Vertebrate Transposons.PDF

See online version for legend and references192 Cell 135,October 3,2008 2008 Elsevier Inc.DOI 10.1016/j.cell.2008.09.028SnapShot:Vertebrate TransposonsPrabhat K.Mandal and Haig H.Kazazian,Jr.Department of Genetics,University of Pennsylvania School of Medicine,Philadelphia,PA 19104,USAHuman Genome?3200 Mb#of Copies(1000)Total Length(Mb)%of GenomeActiveLINEs868558.820.42LINE1151646216.89ActiveLINE231588.23.22LINE3378.40.31SINEs1558359.613.29Alu11090290.110.6Active using L1 RTMIR39360.12.2MIR3759.30.34SVA12.764.20.15Active using L1 RTLTR retrotransposons4432278.29ERV class I11279.22.89ERV(K)class II88.50.31ERV(L)class III8339.51.44MaLR24099.83.65DNA trans posons29477.62.84hATCharlie18238.11.39Zaphod134.30.16Tc-1Tigger57281.02Tc240.90.03Mariner142.60.1PiggyBac-like20.50.02Unclassified223.20.12Opossum Genome?3600 Mb#of Copies(1000)Total Length(Mb)%of GenomeLINEs2581.46975.2929.17LINE11165.62670.0320.04LINE2833.76158.284.73LINE3317.3469.212.07RTE264.7377.772.32SINEs2306.91348.8910.42SINE/L1577.7396.52.88SINE/RTE562.33100.192.99SINE/other1166.85152.24.55LTR retrotransposons1123.08355.610.63ERV-internal309.16124.253.71ERV-LTR813.92231.356.92DNA trans posons353.1958.121.73hAT177.9825.60.76Mariner74.4416.170.48Other100.7716.350.48Platypus Genome?2300 Mb#of Copies(1000)Total Length(Mb)%of GenomeLINEs2050.2389.221.04LINE10.060.010LINE21910.97360.2319.47LINE38.040.80.04CR143.768.560.46RTE85.6919.171.04Dong/R41.70.410.02SINEs2275.141522.43L2-Mon12145.38394.0421.3RTE-SINE52.8812.120.66MIR35.263.090.17MIR32.560.240.01Other39.025.440.29LTR retrotransposons5.792.720.15ERV class I1.950.910.05ERV(K)class II0.410.320.02ERV(L)class III0.020.010.01Gypsy0.040.010.01Other3.381.490.08DNA transposons58.1310.270.56Tc-1/Tigger49.768.910.48hAThAT7.251.050.06Charlie0.420.070.01AcHobo0.40.220.01MER10.30.020.01Tip1000.010.010.01Chicken Genome?1200 Mb#of Copies(1000)Total Length(Mb)%of GenomeLINEs96.2337.163.1CR196.2337.163.1LTR retrotransposons17.047.280.6Birddwag/gypsy7.42.690.22Kronos/gypsy4.963.020.25Soprano1.360.760.06Hitchcock3.320.810.07DNA transposons16.017.340.61Tc-1/Galluhop13.726.140.51hAT/Charlie2.291.20.1Fugu Genome?400 Mb#of Copies(1000)Total Length(Mb)%of GenomeLINEs4.365.291.323NeSL/Zebulon0.030.0360.009R4/Rex60.280.340.086LINE1/Tx10.180.220.055RTE/Rex31.291.580.394LINE2/Maui1.752.140.534Rex/Babar0.80.980.245SINEs5SINE-FR/Alu,MIR5LTR retro transposons0.981.2040.301Ty3/gypsySURL0.020.0240.006SURL-like0.010.0120.003Jule0.010.0120.003CsRn10.140.1760.044Sushi0.290.3560.089Barthez0.0250.0280.007Gmr1(-like)0.050.0680.017Rex80.010.0120.003Ty1/Copia0.050.0560.014DIRS10.020.0280.007BEL0.050.0680.017FERV-R0.30.3640.091DNA transposonsPiggyback/Pigibaku0.22IS5/Harbinger/Senkusha0.75Pogo/Tc1/IS630Tc1 FR1.4Pogo/Tiggu0.5Tc2 FR1.8hATChaplin/Charlie1.5Trillian/Zaphod0.15Furousha0.15Mouse Genome?2800 Mb#of Copies(1000)Total Length(Mb)%of GenomeActiveLINEs660475.319.21LINE11599464.818.78ActiveLINE2539.40.38LINE381.20.05SINEs1498202.98.22B1(Alu)156467.32.66Active using L1 RTMIR/MIR311514.10.57B2134859.62.39Active using L1 RTB4/RSINE39157.12.36ID795.30.25LTR retrotransposons631244.39.87ERV class I3416.80.68ActiveERV class II212779.13.14ActiveERV class III37140.58ActiveMaLR(III)388112.24.82ActiveDNA transposons11221.80.88hATCharlie8215.20.62Other hATs81.60.06Tc-1Tigger244.40.17Mariner10.20.011Target site preference:5-TT/AAAA-32IAP(1000 copies)and ETn(300-400 copies)are members of this classSnapShot:Vertebrate TransposonsPrabhat K.Mandal and Haig H.Kazazian,Jr.Department of Genetics,University of Pennsylvania School of Medicine,Philadelphia,PA 19104,USA192.e1 Cell 135,October 3,2008 2008 Elsevier Inc.DOI 10.1016/j.cell.2008.09.028Transposable elements,originally discovered in maize by Barbara McClintock,are discrete DNA segments that can insert into new chromosomal locations either by a“cut and paste”or by a“copy and paste”mechanism.Transposable elements are involved in a wide variety of biological transactions including genome alteration by element insertion or deletion and homologous recombination between element copies.They fall into two classes according to whether their transposition intermediate is RNA(class 1 or retrotransposons)or DNA(class 2 or DNA-based transposons).Recent genome sequencing projects have revealed that transposable elements make up a major portion of most vertebrate genomes.For example,transposable elements account for almost 50%of the human genome.This table summarizes different types of transposable element content in human,mouse,opossum,platypus,chicken,and fugu.Human(Homo sapiens)In the human genome,the most abundant and still active elements are the LINE1(L1)and its SINE partner Alu.The average human genome contains 80100 L1 elements competent for retrotransposition whose encoded proteins mobilize their L1s in cis(see the Review by Goodier and Kazazian,page 23 of this issue).The L1 reverse tran-scriptase(RT)is required for trans-mobilization of Alu and SVA elements.Because some L1s are active retrotransposons,multiple laboratories are testing them for use in gene transfer and insertional mutagenesis.There is no current evidence for long terminal repeat(LTR)or DNA transposon active transposition activity in the human genome.Alus belong to the 7SL RNA-derived SINEs and are present only in primates,whereas MIRs are tRNA-derived SINEs and mammalian specific.Mouse(Mus musculus)Mice have greater transposon activity than humans because of a higher content of lineage-specific repeats(mouse versus human:32.4%versus 24.4%).Endogenous retro-viruses(ERVs)are extinct in humans,whereas all three classes of ERVs have active members in the mouse.MaLR,the single most successful LTR element in mouse and a class III ERV,is still active in mouse but died out some 50 million years ago in humans.Early transposon(ETn)elements are derived from partially deleted musD endogenous retroviruses and,unlike L1s,are mobilized in trans.Retrotransposing intracisternal A particles(IAP)elements are mostly defective but can be mobilized in trans using the protein machinery of a small number of intact IAPs in the mouse genome.Opossum(Monodelphis domestica)The opossum genome size of 3600 Mb is greater than in any amniotic lineage studied to date.Five hundred families of interspersed repeats cover around 52%of the genome.The genome is significantly rich in non-LTR retrotransposons(they cover 29%of the genome).RTE(retrotransposable element)-like non-LTR elements that were originally discovered in C.elegans have been identified in opossum.Several families of SINEs appear to use RTE elements for mobilization.The L3/CR1 fraction of the genome is significantly greater in Monodelphis,comprising 2.1%of the genome.This is seven times than that of human(0.3%)and 42 times greater than that of mouse(0.05%).Platypus(Ornithorhynchus anatinus)About one-half of the Platypus genome is derived from transposable elements.The most abundant and still active repeats are LINE2 and its nonautonomous partner SINE,Mon1.snoRTE,a unique SINE-like retrotransposon related to small nucleolar RNA(snoRNA),has been identified.snoRTE retrotransposes by means of an RTE class of non-LTR transposable element.Gypsy,an ancient class of LTR element,is present in the platypus genome and has not been identified in any other mammalian genome sequenced.Chicken(Gallus gallus)A small portion(4.3%)of the chicken genome is occupied by transposable elements.SINE-like elements have not been identified.Fugu(Takifugu rubripes)Although the Fugu genome contains a lower abundance of interspersed repeats,the level of retrotransposon diversity is greater than in mammals as numerous clades have been identified that are not present in mammals.AbbreviationsLINEs,long interspersed nucleotide elements;SINEs,short interspersed nucleotide elements;SVA,SINE-Ra HERV-K(HML2)LTR/VNTRvariable number of tandem re-peats/Alu;MIR,mammalian-wide interspersed repeat;LTR,long terminal repeat;ERV,endogenous retrovirus;MaLR,mammalian apparent LTR-retrotransposon;B2 and ID,closely resemble Ala-tRNA;B4,resemble a fusion between B1 and B2;ETn,early transposon;hAT,hobo-activator-Tam;IAP,intracisternal A particle;RTE,retrotransposable element;CR1,chicken repeat 1;ID,identifier(BC1 derived,neuronally expressed);RT,reverse transcriptase.ACkNOwLEDGMENTSWe thank J.L.Goodier and A.D.Ewing for their helpful discussions.We also thank J.Jurka for critical reading and helpful comments.REFERENCESAparicio,S.,Chapman,J.,Stupka,E.,Putnam,N.,Chia,J.M.,Dehal,P.,Christoffels,A.,Rash,S.,Hoon,S.,Smit,A.,et al.(2002).Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes.Science 297,13011310.Gentles,A.J.,Wakefield,M.J.,Kohan,O.,Gu,W.,Batzer,M.A.,Pollock,D.D.,and Jurka,J.(2007).Evolutionary dynamics of transposable elements in the short-tailed opos-sum Monodelphis domestica.Genome 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