title: MicroRNAs show a wide diversity of expression profiles in the developing and mature central nervous system.
abstract: BACKGROUND
  MicroRNA (miRNA) encoding genes are abundant in vertebrate genomes but very few have been studied in any detail. Bioinformatic tools allow prediction of miRNA targets and this information coupled with knowledge of miRNA expression profiles facilitates formulation of hypotheses of miRNA function. Although the central nervous system (CNS) is a prominent site of miRNA expression, virtually nothing is known about the spatial and temporal expression profiles of miRNAs in the brain. To provide an overview of the breadth of miRNA expression in the CNS, we performed a comprehensive analysis of the neuroanatomical expression profiles of 38 abundant conserved miRNAs in developing and adult zebrafish brain.
  
  
  RESULTS
  Our results show miRNAs have a wide variety of different expression profiles in neural cells, including: expression in neuronal precursors and stem cells (for example, miR-92b); expression associated with transition from proliferation to differentiation (for example, miR-124); constitutive expression in mature neurons (miR-124 again); expression in both proliferative cells and their differentiated progeny (for example, miR-9); regionally restricted expression (for example, miR-222 in telencephalon); and cell-type specific expression (for example, miR-218a in motor neurons).
  
  
  CONCLUSIONS
  The data we present facilitate prediction of likely modes of miRNA function in the CNS and many miRNA expression profiles are consistent with the mutual exclusion mode of function in which there is spatial or temporal exclusion of miRNAs and their targets. However, some miRNAs, such as those with cell-type specific expression, are more likely to be co-expressed with their targets. Our data provide an important resource for future functional studies of miRNAs in the CNS.
authors: Department of Anatomy and Developmental Biology, UCL, Gower Street, London WC1E 6BT, UK. kapsimal@biologie.ens.fr
authors: Marika
authors: M
authors: Kapsimali
authors: Wigard P
authors: WP
authors: Kloosterman
authors: Ewart
authors: E
authors: de Bruijn
authors: Frederic
authors: F
authors: Rosa
authors: Ronald H A
authors: RH
authors: Plasterk
authors: Stephen W
authors: SW
authors: Wilson
mesh_terms: D000818:Animals; D001921:Brain / Q000166:cytology / Q000254:growth & development*; D002454:Cell Differentiation / Q000235:genetics; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D007814:Larva / Q000737:chemistry / Q000166:cytology / Q000235:genetics / Q000254:growth & development; D035683:MicroRNAs / Q000032:analysis / Q000235:genetics* / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D038081:Organogenesis / Q000235:genetics*; D015027:Zebrafish / Q000235:genetics / Q000254:growth & development*
chemical_list: D035683:MicroRNAs
references: Proc Natl Acad Sci U S A. 2006 Mar 14;103(11):4034-9
references: 16495412
references: Cancer Res. 2005 Jul 15;65(14):6029-33
references: 16024602
references: Science. 2006 Apr 7;312(5770):75-9
references: 16484454
references: Nucleic Acids Res. 2006;34(9):2558-69
references: 16698962
references: Nat Genet. 2006 Jun;38 Suppl:S20-4
references: 16736020
references: RNA. 2006 Jul;12(7):1161-7
references: 16738409
references: Dev Biol. 2006 Jul 1;295(1):263-77
references: 16682018
references: Dev Biol. 2006 Jul 1;295(1):278-93
references: 16828638
references: Genes Dev. 2006 Aug 15;20(16):2202-7
references: 16882971
references: Methods Mol Biol. 2006;342:129-38
references: 16957372
references: Nat Rev Genet. 2006 Oct;7(10):793-803
references: 16983375
references: Cell. 2006 Sep 22;126(6):1203-17
references: 16990141
references: J Neurosci. 2000 Jan 1;20(1):206-18
references: 10627598
references: Dev Biol. 2000 Nov 15;227(2):279-93
references: 11071755
references: Anat Embryol (Berl). 2000 Nov;202(5):385-400
references: 11089930
references: Nature. 2001 Jan 18;409(6818):363-6
references: 11201747
references: J Anat. 2001 Jul-Aug;199(Pt 1-2):63-84
references: 11523830
references: Biochem Biophys Res Commun. 2005 Sep 9;334(4):1351-8
references: 16039986
references: Science. 2005 Sep 2;309(5740):1573-6
references: 16081698
references: Science. 2005 Oct 14;310(5746):317-20
references: 16224024
references: Proc Natl Acad Sci U S A. 2005 Nov 8;102(45):16426-31
references: 16260724
references: Development. 2005 Dec;132(23):5329-39
references: 16284123
references: Science. 2005 Dec 16;310(5755):1817-21
references: 16308420
references: Cell. 2005 Dec 16;123(6):1133-46
references: 16337999
references: Nat Methods. 2006 Jan;3(1):27-9
references: 16369549
references: Nature. 2006 Jan 19;439(7074):283-9
references: 16421561
references: Proc Natl Acad Sci U S A. 2006 Feb 14;103(7):2422-7
references: 16461918
references: Mol Cell. 2006 Feb 17;21(4):533-42
references: 16483934
references: Proc Natl Acad Sci U S A. 2006 Mar 7;103(10):3687-92
references: 16505370
references: Nat Neurosci. 2006 Oct;9(10):1247-56
references: 16980963
references: Proc Natl Acad Sci U S A. 2006 Sep 26;103(39):14385-9
references: 16983084
references: Dev Cell. 2006 Oct;11(4):441-50
references: 17011485
references: Science. 2006 Oct 6;314(5796):144-8
references: 17023663
references: Genes Dev. 2006 Oct 15;20(20):2793-805
references: 17015424
references: Curr Biol. 2006 Nov 7;16(21):2135-42
references: 17084698
references: Nat Genet. 2006 Dec;38(12):1452-6
references: 17072316
references: PLoS Biol. 2006 Oct;4(10):e309
references: 17048983
references: Gene. 2007 Apr 15;391(1-2):39-44
references: 17229533
references: Genes Dev. 2007 Apr 1;21(7):744-9
references: 17403776
references: Neuron. 2007 Jun 7;54(5):813-29
references: 17553428
references: Curr Biol. 2002 Apr 30;12(9):735-9
references: 12007417
references: RNA. 2003 Feb;9(2):180-6
references: 12554860
references: Trends Neurosci. 2003 Sep;26(9):469-76
references: 12948657
references: Nature. 2003 Sep 25;425(6956):415-9
references: 14508493
references: Genome Biol. 2004;5(3):R13
references: 15003116
references: Neuron. 2004 Jun 10;42(5):703-16
references: 15182712
references: Nature. 2004 Aug 12;430(7001):785-9
references: 15306811
references: Annu Rev Cell Dev Biol. 2004;20:505-23
references: 15473850
references: Nature. 2004 Nov 11;432(7014):226-30
references: 15538371
references: Cell. 2005 Jan 14;120(1):15-20
references: 15652477
references: Cell. 2005 Jan 14;120(1):21-4
references: 15652478
references: Curr Biol. 2005 Feb 8;15(3):238-43
references: 15694307
references: Nature. 2005 Feb 17;433(7027):769-73
references: 15685193
references: Eur J Neurosci. 2005 Mar;21(6):1469-77
references: 15845075
references: Science. 2005 May 6;308(5723):833-8
references: 15774722
references: Genes Dev. 2005 Jun 1;19(11):1288-93
references: 15937218
references: Nat Cell Biol. 2005 Jul;7(7):719-23
references: 15937477
references: Nat Genet. 2005 Jul;37(7):766-70
references: 15965474
references: Science. 2005 Jul 8;309(5732):310-1
references: 15919954
references: Nat Neurosci. 2006 Apr;9(4):511-8
references: 16520734