title: RNA sequencing reveals small RNAs differentially expressed between incipient Japanese threespine sticklebacks.
abstract: BACKGROUND
  Non-coding small RNAs, ranging from 20 to 30 nucleotides in length, mediate the regulation of gene expression and play important roles in many biological processes. One class of small RNAs, microRNAs (miRNAs), are highly conserved across taxa and mediate the regulation of the chromatin state and the post-transcriptional regulation of messenger RNA (mRNA). Another class of small RNAs is the Piwi-interacting RNAs, which play important roles in the silencing of transposons and other functional genes. Although the biological functions of the different small RNAs have been elucidated in several laboratory animals, little is known regarding naturally occurring variation in small RNA transcriptomes among closely related species.
  
  
  RESULTS
  We employed next-generation sequencing technology to compare the expression profiles of brain small RNAs between sympatric species of the Japanese threespine stickleback (Gasterosteus aculeatus). We identified several small RNAs that were differentially expressed between sympatric Pacific Ocean and Japan Sea sticklebacks. Potential targets of several small RNAs were identified as repetitive sequences. Female-biased miRNA expression from the old X chromosome was also observed, and it was attributed to the degeneration of the Y chromosome.
  
  
  CONCLUSIONS
  Our results suggest that expression patterns of small RNA can differ between incipient species and may be a potential mechanism underlying differential mRNA expression and transposon activity.
authors.affiliation: Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka, Japan. jkitano@lab.nig.ac.jp
authors.forename: Jun
authors.initials: J
authors.lastname: Kitano
authors.forename: Kohta
authors.initials: K
authors.lastname: Yoshida
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Suzuki
mesh_terms: D000818:Animals; D001921:Brain / Q000378:metabolism; D005260:Female; D008297:Male; D035683:MicroRNAs / Q000235:genetics; D058727:RNA, Small Untranslated / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid; D017423:Sequence Analysis, RNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D023701:Smegmamorpha / Q000235:genetics*; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D058727:RNA, Small Untranslated
references.citation: PLoS Genet. 2008 Apr 25;4(4):e1000056
references.pmid: 18437202
references.citation: Evolution. 2010 Apr 1;64(4):1029-47
references.pmid: 19895556
references.citation: Curr Biol. 2012 Jan 24;22(2):166-70
references.pmid: 22206705
references.citation: Nature. 2011 Oct 30;479(7374):534-7
references.pmid: 22037309
references.citation: Nat Rev Neurosci. 2006 Dec;7(12):911-20
references.pmid: 17115073
references.citation: Evolution. 2008 Sep;62(9):2155-77
references.pmid: 18616572
references.citation: FASEB J. 2007 Feb;21(2):415-26
references.pmid: 17167072
references.citation: Science. 2008 Nov 28;322(5906):1387-92
references.pmid: 19039138
references.citation: Evolution. 1986 Jan;40(1):129-141
references.pmid: 28564117
references.citation: Genome Med. 2012 Aug 24;4(8):62
references.pmid: 22906193
references.citation: Trends Cell Biol. 2008 Oct;18(10):505-16
references.pmid: 18774294
references.citation: Genome Res. 2010 Jun;20(6):816-25
references.pmid: 20354124
references.citation: Proc Natl Acad Sci U S A. 2007 Feb 27;104(9):3300-5
references.pmid: 17360642
references.citation: Genome Biol Evol. 2012;4(5):687-702
references.pmid: 22534163
references.citation: Genetica. 2007 Jan;129(1):105-26
references.pmid: 16897450
references.citation: Cell. 2009 Jan 9;136(1):26-36
references.pmid: 19135886
references.citation: Annu Rev Biomed Eng. 2010 Aug 15;12:1-27
references.pmid: 20415587
references.citation: Evolution. 2007 May;61(5):995-1016
references.pmid: 17492956
references.citation: Nat Rev Genet. 2004 May;5(5):396-400
references.pmid: 15143321
references.citation: Philos Trans R Soc Lond B Biol Sci. 2000 Nov 29;355(1403):1563-72
references.pmid: 11127901
references.citation: Nat Rev Mol Cell Biol. 2009 Feb;10(2):126-39
references.pmid: 19165215
references.citation: Genome Res. 2012 Jul;22(7):1243-54
references.pmid: 22456605
references.citation: Evolution. 2001 Mar;55(3):512-21
references.pmid: 11327159
references.citation: Nature. 2004 Apr 15;428(6984):717-23
references.pmid: 15085123
references.citation: Nucleic Acids Res. 2008 Nov;36(19):6048-55
references.pmid: 18820301
references.citation: Mol Ecol Resour. 2011 Jul;11(4):650-61
references.pmid: 21481219
references.citation: RNA. 2012 May;18(5):915-29
references.pmid: 22408181
references.citation: Trends Neurosci. 2012 May;35(5):325-34
references.pmid: 22436491
references.citation: Curr Opin Genet Dev. 2007 Jun;17(3):166-76
references.pmid: 17467975
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D173-7
references.pmid: 17881367
references.citation: Dev Dyn. 2005 Dec;234(4):815-23
references.pmid: 16252286
references.citation: Nature. 2000 Nov 2;408(6808):86-9
references.pmid: 11081512
references.citation: Curr Biol. 2010 Dec 7;20(23):2124-30
references.pmid: 21093265
references.citation: PLoS Genet. 2012;8(8):e1002861
references.pmid: 22916025
references.citation: Proc Natl Acad Sci U S A. 1991 Mar 15;88(6):2326-30
references.pmid: 1848699
references.citation: Nat Rev Genet. 2009 Feb;10(2):94-108
references.pmid: 19148191
references.citation: Nat Biotechnol. 2009 May;27(5):472-7
references.pmid: 19396161
references.citation: Genome Biol. 2006;7(12):R116
references.pmid: 17156454
references.citation: Methods Mol Biol. 2010;629:239-55
references.pmid: 20387153
references.citation: Cell. 2006 Mar 10;124(5):901-14
references.pmid: 16530039
references.citation: Nature. 2008 May 22;453(7194):534-8
references.pmid: 18404147
references.citation: Cell. 2012 Apr 27;149(3):693-707
references.pmid: 22541438
references.citation: J Fish Biol. 2009 Nov;75(8):2000-36
references.pmid: 20738669
references.citation: Nature. 2004 Jul 1;430(6995):85-8
references.pmid: 15229602
references.citation: Annu Rev Cell Dev Biol. 2009;25:355-76
references.pmid: 19575643
references.citation: PLoS One. 2012;7(5):e37877
references.pmid: 22655075
references.citation: Science. 2008 May 23;320(5879):1077-81
references.pmid: 18403677
references.citation: Nat Rev Mol Cell Biol. 2011 Apr;12(4):246-58
references.pmid: 21427766
references.citation: Proc Natl Acad Sci U S A. 2006 Oct 17;103(42):15669-74
references.pmid: 17028171
references.citation: RNA. 2011 Jun;17(6):1090-9
references.pmid: 21515829
references.citation: Cancer Res. 2008 May 15;68(10):3566-72
references.pmid: 18483236
references.citation: Mol Ecol. 2010 Dec;19(24):5389-403
references.pmid: 21087448
references.citation: Nat Rev Genet. 2008 Feb;9(2):102-14
references.pmid: 18197166
references.citation: Mol Ecol. 2013 Feb;22(3):774-86
references.pmid: 22971109
references.citation: Nature. 2008 Jun 5;453(7196):793-7
references.pmid: 18463636
references.citation: RNA. 2006 Apr;12(4):589-97
references.pmid: 16489184
references.citation: Mol Cell. 2010 May 14;38(3):465-75
references.pmid: 20381393
references.citation: Annu Rev Genet. 2012;46:537-60
references.pmid: 22974302
references.citation: Nat Rev Genet. 2007 Feb;8(2):93-103
references.pmid: 17230196
references.citation: Nature. 2008 Jun 5;453(7196):798-802
references.pmid: 18463631
references.citation: Nature. 2009 Oct 22;461(7267):1079-83
references.pmid: 19783981
references.citation: PLoS One. 2010 Jun 11;5(6):e11070
references.pmid: 20552018
references.citation: Genome Biol Evol. 2011;3:55-65
references.pmid: 21169229
references.citation: J Hum Genet. 2008;53(6):515
references.pmid: 18465083
references.citation: BMC Bioinformatics. 2006 Oct 25;7:474
references.pmid: 17064419
references.citation: Heredity (Edinb). 2010 Mar;104(3):289-301
references.pmid: 20087395
references.citation: Science. 2005 Oct 14;310(5746):317-20
references.pmid: 16224024
references.citation: Nucleic Acids Res. 2012 Sep;40(16):8001-10
references.pmid: 22684503
references.citation: PLoS One. 2012;7(1):e30737
references.pmid: 22303453
references.citation: Stroke. 2011 Apr;42(4):1105-9
references.pmid: 21311060
references.citation: Mol Ecol. 2011 May;20(9):1813-28
references.pmid: 21410806
references.citation: Nat Genet. 2006 Jul;38(7):813-8
references.pmid: 16751773
references.citation: RNA. 2009 Dec;15(12):2147-60
references.pmid: 19850906
references.citation: J Cell Sci. 2010 Oct 15;123(Pt 20):3515-24
references.pmid: 20841382
references.citation: Mol Biol Evol. 2010 Jul;27(7):1495-503
references.pmid: 20142438
references.citation: BMC Genomics. 2012 Sep 13;13:476
references.pmid: 22974136
references.citation: Nature. 2008 May 22;453(7194):539-43
references.pmid: 18404146
references.citation: Mol Biol Evol. 2003 Oct;20(10):1659-68
references.pmid: 12885966
references.citation: RNA. 2010 Apr;16(4):673-95
references.pmid: 20181738
references.citation: Trends Immunol. 2008 Jul;29(7):343-51
references.pmid: 18515182
references.citation: PLoS One. 2011;6(12):e29253
references.pmid: 22216225
references.citation: Mol Ecol. 2008 Apr;17(7):1636-47
references.pmid: 18266620
references.citation: Cell. 2008 Jul 11;134(1):25-36
references.pmid: 18614008
references.citation: Cell. 2007 Dec 14;131(6):1179-89
references.pmid: 18083106
references.citation: Philos Trans R Soc Lond B Biol Sci. 2010 Aug 27;365(1552):2581-90
references.pmid: 20643748