title: A novel RNA motif mediates the strict nuclear localization of a long noncoding RNA.
abstract: The ubiquitous presence of long noncoding RNAs (lncRNAs) in eukaryotes points to the importance of understanding how their sequences impact function. As many lncRNAs regulate nuclear events and thus must localize to nuclei, we analyzed the sequence requirements for nuclear localization in an intergenic lncRNA named BORG (BMP2-OP1-responsive gene), which is both spliced and polyadenylated but is strictly localized in nuclei. Subcellular localization of BORG was not dependent on the context or level of its expression or decay but rather depended on the sequence of the mature, spliced transcript. Mutational analyses indicated that nuclear localization of BORG was mediated through a novel RNA motif consisting of the pentamer sequence AGCCC with sequence restrictions at positions -8 (T or A) and -3 (G or C) relative to the first nucleotide of the pentamer. Mutation of the motif to a scrambled sequence resulted in complete loss of nuclear localization, while addition of even a single copy of the motif to a cytoplasmically localized RNA was sufficient to impart nuclear localization. Further, the presence of this motif in other cellular RNAs showed a direct correlation with nuclear localization, suggesting that the motif may act as a general nuclear localization signal for cellular RNAs.
authors.affiliation: Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.
authors.forename: Bing
authors.initials: B
authors.lastname: Zhang
authors.affiliation: Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.
authors.forename: Lalith
authors.initials: L
authors.lastname: Gunawardane
authors.affiliation: Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.
authors.forename: Farshad
authors.initials: F
authors.lastname: Niazi
authors.affiliation: Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.
authors.forename: Fereshteh
authors.initials: F
authors.lastname: Jahanbani
authors.affiliation: Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.
authors.forename: Xin
authors.initials: X
authors.lastname: Chen
authors.affiliation: Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA saba.valadkhan@case.edu.
authors.forename: Saba
authors.initials: S
authors.lastname: Valadkhan
mesh_terms: D000818:Animals; D001483:Base Sequence; D002467:Cell Nucleus / Q000378:metabolism*; D057809:HEK293 Cells; D006367:HeLa Cells; D006801:Humans; D051379:Mice; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics; D019913:Nuclear Localization Signals / Q000378:metabolism; D059372:Nucleotide Motifs / Q000235:genetics*; D026723:Polyadenylation / Q000235:genetics; D012326:RNA Splicing / Q000235:genetics; D034443:RNA Transport / Q000235:genetics*; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D013347:Subcellular Fractions / Q000378:metabolism
chemical_list: D019913:Nuclear Localization Signals; D062085:RNA, Long Noncoding; D012333:RNA, Messenger
references.citation: Proc Natl Acad Sci U S A. 2009 Jul 14;106(28):11667-72
references.pmid: 19571010
references.citation: Cell. 2013 Jul 3;154(1):26-46
references.pmid: 23827673
references.citation: Genome Res. 2012 May;22(5):885-98
references.pmid: 22406755
references.citation: Curr Opin Cell Biol. 2005 Jun;17(3):302-8
references.pmid: 15901501
references.citation: Genes Cells. 2011 May;16(5):479-90
references.pmid: 21463453
references.citation: J Cell Biol. 1994 Aug;126(4):877-99
references.pmid: 7519622
references.citation: RNA. 2012 Apr;18(4):825-43
references.pmid: 22361292
references.citation: BMC Genomics. 2012 Oct 30;13:574
references.pmid: 23110385
references.citation: Cell. 2005 Oct 21;123(2):249-63
references.pmid: 16239143
references.citation: Chromosoma. 2007 Aug;116(4):373-83
references.pmid: 17333237
references.citation: Mol Ther Nucleic Acids. 2013 Jul 09;2:e104
references.pmid: 23839098
references.citation: Nat Struct Mol Biol. 2013 Apr;20(4):440-6
references.pmid: 23435381
references.citation: Mol Cell. 2011 Sep 16;43(6):904-14
references.pmid: 21925379
references.citation: PLoS Genet. 2013 Apr;9(4):e1003470
references.pmid: 23637635
references.citation: Biochimie. 2011 Apr;93(4):633-44
references.pmid: 21111023
references.citation: Nature. 2011 Jul 20;475(7356):333-41
references.pmid: 21776079
references.citation: Genome Biol. 2012 Nov 26;13(11):R107
references.pmid: 23181609
references.citation: Science. 2012 Dec 14;338(6113):1435-9
references.pmid: 23239728
references.citation: Nucleic Acids Res. 2008 Feb;36(3):1037-49
references.pmid: 18096623
references.citation: Science. 2007 Jun 8;316(5830):1484-8
references.pmid: 17510325
references.citation: Semin Cell Dev Biol. 2011 Jun;22(4):366-76
references.pmid: 21256239
references.citation: Genes Dev. 2002 Nov 1;16(21):2761-6
references.pmid: 12414728
references.citation: Nature. 2001 Nov 1;414(6859):82-4
references.pmid: 11689947
references.citation: J Virol. 1989 Oct;63(10):4386-94
references.pmid: 2550672
references.citation: Cold Spring Harb Symp Quant Biol. 2006;71:407-17
references.pmid: 17381323
references.citation: Nat Rev Genet. 2009 Mar;10(3):155-9
references.pmid: 19188922
references.citation: Int J Oncol. 2011 Jul;39(1):169-75
references.pmid: 21503572
references.citation: Proc Natl Acad Sci U S A. 2010 Dec 21;107(51):22196-201
references.pmid: 21135235
references.citation: Proc Natl Acad Sci U S A. 2007 Jun 19;104(25):10412-7
references.pmid: 17563387
references.citation: Cell Cycle. 2008 Nov 1;7(21):3294-301
references.pmid: 18948735
references.citation: J Biol Chem. 1998 Jul 3;273(27):17079-85
references.pmid: 9642273
references.citation: Genes Dev. 2007 Jan 1;21(1):11-42
references.pmid: 17210785
references.citation: Genome Res. 2012 Sep;22(9):1775-89
references.pmid: 22955988
references.citation: Nature. 2012 Feb 15;482(7385):339-46
references.pmid: 22337053
references.citation: Science. 2005 Sep 2;309(5740):1559-63
references.pmid: 16141072
references.citation: Mol Cell Biol. 1999 Dec;19(12):8412-21
references.pmid: 10567566
references.citation: Cold Spring Harb Protoc. 2010 Jun;2010(6):pdb.prot5441
references.pmid: 20516179
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D48-55
references.pmid: 23203987
references.citation: Nature. 2012 Sep 6;489(7414):57-74
references.pmid: 22955616
references.citation: Trends Cell Biol. 2013 Aug;23(8):365-73
references.pmid: 23583578
references.citation: RNA Biol. 2012 Dec;9(12):1413-7
references.pmid: 23187719
references.citation: Mol Cell Biol. 2000 Jun;20(11):3996-4005
references.pmid: 10805742
references.citation: Annu Rev Biochem. 2012;81:145-66
references.pmid: 22663078
references.citation: Genome Res. 2004 Jun;14(6):1188-90
references.pmid: 15173120
references.citation: RNA. 1995 May;1(3):273-83
references.pmid: 7489499
references.citation: Mol Cell Biol. 1992 Aug;12(8):3514-21
references.pmid: 1630459
references.citation: RNA. 2012 Apr;18(4):738-51
references.pmid: 22355166
references.citation: Mol Cell. 2011 Nov 18;44(4):667-78
references.pmid: 21963238
references.citation: Proc Natl Acad Sci U S A. 2011 Nov 1;108(44):17985-90
references.pmid: 22010220
references.citation: Methods Mol Biol. 2004;257:75-84
references.pmid: 14769997
references.citation: Nat Struct Mol Biol. 2012 Nov;19(11):1068-75
references.pmid: 23132386
references.citation: Proc Natl Acad Sci U S A. 2007 Aug 21;104(34):13684-9
references.pmid: 17699631
references.citation: EMBO J. 1999 Mar 15;18(6):1642-52
references.pmid: 10075934
references.citation: Mol Cell. 2009 Aug 28;35(4):467-78
references.pmid: 19716791
references.citation: Proc Natl Acad Sci U S A. 2012 Nov 20;109(47):19202-7
references.pmid: 23129630
references.citation: Nucleic Acids Res. 1992 Jun 25;20(12):3191-8
references.pmid: 1620616
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D64-9
references.pmid: 23155063
references.citation: Nucleic Acids Res. 2013 Feb 1;41(4):2517-25
references.pmid: 23275560
references.citation: Cell. 2013 Mar 14;152(6):1298-307
references.pmid: 23498938
references.citation: Mol Cell Biol. 1996 Apr;16(4):1534-42
references.pmid: 8657127
references.citation: Cell Rep. 2012 Jul 26;2(1):26-32
references.pmid: 22840393
references.citation: Genes Dev. 1998 Nov 1;12(21):3303-19
references.pmid: 9808617
references.citation: RNA. 2009 Oct;15(10):1917-28
references.pmid: 19703940
references.citation: Curr Opin Cell Biol. 2010 Jun;22(3):357-64
references.pmid: 20356723
references.citation: Crit Rev Biochem Mol Biol. 2010 Jun;45(3):215-32
references.pmid: 20446804
references.citation: EMBO J. 1998 Jun 1;17(11):3176-87
references.pmid: 9606199
references.citation: Nucleic Acids Res. 2008 Nov;36(20):6482-93
references.pmid: 18854356
references.citation: PLoS Comput Biol. 2011 May;7(5):e1002031
references.pmid: 21573207
references.citation: Genetics. 2013 Mar;193(3):651-69
references.pmid: 23463798
references.citation: Nat Struct Mol Biol. 2013 Mar;20(3):300-7
references.pmid: 23463315
references.citation: PLoS One. 2013;8(1):e55684
references.pmid: 23383264