speciﬁcally expressed in the rat epididymis. Biol. Reprod., 76, 63–73. 24. Hu,H.Y., Yan,Z., Xu,Y., Hu,H., Menzel,C., Zhou,Y.H., Chen,W. and Khaitovich,P. (2009) Sequence features associated with microRNA strand selection in humans and ﬂies. BMC Genomics, 10, 413. 25. Langmead,B., Trapnell,C., Pop,M. and Salzberg,S.L. (2009) Ultrafast and memory-efﬁcient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25. 26. Vagin,V.V., Wohlschlegel,J., Qu,J., Jonsson,Z., Huang,X., Chuma,S., Girard,A., Sachidanandam,R., Hannon,G.J. and Aravin,A.A. (2009) Proteomic analysis of murine Piwi proteins reveals a role for arginine methylation in specifying interaction with Tudor family members. Genes Dev., 23, 1749–1762. 27. Reuter,M., Chuma,S., Tanaka,T., Franz,T., Stark,A. and Pillai,R.S. (2009) Loss of the Mili-interacting Tudor domain-containing protein-1 activates transposons and alters the Mili-associated small RNA proﬁle. Nat. Struct. Mol. Biol., 16, 639–646. 28. Kuchen,S., Resch,W., Yamane,A., Kuo,N., Li,Z., Chakraborty,T., Wei,L., Laurence,A., Yasuda,T., Peng,S. et al. Regulation of microRNA expression and abundance during lymphopoiesis. Immunity, 32, 828–839. 29. Chung,W.J., Okamura,K., Martin,R. and Lai,E.C. (2008) Endogenous RNA interference provides a somatic defense against Drosophila transposons. Curr. Biol., 18, 795–802. 30. Ghildiyal,M., Xu,J., Seitz,H., Weng,Z. and Zamore,P.D. Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway. RNA, 16, 43–56. 31. Okamura,K., Chung,W.J., Ruby,J.G., Guo,H., Bartel,D.P. and Lai,E.C. (2008) The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs. Nature, 453, 803–806. 32. Czech,B., Malone,C.D., Zhou,R., Stark,A., Schlingeheyde,C., Dus,M., Perrimon,N., Kellis,M., Wohlschlegel,J.A., Sachidanandam,R. et al. (2008) An endogenous small interfering RNA pathway in Drosophila. Nature, 453, 798–802. 33. Ruby,J.G., Stark,A., Johnston,W.K., Kellis,M., Bartel,D.P. and Lai,E.C. (2007) Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res., 17, 1850–1864. 34. Rhead,B., Karolchik,D., Kuhn,R.M., Hinrichs,A.S., Zweig,A.S., Fujita,P.A., Diekhans,M., Smith,K.E., Rosenbloom,K.R., Raney,B.J. et al. The UCSC Genome Browser database: update 2010. Nucleic Acids Res., 38, D613–D619. 35. Hubbard,T.J., Aken,B.L., Ayling,S., Ballester,B., Beal,K., Bragin,E., Brent,S., Chen,Y., Clapham,P., Clarke,L. et al. (2009) Ensembl 2009. Nucleic. Acids Res., 37, D690–D697. 36. Grifﬁths-Jones,S., Saini,H.K., van Dongen,S. and Enright,A.J. (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res., 36, D154–D158. Nucleic Acids Research, 2011, Vol. 39, No. 15 6607 37. Grifﬁths-Jones,S., Grocock,R.J., van Dongen,S., Bateman,A. and Enright,A.J. (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucl. Acids Res., 34, D140–D144. 38. Grifﬁths-Jones,S. (2004) The microRNA Registry. Nucleic Acids Res., 32, D109–111. 39. Pruitt,K.D., Tatusova,T. and Maglott,D.R. (2007) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 35, D61–D65. 40. Silahtaroglu,A.N., Nolting,D., Dyrskjot,L., Berezikov,E., Moller,M., Tommerup,N. and Kauppinen,S. (2007) Detection of microRNAs in frozen tissue sections by ﬂuorescence in situ hybridization using locked nucleic acid probes and tyramide signal ampliﬁcation. Nat. Protoc., 2, 2520–2528. 41. Jankowsky,J.L., Derrick,B.E. and Patterson,P.H. (2000) Cytokine responses to LTP induction in the rat hippocampus: a comparison of in vitro and in vivo techniques. Learn. Mem., 7, 400–412. 42. Xu,M., Medvedev,S., Yang,J. and Hecht,N.B. (2009) MIWI-independent small RNAs (MSY-RNAs) bind to the RNA-binding protein, MSY2, in male germ cells. Proc. Natl Acad. Sci. USA, 106, 12371–12376. 43. Ohara,T., Sakaguchi,Y., Suzuki,T., Ueda,H. and Miyauchi,K. (2007) The 30 termini of mouse Piwi-interacting RNAs are 2’-O-methylated. Nat. Struct. Mol. Biol., 14, 349–350. 44. Kirino,Y. and Mourelatos,Z. (2007) 20-O-methyl modiﬁcation in mouse piRNAs and its methylase. Nucleic Acids Symp. Ser., 417–418. 45. Kirino,Y. and Mourelatos,Z. (2007) Mouse Piwi-interacting RNAs are 2’-O-methylated at their 3’ termini. Nat. Struct. Mol. Biol., 14, 347–348. 46. Kirino,Y. and Mourelatos,Z. (2007) The mouse homolog of HEN1 is a potential methylase for Piwi-interacting RNAs. RNA, 13, 1397–1401. 47. Sugimoto,K., Kage,H., Aki,N., Sano,A., Kitagawa,H., Nagase,T., Yatomi,Y., Ohishi,N. and Takai,D. (2007) The induction of H3K9 methylation by PIWIL4 at the p16Ink4a locus. Biochem. Biophys. Res. Commun., 359, 497–502. 48. Ahn,H.W., Morin,R.D., Zhao,H., Harris,R.A., Coarfa,C., Chen,Z.J., Milosavljevic,A., Marra,M.A. and Rajkovic,A. MicroRNA transcriptome in the newborn mouse ovaries determined by massive parallel sequencing. Mol. Hum. Reprod., 16, 463–471. 49. Ro,S., Song,R., Park,C., Zheng,H., Sanders,K.M. and Yan,W. (2007) Cloning and expression proﬁling of small RNAs expressed in the mouse ovary. RNA, 13, 2366–2380.