title: Non-coding RNAs in crop genetic modification: considerations and predictable environmental risk assessments (ERA).
abstract: Of late non-coding RNAs (ncRNAs)-mediated gene silencing is an influential tool deliberately deployed to negatively regulate the expression of targeted genes. In addition to the widely employed small interfering RNA (siRNA)-mediated gene silencing approach, other variants like artificial miRNA (amiRNA), miRNA mimics, and artificial transacting siRNAs (tasiRNAs) are being explored and successfully deployed in developing non-coding RNA-based genetically modified plants. The ncRNA-based gene manipulations are typified with mobile nature of silencing signals, interference from viral genome-derived suppressor proteins, and an obligation for meticulous computational analysis to prevaricate any inadvertent effects. In a broad sense, risk assessment inquiries for genetically modified plants based on the expression of ncRNAs are competently addressed by the environmental risk assessment (ERA) models, currently in vogue, designed for the first generation transgenic plants which are based on the expression of heterologous proteins. Nevertheless, transgenic plants functioning on the foundation of ncRNAs warrant due attention with respect to their unique attributes like off-target or non-target gene silencing effects, small RNAs (sRNAs) persistence, food and feed safety assessments, problems in detection and tracking of sRNAs in food, impact of ncRNAs in plant protection measures, effect of mutations etc. The role of recent developments in sequencing techniques like next generation sequencing (NGS) and the ERA paradigm of the different countries in vogue are also discussed in the context of ncRNA-based gene manipulations.
authors: Directorate of Soybean Research, Indian Council of Agricultural Research-ICAR, Indore 452001, India. rameshsvbio@gmail.com
authors: S V
authors: SV
authors: Ramesh
mesh_terms: D018506:Gene Expression Regulation, Plant; D020868:Gene Silencing; D005818:Genetic Engineering / Q000941:ethics / Q000331:legislation & jurisprudence; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D035683:MicroRNAs / Q000235:genetics; D010944:Plants / Q000235:genetics*; D030821:Plants, Genetically Modified; D018749:RNA, Plant / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics*; D018570:Risk Assessment; D019076:Transgenes
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant; D034741:RNA, Small Interfering; D022661:RNA, Untranslated
references: Transgenic Res. 2008 Jun;17(3):367-77
references: 17605085
references: Genes Dev. 2003 Jan 1;17(1):49-63
references: 12514099
references: BMC Biotechnol. 2012 Apr 30;12:15
references: 22546148
references: Biotechnol Adv. 2010 May-Jun;28(3):301-7
references: 20067828
references: Environ Biosafety Res. 2006 Jul-Sep;5(3):119-25
references: 17445509
references: Science. 1994 Mar 11;263(5152):1423-5
references: 8128222
references: Transgenic Res. 2005 Dec;14(6):989-94
references: 16315100
references: Plant J. 2008 Feb;53(4):674-90
references: 18269576
references: Plant Cell. 2006 May;18(5):1121-33
references: 16531494
references: Transgenic Res. 2010 Jun;19(3):425-36
references: 19757133
references: Plant J. 2001 Sep;27(6):581-90
references: 11576441
references: Mol Plant Microbe Interact. 2012 Jan;25(1):97-106
references: 21936664
references: Nat Biotechnol. 2004 Dec;22(12):1559-66
references: 15543134
references: PLoS Genet. 2012;8(8):e1002885
references: 22916030
references: Nat Biotechnol. 2006 Nov;24(11):1420-8
references: 17057702
references: Toxicology. 2002 Dec 27;181-182:421-6
references: 12505346
references: Environ Int. 2011 Oct;37(7):1285-93
references: 21624662
references: PLoS One. 2008 Mar 19;3(3):e1829
references: 18350165
references: Science. 2010 May 14;328(5980):912-6
references: 20413458
references: Nat Biotechnol. 2007 Nov;25(11):1322-6
references: 17982443
references: PLoS One. 2011 Apr 11;6(4):e18644
references: 21494551
references: Appl Microbiol Biotechnol. 2009 Aug;84(2):323-33
references: 19330324
references: J Agric Food Chem. 2009 Jan 28;57(2):509-16
references: 19123817
references: Trends Biotechnol. 2004 Sep;22(9):463-9
references: 15331227
references: Mol Biol Evol. 2012 Nov;29(11):3297-307
references: 22593223
references: Biochem Biophys Res Commun. 2011 Mar 18;406(3):315-9
references: 21329663
references: Cell. 2000 Sep 29;103(1):157-67
references: 11051555
references: Proc Natl Acad Sci U S A. 1990 Mar;87(5):1820-4
references: 2308940
references: Cell Res. 2012 Jan;22(1):107-26
references: 21931358
references: Nat Biotechnol. 2003 Jun;21(6):635-7
references: 12754523
references: Nat Methods. 2006 Mar;3(3):199-204
references: 16489337
references: Transgenic Res. 2007 Jun;16(3):363-75
references: 17103244
references: EMBO J. 2001 Dec 3;20(23):6877-88
references: 11726523
references: Trends Plant Sci. 2009 Dec;14(12):643-4
references: 19822452
references: Mol Plant Microbe Interact. 1999 Feb;12(2):153-62
references: 9926415
references: Proc Natl Acad Sci U S A. 2006 Sep 26;103(39):14302-6
references: 16985000
references: Nature. 2003 Jun 19;423(6942):823
references: 12815419
references: Proc Natl Acad Sci U S A. 2008 Mar 4;105(9):3640-5
references: 18303117
references: EMBO Rep. 2006 Nov;7(11):1168-75
references: 17039251
references: Nat Genet. 2007 Aug;39(8):1033-7
references: 17643101
references: Genes Dev. 2004 Oct 1;18(19):2368-79
references: 15466488
references: GM Crops. 2010 Jul-Sep;1(4):207-13
references: 21844675
references: Plant Physiol. 2008 Jun;147(2):494-502
references: 18524880
references: J Agric Food Chem. 2006 Jan 11;54(1):130-7
references: 16390189
references: J Virol. 2006 Jun;80(12):5747-56
references: 16731914
references: Plant Physiol. 2003 Jan;131(1):245-53
references: 12529532
references: Mol Cell. 2004 Oct 8;16(1):69-79
references: 15469823
references: Cell. 2005 Apr 22;121(2):207-21
references: 15851028
references: Nat Genet. 2006 Jun;38(6):721-5
references: 16699516
references: Nucleic Acids Res. 2003 Jan 15;31(2):589-95
references: 12527766
references: Genes Dev. 2006 Dec 1;20(23):3255-68
references: 17158744
references: Virus Res. 2004 Jun 1;102(1):85-96
references: 15068884
references: Trends Microbiol. 2002 Jul;10(7):306-8
references: 12110203
references: Proc Natl Acad Sci U S A. 1998 Nov 10;95(23):13959-64
references: 9811908
references: Nat Biotechnol. 2007 Nov;25(11):1307-13
references: 17982444
references: PLoS One. 2012;7(10):e44803
references: 23077485
references: Food Chem Toxicol. 2009 Feb;47(2):353-60
references: 19068223
references: EMBO J. 1998 Nov 16;17(22):6739-46
references: 9822616
references: Nat Rev Genet. 2003 Jan;4(1):29-38
references: 12509751
references: Nat Biotechnol. 2007 Nov;25(11):1231-2
references: 17989682
references: Genome Biol. 2011;12(1):215
references: 21235831
references: Respirology. 2011 Feb;16(2):210-22
references: 21077988
references: EMBO J. 2002 Jun 17;21(12):3070-80
references: 12065420
references: Virology. 1992 Apr;187(2):525-33
references: 1546451
references: Science. 1997 Jun 6;276(5318):1558-60
references: 18610513
references: PLoS One. 2011;6(6):e21330
references: 21731706
references: Hum Mol Genet. 2003 Oct 15;12(20):2637-44
references: 12928480
references: Plant Physiol. 2008 Jun;147(2):543-51
references: 18441221
references: J Biotechnol. 2006 May 17;123(2):137-48
references: 16466822
references: Planta. 2006 Jun;224(1):125-32
references: 16395584
references: Genome Biol. 2007;8(6):R96
references: 17543110
references: Curr Biol. 2001 Mar 20;11(6):436-40
references: 11301254
references: Nucleic Acids Res. 2005 Mar 30;33(6):1834-47
references: 15800213
references: Genes Dev. 2004 May 15;18(10):1179-86
references: 15131083
references: Nature. 2000 Sep 21;407(6802):319-20
references: 11014180
references: Transgenic Res. 2010 Feb;19(1):45-55
references: 19548101
references: Genetics. 2003 Sep;165(1):387-97
references: 14504244
references: Nucleic Acids Res. 2005 Aug 09;33(14):4527-35
references: 16091630
references: PLoS One. 2009 Sep 30;4(9):e7232
references: 19789634
references: Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):7195-200
references: 12782788
references: Trends Genet. 2004 Nov;20(11):521-4
references: 15475108
references: Plant Physiol. 2006 Oct;142(2):429-40
references: 16920874
references: Annu Rev Phytopathol. 2007;45:173-202
references: 17408355
references: Genomics. 2008 Nov;92(5):255-64
references: 18703132
references: Virology. 2006 Jan 5;344(1):158-68
references: 16364747