Oligonucleotide-based tools for studying zebrafish development.
Synthetic and nonnatural oligonucleotides have been used extensively to interrogate gene function in zebrafish. In this review, we survey the capabilities and limitations of various oligonucleotide-based technologies for perturbing RNA function and tracking RNA expression. We also examine recent strategies for achieving spatiotemporal control of oligonucleotide function, particularly light-gated technologies that exploit the optical transparency of zebrafish embryos.
Shestopalov
Ilya A
IA
Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA.
Chen
James K
JK
D000818:Animals; D018507:Gene Expression Regulation, Developmental; D005821:Genetic Techniques; D009841:Oligonucleotides / Q000235:genetics*; D012313:RNA / Q000235:genetics; D015027:Zebrafish / Q000235:genetics* / Q000254:growth & development*
D009841:Oligonucleotides; D012313:RNA
Nat Chem Biol. 2008 Jan;4(1):33-41
18026094
Chembiochem. 2008 Dec 15;9(18):2937-40
19021142
Nucleic Acids Res. 2008 Jul;36(12):4158-71
18558618
Methods. 2008 Jan;44(1):55-60
18158133
Development. 1999 Nov;126(21):4817-26
10518498
Chem Soc Rev. 2007 Aug;36(8):1249-62
17619685
Development. 2006 Jun;133(11):2137-47
16672347
Development. 2006 Aug;133(16):3265-76
16873584
Angew Chem Int Ed Engl. 2005 Feb 18;44(9):1328-32
15643658
Science. 2005 Jul 8;309(5732):310-1
15919954
Nature. 1993 Oct 7;365(6446):566-8
7692304
Cell. 2009 Feb 20;136(4):642-55
19239886
Mol Pharm. 2009 May-Jun;6(3):686-95
19397332
Cytokine Growth Factor Rev. 2007 Oct-Dec;18(5-6):363-71
17698400
Development. 2008 May;135(10):1735-43
18403413
PLoS Genet. 2007 May 25;3(5):e78
17530925
Mol Biosyst. 2008 May;4(5):431-40
18414741
Nature. 2005 Dec 1;438(7068):685-9
16258535
Nat Methods. 2006 Jan;3(1):27-9
16369549
Biochim Biophys Acta. 1999 Dec 10;1489(1):117-30
10807002
Nucleic Acids Res. 2004 Dec 07;32(21):6284-91
15585662
Genesis. 2008 Jan;46(1):1-7
18196596
Mar Biotechnol (NY). 2008 May-Jun;10(3):262-9
18214611
Biochim Biophys Acta. 1999 Dec 10;1489(1):141-58
10807004
RNA Biol. 2005 Jul-Sep;2(3):101-5
17114924
Antisense Nucleic Acid Drug Dev. 1997 Jun;7(3):187-95
9212909
PLoS One. 2009 Jul 03;4(7):e6125
19582161
Mar Biotechnol (NY). 2008 Sep-Oct;10(5):511-7
18322750
Biochem Biophys Res Commun. 2007 Jun 29;358(2):521-7
17493584
Biochem Biophys Res Commun. 1999 Sep 16;263(1):156-61
10486270
Nat Protoc. 2008;3(1):59-69
18193022
Nat Chem Biol. 2007 Oct;3(10):650-1
17717538
Nat Genet. 2001 Aug;28(4):317-25
11479592
Molecules. 2009 Mar 25;14(3):1304-23
19325525
Angew Chem Int Ed Engl. 2007;46(37):6966-84
17722137
J Biomed Sci. 2007 Nov;14(6):767-76
17624603
Dev Biol. 2000 Jan 15;217(2):394-405
10625563
Dev Dyn. 2003 Nov;228(3):405-13
14579379
PLoS Biol. 2007 Aug;5(8):e203
17676975
Org Lett. 2008 Jan 17;10(2):249-51
18076183
Dev Biol. 2000 Aug 1;224(1):20-8
10898958
Org Lett. 2007 May 10;9(10):1903-6
17447773
Methods. 2001 Apr;23(4):345-58
11316436
Nat Genet. 2000 Oct;26(2):216-20
11017081
J Am Chem Soc. 2009 Sep 23;131(37):13255-69
19708646
Blood Cells Mol Dis. 2010 Mar 15;44(3):169-74
20045356
J Am Chem Soc. 2007 Sep 12;129(36):11000-1
17711280
Nat Genet. 2003 Nov;35(3):217-8
14528306
Drugs Today (Barc). 2001 Apr;37(4):245-255
12768225
Zebrafish. 2009 Mar;6(1):69-77
19374550
Chem Soc Rev. 2008 Jul;37(7):1294-307
18568156
Br J Pharmacol. 2002 Nov;137(6):782-92
12411408
Dev Biol. 2001 Jan 1;229(1):215-23
11133165
Genesis. 2009 Nov;47(11):736-43
19644983
Genetika. 2009 Sep;45(9):1187-93
19824538