulation of its host gene by modulating the levels of AATK mRNA, a kinase which plays a role during differentiation, apoptosis and possibly in neuronal degeneration.
References
[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.
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.
