A Highly Conserved, Small LTR Retrotransposon that Preferentially Targets Genes in Grass Genomes
Tóm tắt
Từ khóa
Tài liệu tham khảo
C Feschotte, 2002, Plant transposable elements: where genetics meets genomics., Nat Rev Genet, 3, 329, 10.1038/nrg793
R Cordaux, 2009, The impact of retrotransposons on human genome evolution., Nat Rev Genet, 10, 691, 10.1038/nrg2640
JF Wendel, 2000, Retrotransposon-mediated genome evolution on a local ecological scale., Proc Natl Acad Sci U S A, 97, 6250, 10.1073/pnas.97.12.6250
HH Kazazian Jr, 2004, Mobile elements: drivers of genome evolution., Science, 303, 1626, 10.1126/science.1089670
SR Wessler, 2006, Transposable elements and the evolution of eukaryotic genomes., Proc Natl Acad Sci U S A, 103, 17600, 10.1073/pnas.0607612103
Z Lippman, 2004, The role of RNA interference in heterochromatic silencing., Nature, 431, 364, 10.1038/nature02875
PH Maxwell, 2006, Identification of multiple transcription initiation, polyadenylation, and splice sites in the Drosophila melanogaster TART family of telomeric retrotransposons., Nucleic Acids Res, 34, 5498, 10.1093/nar/gkl709
T Wicker, 2007, A unified classification system for eukaryotic transposable elements., Nat Rev Genet, 8, 973, 10.1038/nrg2165
PS Schnable, 2009, The B73 maize genome: complexity, diversity, and dynamics., Science, 326, 1112, 10.1126/science.1178534
CP Witte, 2001, Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes., Proc Natl Acad Sci USA, 98, 13778, 10.1073/pnas.241341898
ER Havecker, 2004, The diversity of LTR retrotransposons., Genome Biol, 5, 225, 10.1186/gb-2004-5-6-225
R Kalendar, 2004, Large retrotransposon derivatives: abundant, conserved but nonautonomous retroelements of barley and related genomes., Genetics, 166, 1437, 10.1534/genetics.166.3.1437
R Kalendar, 2008, Cassandra retrotransposons carry independently transcribed 5S RNA., Proc Natl Acad Sci USA, 105, 5833, 10.1073/pnas.0709698105
N Jiang, 2002, Dasheng: a recently amplified nonautonomous long terminal repeat element that is a major component of pericentromeric regions in rice., Genetics, 161, 1293, 10.1093/genetics/161.3.1293
VD Soleimani, 2006, Quantification of the retrotransposon BARE-1 reveals the dynamic nature of the barley genome., Genome, 49, 389, 10.1139/G05-119
T Pélissier, 1996, DNA regions flanking the major Arabidopsis thaliana satellite are principally enriched in Athila retroelement sequences., Genetica, 97, 141, 10.1007/BF00054621
GG Presting, 1998, A Ty3/gypsy retrotransposon-like sequence localizes to the centromeric regions of cereal chromosomes., Plant J, 16, 721, 10.1046/j.1365-313x.1998.00341.x
Z Cheng, 2002, Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon., Plant Cell, 14, 1691, 10.1105/tpc.003079
KM Devos, 2002, Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis., Genome Res, 12, 1075, 10.1101/gr.132102
JS Ammiraju, 2007, Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza., Plant J, 52, 342, 10.1111/j.1365-313X.2007.03242.x
D Gao, 2009, A lineage-specific centromere retrotransposon in <italic>Oryza brachyantha</italic>., Plant J, 60, 820, 10.1111/j.1365-313X.2009.04005.x
P Neumann, 2003, Highly abundant pea LTR retrotransposon Ogre is constitutively transcribed and partially spliced., Plant Mol Biol, 53, 399, 10.1023/B:PLAN.0000006945.77043.ce
C Vitte, 2007, LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss., BMC Genomics, 8, 218, 10.1186/1471-2164-8-218
SR Wessler, 2001, Plant transposable elements. A hard act to follow., Plant Physiol, 125, 149, 10.1104/pp.125.1.149
B Piegu, 2006, Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice., Genome Res, 16, 1262, 10.1101/gr.5290206
Y Ding, 2007, SDG714, a histone H3K9 methyltransferase, is involved in Tos17 DNA methylation and transposition in rice., Plant Cell, 19, 9, 10.1105/tpc.106.048124
M Mirouze, 2009, Selective epigenetic control of retrotransposition in Arabidopsis., Nature, 461, 427, 10.1038/nature08328
K Shirasu, 2000, A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion., Genome Res, 10, 908, 10.1101/gr.10.7.908
C Vitte, 2003, Formation of solo-LTRs through unequal homologous recombination counterbalances amplifications of LTR retrotransposons in rice Oryza sativa L., Mol Biol Evol, 20, 528, 10.1093/molbev/msg055
Z Xu, 2007, LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons., Nucleic Acids Res, 35, W265, 10.1093/nar/gkm286
BS Gaut, 2002, Evolutionary dynamics of grass genomes., New Phytol, 154, 15, 10.1046/j.1469-8137.2002.00352.x
M Charles, 2009, Sixty million years in evolution of soft grain trait in grasses: emergence of the softness locus in the common ancestor of Pooideae and Ehrhartoideae, after their divergence from Panicoideae., Mol Biol Evol, 26, 1651, 10.1093/molbev/msp076
P SanMiguel, 1998, The paleontology of intergene retrotransposons of maize., Nat Genet, 20, 43, 10.1038/1695
J Ma, 2004, Rapid recent growth and divergence of rice nuclear genomes., Proc Natl Acad Sci USA, 101, 12404, 10.1073/pnas.0403715101
T Sang, 2007, Genetics and phylogenetics of rice domestication., Curr Opin Genet Dev, 17, 533, 10.1016/j.gde.2007.09.005
S Kikuchi, 2003, Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice., Science, 301, 376, 10.1126/science.1081288
S Ouyang, 2007, The TIGR Rice Genome Annotation Resource: improvements and new features., Nucleic Acids Research, 35, D883, 10.1093/nar/gkl976
T Tanaka, 2008, The Rice Annotation Project Database (RAP-DB): 2008 update., Nucleic Acids Res, D1028
H Ito, 2011, An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress., Nature, 472, 115, 10.1038/nature09861
MA German, 2009, Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome., Nat Protoc, 4, 356, 10.1038/nprot.2009.8
Y Xiong, 1990, Origin and evolution of retroelements based upon their reverse-transcriptase sequences., EMBO J, 9, 3353, 10.1002/j.1460-2075.1990.tb07536.x
HS Malik, 2001, Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses., Genome Res, 11, 1187, 10.1101/gr.185101
I Marín, 2000, Ty3/Gypsy retrotransposons: description of new Arabidopsis thaliana elements and evolutionary perspectives derived from comparative genomic data., Mol Biol Evol, 17, 1040, 10.1093/oxfordjournals.molbev.a026385
X Diao, 2006, Horizontal transfer of a plant transposon., PLoS Biol, 4, e5, 10.1371/journal.pbio.0040005
A Roulin, 2008, Evidence of multiple horizontal transfers of the long terminal repeat retrotransposon RIRE1 within the genus Oryza., Plant J, 53, 950, 10.1111/j.1365-313X.2007.03388.x
H Yan, 2010, Genome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with genes and centromeres in rice., Plant J, 63, 353, 10.1111/j.1365-313X.2010.04246.x
JA Bedell, 2005, Sorghum genome sequencing by methylation filtration., PLoS Biol, 3, e13, 10.1371/journal.pbio.0030013
C Feschotte, 2002, Mariner-like transposases are widespread and diverse in flowering plants., Proc Natl Acad Sci U S A, 99, 280, 10.1073/pnas.022626699
2002, Initial sequencing and comparative analysis of the mouse genome., Nature, 420, 520, 10.1038/nature01262
TE Bureau, 1992, Tourist: a large family of small inverted repeat elements frequently associated with maize genes., Plant Cell, 4, 1283, 10.1105/tpc.4.10.1283
TE Bureau, 1994, Stowaway: a new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants., Plant Cell, 6, 907, 10.1105/tpc.6.6.907
K Naito, 2006, Dramatic amplification of a rice transposable element during recent domestication., Proc Natl Acad Sci U S A, 103, 17620, 10.1073/pnas.0605421103
G Yang, 2001, Kiddo, a new transposable element family closely associated with rice genes., Mol Genet Genomics, 266, 417, 10.1007/s004380100530
SM Berget, 1977, Spliced segments at the 5′ terminus of adenovirus 2 late mRNA., Proc Natl Acad Sci U S A, 74, 3171, 10.1073/pnas.74.8.3171
W Li, 2009, Extensive, recent intron gains in Daphnia populations., Science, 326, 1260, 10.1126/science.1179302
A Girard, 2008, Conserved themes in small-RNA-mediated transposon control., Trends Cell Biol, 18, 136, 10.1016/j.tcb.2008.01.004
S Tsukahara, 2009, Bursts of retrotransposition reproduced in Arabidopsis., Nature, 461, 423, 10.1038/nature08351
J Liu, 2004, siRNAs targeting an intronic transposon in the regulation of natural flowering behavior in Arabidopsis., Genes Dev, 18, 2873, 10.1101/gad.1217304
SY Ying, 2010, Intron-mediated RNA interference, intronic microRNAs, and applications., Methods Mol Biol, 629, 205
SD Ehrlich, 1989, Illegitimate recombination in bacteria., 799
N Sugawara, 1992, Characterization of double-strand break-induced recombination: Homology requirements and single-stranded DNA formation., Mol Cell Biol, 12, 563, 10.1128/MCB.12.2.563
J Fernandes, 2004, Genome-wide mutagenesis of Zea mays L. using RescueMu transposons., Genome Biol, 5, R82, 10.1186/gb-2004-5-10-r82
L Bai, 2011, The activator/dissociation transposable elements comprise a two-component gene regulatory switch that controls endogenous gene expression in maize., Genetics, 187, 749, 10.1534/genetics.110.124149
H Hirochika, 1996, Retrotransposons of rice involved in mutations induced by tissue culture., Proc Natl Acad Sci USA, 93, 7783, 10.1073/pnas.93.15.7783
DG Higgins, 1996, Using CLUSTAL for multiple sequence alignments., Methods Enzymol, 266, 383, 10.1016/S0076-6879(96)66024-8
K Tamura, 2007, MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0., Molecular Biology and Evolution, 24, 1596, 10.1093/molbev/msm092
KJ Livak, 2001, Analysis of relative gene expression data using real-time quantitative PCR and the 2(-delta delta C(T)) method., Methods, 25, 402, 10.1006/meth.2001.1262