title: RNA-Mediated Gene Duplication and Retroposons: Retrogenes, LINEs, SINEs, and Sequence Specificity.
abstract: A substantial number of "retrogenes" that are derived from the mRNA of various intron-containing genes have been reported. A class of mammalian retroposons, long interspersed element-1 (LINE1, L1), has been shown to be involved in the reverse transcription of retrogenes (or processed pseudogenes) and non-autonomous short interspersed elements (SINEs). The 3'-end sequences of various SINEs originated from a corresponding LINE. As the 3'-untranslated regions of several LINEs are essential for retroposition, these LINEs presumably require "stringent" recognition of the 3'-end sequence of the RNA template. However, the 3'-ends of mammalian L1s do not exhibit any similarity to SINEs, except for the presence of 3'-poly(A) repeats. Since the 3'-poly(A) repeats of L1 and Alu SINE are critical for their retroposition, L1 probably recognizes the poly(A) repeats, thereby mobilizing not only Alu SINE but also cytosolic mRNA. Many flowering plants only harbor L1-clade LINEs and a significant number of SINEs with poly(A) repeats, but no homology to the LINEs. Moreover, processed pseudogenes have also been found in flowering plants. I propose that the ancestral L1-clade LINE in the common ancestor of green plants may have recognized a specific RNA template, with stringent recognition then becoming relaxed during the course of plant evolution.
authors: Graduate School of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama 526-0829, Japan.
authors: Kazuhiko
authors: K
authors: Ohshima
references: Genetics. 2004 Dec;168(4):2037-47
references: 15611173
references: Cell. 2002 Nov 1;111(3):433-44
references: 12419252
references: Mol Biol Evol. 1999 Sep;16(9):1238-50
references: 10486979
references: Mol Cell Biol. 2004 Sep;24(18):7902-13
references: 15340053
references: Nucleic Acids Res. 1988 Feb 25;16(4):1431-52
references: 2831500
references: Proc Natl Acad Sci U S A. 2006 Feb 28;103(9):3220-5
references: 16492757
references: Mol Biol Evol. 2003 Jan;20(1):38-46
references: 12519904
references: BMC Genomics. 2009 Oct 16;10:480
references: 19835609
references: EMBO J. 2002 Feb 1;21(3):408-17
references: 11823433
references: RNA. 1997 Jan;3(1):1-16
references: 8990394
references: Proc Natl Acad Sci U S A. 2004 Apr 13;101(15):5589-94
references: 15064405
references: Genome Res. 2002 Feb;12(2):316-24
references: 11827951
references: Mol Biol Evol. 2011 Oct;28(10):2727-30
references: 21512106
references: J Mol Biol. 2000 May 5;298(3):365-77
references: 10772856
references: Eur J Biochem. 1990 Apr 20;189(1):25-31
references: 1691979
references: Gene. 2008 Dec 1;425(1-2):1-8
references: 18796327
references: Mol Biol Evol. 2004 Apr;21(4):705-15
references: 15014157
references: Cell. 1996 Nov 29;87(5):917-27
references: 8945518
references: Gene. 2002 Sep 4;297(1-2):229-39
references: 12384304
references: Genome Res. 2003 Dec;13(12):2541-58
references: 14656962
references: Nat Rev Genet. 2003 Nov;4(11):865-75
references: 14634634
references: Mol Biol Evol. 2001 Dec;18(12):2315-22
references: 11719581
references: Mol Cell Biol. 1995 Jul;15(7):3882-91
references: 7540721
references: Genome Res. 2002 Sep;12(9):1333-44
references: 12213770
references: Proc Natl Acad Sci U S A. 1996 Feb 6;93(3):1077-81
references: 8577717
references: Genome Res. 2002 Mar;12(3):391-9
references: 11875026
references: Proc Natl Acad Sci U S A. 1993 Jul 15;90(14):6562-6
references: 8341669
references: Gene. 1997 Dec 31;205(1-2):229-43
references: 9461397
references: J Biol Chem. 2002 May 17;277(20):17877-82
references: 11882661
references: Cell. 1993 Feb 26;72(4):595-605
references: 7679954
references: Mol Biol Evol. 2007 Sep;24(9):2009-15
references: 17602167
references: Plant Physiol. 2005 Jun;138(2):935-48
references: 15923328
references: Cytogenet Genome Res. 2005;110(1-4):462-7
references: 16093699
references: Cell. 2008 Oct 3;135(1):23-35
references: 18854152
references: Nucleic Acids Res. 1995 Jan 11;23(1):98-102
references: 7870595
references: Genome Res. 2008 Jun;18(6):1005-10
references: 18463303
references: Proc Natl Acad Sci U S A. 2013 Jan 15;110(3):1012-6
references: 23277587
references: Curr Opin Genet Dev. 1996 Dec;6(6):743-8
references: 8994846
references: Nucleic Acids Res. 2013 Jan;41(Database issue):D83-9
references: 23203982
references: Nat Struct Mol Biol. 2011 Aug 07;18(9):1006-14
references: 21822284
references: Cell. 1996 Nov 29;87(5):905-16
references: 8945517
references: Mol Biol Evol. 1999 Dec;16(12):1675-86
references: 10605110
references: Proc Natl Acad Sci U S A. 1986 Jan;83(2):251-5
references: 3455763
references: Plant Cell. 2003 Aug;15(8):1934-44
references: 12897263
references: Genes Genet Syst. 2011;86(1):19-25
references: 21498919
references: Plant Mol Biol. 2006 May;61(1-2):79-94
references: 16786293
references: J Mol Evol. 2006 May;62(5):630-44
references: 16612539
references: Gene. 1999 Sep 30;238(1):115-34
references: 10570990
references: Nat Genet. 1997 May;16(1):6-7
references: 9140383
references: BMC Evol Biol. 2009 Oct 15;9:252
references: 19832993
references: Plant Mol Biol. 2006 Jun;61(3):505-14
references: 16830182
references: Gene. 2009 Jul 15;441(1-2):111-8
references: 19118606
references: Mol Biol Evol. 2007 Aug;24(8):1656-66
references: 17470437
references: Proc Natl Acad Sci U S A. 1994 Apr 26;91(9):3911-5
references: 7513427
references: J Exp Bot. 2012 Sep;63(14):5061-77
references: 22865910
references: Nucleic Acids Res. 2005 Apr 06;33(6):1993-2002
references: 15814816
references: Science. 2001 Dec 14;294(5550):2351-3
references: 11743201
references: Mol Biol Evol. 2009 Jun;26(6):1405-20
references: 19289598
references: Mol Biol Evol. 1998 Apr;15(4):391-407
references: 9549090
references: Nat Genet. 2004 Oct;36(10):1061-3
references: 15378063
references: Cytogenet Genome Res. 2005;110(1-4):441-7
references: 16093696
references: Proc Natl Acad Sci U S A. 1991 Mar 15;88(6):2326-30
references: 1848699
references: Genes Genet Syst. 2005 Jun;80(3):161-71
references: 16172529
references: PLoS Biol. 2008 Jun 10;6(6):e140
references: 18547142
references: Curr Opin Cell Biol. 2002 Jun;14(3):343-50
references: 12067657
references: PLoS Genet. 2009 Nov;5(11):e1000732
references: 19936065
references: Plant J. 2009 Sep;59(6):872-82
references: 19473321
references: Mol Biol Evol. 2012 Nov;29(11):3255-9
references: 22675029
references: Nucleic Acids Res. 2003 Jul 1;31(13):3406-15
references: 12824337
references: PLoS Genet. 2009 Apr;5(4):e1000458
references: 19390602
references: Proc Natl Acad Sci U S A. 2011 Feb 8;108(6):2322-7
references: 21252301
references: Mol Biol Evol. 2011 Jan;28(1):17-20
references: 20716533
references: Mol Biol Evol. 2010 Nov;27(11):2522-33
references: 20525901
references: J Mol Evol. 2006 May;62(5):511-22
references: 16612535
references: Mol Biol Evol. 2003 May;20(5):694-702
references: 12679554
references: Nat Genet. 2003 Sep;35(1):41-8
references: 12897783
references: PLoS Biol. 2005 Nov;3(11):e357
references: 16201836
references: Syst Biol. 2006 Dec;55(6):886-901
references: 17345671
references: BMC Genomics. 2008 Oct 08;9:466
references: 18842134
references: Mol Cell Biol. 1996 Jul;16(7):3756-64
references: 8668192
references: Proc Natl Acad Sci U S A. 1986 May;83(10):3156-60
references: 3458171
references: Eur J Biochem. 1988 Sep 15;176(2):255-64
references: 2843369
references: Mol Biol Evol. 1998 Nov;15(11):1460-71
references: 12572609
references: Biochem Biophys Res Commun. 1996 Mar 7;220(1):233-7
references: 8602850
references: J Mol Evol. 1997;44 Suppl 1:S52-6
references: 9071012
references: Proc Natl Acad Sci U S A. 1997 Jul 22;94(15):7704-11
references: 9223252
references: J Mol Evol. 2005 May;60(5):677-87
references: 15983875
references: Science. 2004 Mar 12;303(5664):1626-32
references: 15016989
references: Proc Natl Acad Sci U S A. 1999 Mar 16;96(6):2869-74
references: 10077603
references: Proc Natl Acad Sci U S A. 1995 Nov 21;92(24):11125-9
references: 7479950
references: Mol Biol Evol. 2013 Jan;30(1):88-99
references: 22918960
references: Annu Rev Genet. 1985;19:253-72
references: 3909943
references: Nucleic Acids Res. 1995 Jan 11;23(1):170-5
references: 7870583
references: Nat Genet. 2000 Apr;24(4):363-7
references: 10742098
references: Gene. 2007 Mar 15;389(2):196-203
references: 17196768
references: Trends Ecol Evol. 1991 Nov;6(11):358-61
references: 21232509
references: Mol Biol Evol. 1999 Jun;16(6):793-805
references: 10368957
references: Phytochemistry. 2009 Mar;70(4):508-16
references: 19254800
references: Gene. 1995 Jan 23;152(2):261-4
references: 7835712
references: Trends Genet. 2004 Jan;20(1):9-14
references: 14698614
references: Anim Genet. 1993 Feb;24(1):33-9
references: 8498711
references: Gene. 2008 Jan 15;407(1-2):75-85
references: 17976929
references: Syst Biol. 2006 Dec;55(6):949-56
references: 17345676
references: Genome Res. 2004 Oct;14(10A):1911-5
references: 15364902
references: Nucleic Acids Res. 2005 Apr 28;33(8):2374-83
references: 15860774
references: Mol Biol Evol. 2003 Apr;20(4):522-7
references: 12654932
references: Science. 1991 Feb 15;251(4995):753
references: 1990437
references: Proc Natl Acad Sci U S A. 2007 Dec 4;104(49):19363-8
references: 18048334
references: Mol Biol Evol. 1997 Dec;14(12):1206-17
references: 9402732
references: BMC Bioinformatics. 2007 Aug 24;8:308
references: 17718914
references: Science. 1999 Mar 5;283(5407):1530-4
references: 10066175
references: Infect Immun. 2002 Dec;70(12):6798-804
references: 12438355
references: Mol Biol Evol. 2004 Feb;21(2):207-17
references: 12949131
references: Mol Biochem Parasitol. 2007 Mar;152(1):47-52
references: 17178164
references: Genome Biol Evol. 2011;3:1357-68
references: 22042334
references: Gene. 2009 Dec 15;448(2):207-13
references: 19651192
references: Plant Cell Rep. 2011 Dec;30(12):2207-13
references: 21796384
references: Genetics. 2008 May;179(1):113-23
references: 18493044
references: Mol Cell Biol. 2001 Feb;21(4):1429-39
references: 11158327
references: Genome Res. 2005 Aug;15(8):1106-17
references: 16077010
references: Genome Biol. 2003;4(11):R74
references: 14611660
references: Proc Natl Acad Sci U S A. 1997 Mar 4;94(5):1872-7
references: 9050872
references: Genes Genet Syst. 2008 Jun;83(3):227-36
references: 18670134
references: Genome Res. 2006 Jul;16(7):864-74
references: 16717141
references: BMC Genomics. 2009 Feb 19;10:83
references: 19224649
references: Mol Biol Evol. 2013 Feb;30(2):384-96
references: 23066043
references: Cell Mol Life Sci. 2007 Mar;64(5):542-54
references: 17192808
references: Gene. 2011 Jul 1;480(1-2):21-7
references: 21352903
references: Genes Genet Syst. 2001 Jun;76(3):169-79
references: 11569500
references: DNA Res. 2000 Oct 31;7(5):291-303
references: 11089911
references: Mol Biol Evol. 2001 Sep;18(9):1720-33
references: 11504852
references: Nucleic Acids Res. 2006;34(18):5184-93
references: 17000640
references: Cytogenet Genome Res. 2005;110(1-4):475-90
references: 16093701
references: Mol Biol Evol. 1994 Nov;11(6):886-98
references: 7815928
references: J Mol Evol. 1994 Oct;39(4):378-86
references: 7966368
references: Jpn J Genet. 1992 Apr;67(2):155-66
references: 1326298
references: Annu Rev Biochem. 1986;55:631-61
references: 2427017
references: Genome Res. 2007 Aug;17(8):1129-38
references: 17623810
references: Nat Rev Genet. 2009 Jan;10(1):19-31
references: 19030023
references: Mol Biol Evol. 2005 Mar;22(3):673-82
references: 15548748
references: Proc Natl Acad Sci U S A. 1998 Sep 1;95(18):10704-9
references: 9724768
references: EMBO J. 2002 Nov 1;21(21):5899-910
references: 12411507
references: PLoS Biol. 2007 Apr;5(4):e101
references: 17407382