MiRNA profiling of bilateral rat hippocampal CA3 by deep sequencing

Biochemical and Biophysical Research Communications

Volumn 409, Issue 2, 2011, Pages 293-298

  Shinohara, Yoshiaki ^a   Yahagi, Kazuko ^a   Kawano, Mitsuoki ^b   Nishiyori, Hiromi ^b   Kawazu, Chika ^b   Suzuki, Naoko ^b   Manabe, Ri ichiroh ^b   Hirase, Hajime ^a,c  

^a RIKEN BRAIN SCIENCE INSTITUTE   (Japan)

^b RIKEN   (Japan)

^c SAITAMA UNIVERSITY   (Japan)

Author keywords

Deep sequencing; Hippocampus; Left right asymmetry; Let 7

Indexed keywords

MICRORNA; MICRORNA 101A; MICRORNA 101B; MICRORNA 103; MICRORNA 126; MICRORNA 127; MICRORNA 132; MICRORNA 138; MICRORNA 143; MICRORNA 181B; MICRORNA 21; MICRORNA 24; MICRORNA 26A; MICRORNA 27B; MICRORNA 29B; MICRORNA 30A; MICRORNA 30D; MICRORNA 30E; MICRORNA 379; MICRORNA 9; UNCLASSIFIED DRUG;

ANIMAL TISSUE; ARTICLE; GENE EXPRESSION; GENE MAPPING; HIGH THROUGHPUT SEQUENCING; HIPPOCAMPAL CA3 REGION; MALE; NONHUMAN; NUCLEIC ACID DATABASE; PRIORITY JOURNAL; PROTEIN EXPRESSION; RAT; RNA SEQUENCE; STRUCTURAL BIOINFORMATICS;

ANIMALS; CA3 REGION, HIPPOCAMPAL; GENE EXPRESSION PROFILING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MALE; MICRORNAS; RATS; RATS, LONG-EVANS; SEQUENCE ANALYSIS, RNA;

RATTUS;

EID: 79957913002     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2011.05.004     Document Type: Article

References (32)

1. Winter J., Jung S., Keller S., Gregory R.I., Diederichs S. Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat Cell Biol 2009, 11:228-234.
2. Lee R.C., Feinbaum R.L., Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993, 75:843-854.
3. Krichevsky A.M., Sonntag K.C., Isacson O., Kosik K.S. Specific microRNAs modulate embryonic stem cell-derived neurogenesis. Stem Cells 2006, 24:857-864.
4. Smirnova L., Grafe A., Seiler A., Schumacher S., Nitsch R., Wulczyn F.G. Regulation of miRNA expression during neural cell specification. Eur J Neurosci 2005, 21:1469-1477.
5. Chang S., Johnston R.J., Frokjaer-Jensen C., Lockery S., Hobert O. MicroRNAs act sequentially and asymmetrically to control chemosensory laterality in the nematode. Nature 2004, 430:785-789.
6. Kawakami R., Shinohara Y., Kato Y., Sugiyama H., Shigemoto R., Ito I. Asymmetrical allocation of NMDA receptor epsilon2 subunits in hippocampal circuitry. Science 2003, 300:990-994.
7. Shinohara Y., Hirase H., Watanabe M., Itakura M., Takahashi M., Shigemoto R. Left-right asymmetry of the hippocampal synapses with differential subunit allocation of glutamate receptors. Proc Natl Acad Sci USA 2008, 105:19498-19503.
8. Kawakami R., Dobi A., Shigemoto R., Ito I. Right isomerism of the brain in inversus viscerum mutant mice. PLoS ONE 2008, 3:e1945.
9. Tang A.C., Zou B., Reeb B.C., Connor J.A. An epigenetic induction of a right-shift in hippocampal asymmetry: selectivity for short- and long-term potentiation but not post-tetanic potentiation. Hippocampus 2008, 18:5-10.
10. Klur S., Muller C., Pereira de Vasconcelos A., Ballard T., Lopez J., Galani R., Certa U., Cassel J.C. Hippocampal-dependent spatial memory functions might be lateralized in rats: an approach combining gene expression profiling and reversible inactivation. Hippocampus 2009, 19:800-816.
11. Moskal J.R., Kroes R.A., Otto N.J., Rahimi O., Claiborne B.J. Distinct patterns of gene expression in the left and right hippocampal formation of developing rats. Hippocampus 2006, 16:629-634.
12. Landgraf P., Rusu M., Sheridan R., Sewer A., Iovino N., Aravin A., Pfeffer S., Rice A., Kamphorst A.O., Landthaler M., Lin C., Socci N.D., Hermida L., Fulci V., Chiaretti S., Foa R., Schliwka J., Fuchs U., Novosel A., Muller R.U., Schermer B., Bissels U., Inman J., Phan Q., Chien M., Weir D.B., Choksi R., De Vita G., Frezzetti D., Trompeter H.I., Hornung V., Teng G., Hartmann G., Palkovits M., Di Lauro R., Wernet P., Macino G., Rogler C.E., Nagle J.W., Ju J., Papavasiliou F.N., Benzing T., Lichter P., Tam W., Brownstein M.J., Bosio A., Borkhardt A., Russo J.J., Sander C., Zavolan M., Tuschl T. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 2007, 129:1401-1414.
13. Taft R.J., Glazov E.A., Cloonan N., Simons C., Stephen S., Faulkner G.J., Lassmann T., Forrest A.R., Grimmond S.M., Schroder K., Irvine K., Arakawa T., Nakamura M., Kubosaki A., Hayashida K., Kawazu C., Murata M., Nishiyori H., Fukuda S., Kawai J., Daub C.O., Hume D.A., Suzuki H., Orlando V., Carninci P., Hayashizaki Y., Mattick J.S. Tiny RNAs associated with transcription start sites in animals. Nat Genet 2009, 41:572-578.
14. Kawano M., Kawazu C., Lizio M., Kawaji H., Carninci P., Suzuki H., Hayashizaki Y. Reduction of non-insert sequence reads by dimer eliminator LNA oligonucleotide for small RNA deep sequencing. BioTechniques 2010, 49:751-755.
15. De Hoon M.J., Taft R.J., Hashimoto T., Kanamori-Katayama M., Kawaji H., Kawano M., Kishima M., Lassmann T., Faulkner G.J., Mattick J.S., Daub C.O., Carninci P., Kawai J., Suzuki H., Hayashizaki Y. Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. Genome Res 2010, 20:257-264.
16. Friedlander M.R., Chen W., Adamidi C., Maaskola J., Einspanier R., Knespel S., Rajewsky N. Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol 2008, 26:407-415.
17. Pena J.T., Sohn-Lee C., Rouhanifard S.H., Ludwig J., Hafner M., Mihailovic A., Lim C., Holoch D., Berninger P., Zavolan M., Tuschl T. MiRNA in situ hybridization in formaldehyde and EDC-fixed tissues. Nat Methods 2009, 6:139-141.
18. Griffiths-Jones S., Saini H.K., van Dongen S., Enright A.J. MiRBase: tools for microRNA genomics. Nucleic Acids Res 2008, 36:D154-158.
19. Chiang H.R., Schoenfeld L.W., Ruby J.G., Auyeung V.C., Spies N., Baek D., Johnston W.K., Russ C., Luo S., Babiarz J.E., Blelloch R., Schroth G.P., Nusbaum C., Bartel D.P. Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes Dev 2010, 24:992-1009.
20. Grimson A., Srivastava M., Fahey B., Woodcroft B.J., Chiang H.R., King N., Degnan B.M., Rokhsar D.S., Bartel D.P. Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature 2008, 455:1193-1197.
21. Abrahams S., Pickering A., Polkey C.E., Morris R.G. Spatial memory deficits in patients with unilateral damage to the right hippocampal formation. Neuropsychologia 1997, 35:11-24.
22. J. Juhila, T. Sipilä, D. Nicorici, P. Ellonen, D. Greco, I. Hovatta, in: FENS Forum 2010, Amsterdam, 2010, 059.4.
23. Reinhart B.J., Slack F.J., Basson M., Pasquinelli A.E., Bettinger J.C., Rougvie A.E., Horvitz H.R., Ruvkun G. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 2000, 403:901-906.
24. Rybak A., Fuchs H., Hadian K., Smirnova L., Wulczyn E.A., Michel G., Nitsch R., Krappmann D., Wulczyn F.G. The let-7 target gene mouse lin-41 is a stem cell specific E3 ubiquitin ligase for the miRNA pathway protein Ago2. Nat Cell Biol 2009, 11:1411-1420.
25. Rybak A., Fuchs H., Smirnova L., Brandt C., Pohl E.E., Nitsch R., Wulczyn F.G. A feedback loop comprising lin-28 and let-7 controls pre-let-7 maturation during neural stem-cell commitment. Nat Cell Biol 2008, 10:987-993.
26. Wulczyn F.G., Smirnova L., Rybak A., Brandt C., Kwidzinski E., Ninnemann O., Strehle M., Seiler A., Schumacher S., Nitsch R. Post-transcriptional regulation of the let-7 microRNA during neural cell specification. Faseb J 2007, 21:415-426.
27. He Y., Yang C., Kirkmire C.M., Wang Z.J. Regulation of opioid tolerance by let-7 family microRNA targeting the mu opioid receptor. J Neurosci 2010, 30:10251-10258.
28. Schratt G.M., Tuebing F., Nigh E.A., Kane C.G., Sabatini M.E., Kiebler M., Greenberg M.E. MicroRNA regulates dendritic spine development, Nature 2006, 439:283-289.
29. Christensen M., Larsen L.A., Kauppinen S., Schratt G. Recombinant adeno-associated virus-mediated microRNA delivery into the postnatal mouse brain reveals a role for miR-134 in dendritogenesis in vivo. Front Neural Circuits 2009, 3:16.
30. Gao J., Wang W.Y., Mao Y.W., Graff J., Guan J.S., Pan L., Mak G., Kim D., Su S.C., Tsai L.H. A novel pathway regulates memory and plasticity via SIRT1 and miR-134. Nature 2010, 466:1105-1109.
31. Bissels U., Wild S., Tomiuk S., Holste A., Hafner M., Tuschl T., Bosio A. Absolute quantification of microRNAs by using a universal reference. RNA 2009, 15:2375-2384.
32. Olsen L., Klausen M., Helboe L., Nielsen F.C., Werge T. MicroRNAs show mutually exclusive expression patterns in the brain of adult male rats. PLoS ONE 2009, 4:e7225.