Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing.
RNA editing is a widespread post-transcriptional molecular phenomenon that can increase proteomic diversity, by modifying the sequence of completely or partially non-functional primary transcripts, through a variety of mechanistically and evolutionarily unrelated pathways. Editing by base substitution has been investigated in both animals and plants. However, conventional strategies based on directed Sanger sequencing are time-consuming and effectively preclude genome wide identification of RNA editing and assessment of partial and tissue-specific editing sites. In contrast, the high-throughput RNA-Seq approach allows the generation of a comprehensive landscape of RNA editing at the genome level. Short reads from Solexa/Illumina GA and ABI SOLiD platforms have been used to investigate the editing pattern in mitochondria of Vitis vinifera providing significant support for 401 C-to-U conversions in coding regions and an additional 44 modifications in non-coding RNAs. Moreover, 76% of all C-to-U conversions in coding genes represent partial RNA editing events and 28% of them were shown to be significantly tissue specific. Solexa/Illumina and SOLiD platforms showed different characteristics with respect to the specific issue of large-scale editing analysis, and the combined approach presented here reduces the false positive rate of discovery of editing events.
Picardi
Ernesto
E
Dipartimento di Biochimica e Biologia Molecolare E. Quagliariello, Università degli Studi di Bari, Bari, Italy.
Horner
David S
DS
Chiara
Matteo
M
Schiavon
Riccardo
R
Valle
Giorgio
G
Pesole
Graziano
G
D017360:Arabidopsis / Q000235:genetics; D020137:Base Pair Mismatch; D004272:DNA, Mitochondrial / Q000737:chemistry*; D018744:DNA, Plant / Q000737:chemistry; D050259:Genes, Mitochondrial; D054629:Genome, Mitochondrial; D023281:Genomics; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D017393:RNA Editing; D000077278:RNA, Mitochondrial; D018749:RNA, Plant / Q000737:chemistry* / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D027843:Vitis / Q000235:genetics*
D004272:DNA, Mitochondrial; D018744:DNA, Plant; D000077278:RNA, Mitochondrial; D018749:RNA, Plant; D012313:RNA
Nature. 2007 Sep 27;449(7161):463-7
17721507
Cell. 2008 May 2;133(3):523-36
18423832
Annu Rev Genomics Hum Genet. 2008;9:387-402
18576944
Plant J. 2006 Aug;47(3):408-16
16774644
Genome Res. 2004 Dec;14(12):2379-87
15545495
Science. 2009 May 29;324(5931):1210-3
19478186
Curr Top Microbiol Immunol. 2006;307:67-89
16903221
Mol Biol Evol. 2007 Sep;24(9):1971-81
17591603
BMC Plant Biol. 2008 Jul 16;8:79
18631376
Nat Methods. 2008 Jan;5(1):16-8
18165802
Proc Natl Acad Sci U S A. 1999 Dec 21;96(26):15324-9
10611383
IUBMB Life. 2003 Apr-May;55(4-5):227-33
12880203
Mol Genet Genomics. 2002 Dec;268(4):434-45
12471441
Curr Protoc Bioinformatics. 2005 Oct;Chapter 11:Unit11.3
18428744
FEMS Microbiol Rev. 1999 Jun;23(3):297-316
10371035
C R Biol. 2003 Oct-Nov;326(10-11):901-8
14744096
Trends Genet. 2008 Mar;24(3):133-41
18262675
Mol Gen Genet. 2001 Jan;264(5):595-603
11212914
Mol Biol Evol. 2009 Jan;26(1):99-110
18922764
Nucleic Acids Res. 2008 Sep;36(16):e105
18660515
Genome Res. 2009 Jun;19(6):978-86
19420382
Nat Methods. 2008 Dec;5(12):1005-10
19034268
Mitochondrion. 2008 Sep;8(4):319-27
18678284
Nat Biotechnol. 2004 Aug;22(8):1001-5
15258596
J Mol Evol. 2005 Feb;60(2):196-206
15785848
Plant Mol Biol. 1994 Mar;24(5):811-8
8193306
Nucleic Acids Res. 1997 Mar 1;25(5):955-64
9023104
Mitochondrion. 2008 Jan;8(1):35-46
18326075
Genome Biol. 2008;9(12):R175
19087247
J Mol Evol. 1999 Mar;48(3):303-12
10093219
Nat Rev Genet. 2009 Jan;10(1):57-63
19015660
Mol Genet Genomics. 2006 Sep;276(3):285-93
16862402
Stat Med. 1990 Jul;9(7):811-8
2218183
Genome Res. 2004 Jun;14(6):1188-90
15173120
Annu Rev Genet. 2000;34:499-531
11092837
Genetics. 2008 Mar;178(3):1693-708
17565941
Bioinformatics. 2009 Apr 1;25(7):967-8
19218350
Mol Gen Genet. 1994 Jul 8;244(1):67-74
8041363
Plant Cell. 2009 Feb;21(2):558-67
19252080
Curr Protoc Bioinformatics. 2008 Sep;Chapter 2:Unit 2.5
18819075
Methods Enzymol. 2007;424:439-58
17662853
J Mol Evol. 1988 Dec-1989 Feb;28(1-2):87-97
3148746
Nucleic Acids Res. 2003 Oct 15;31(20):5907-16
14530439
Nucleic Acids Res. 2007 Jan;35(Database issue):D173-7
17175530
Genomics. 2008 Nov;92(5):255-64
18703132
FEBS Lett. 1998 Dec 18;441(2):159-60
9883875