Molecular Poltergeists: Mitochondrial DNA Copies () in Sequenced Nuclear Genomes

1. GouldSB

WallerRF

McFaddenGI

2008 Plastid evolution. Annu Rev Plant Biol 59 491 517

2. KleineT

MaierUG

LeisterD

2009 DNA transfer from organelles to the nucleus: the idiosyncratic genetics of endosymbiosis. Annu Rev Plant Biol 60 115 138

3. TimmisJN

AyliffeMA

HuangCY

MartinW

2004 Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat Rev Genet 5 123 135

4. HuangCY

AyliffeMA

TimmisJN

2003 Direct measurement of the transfer rate of chloroplast DNA into the nucleus. Nature 422 72 76

5. RicchettiM

FairheadC

DujonB

1999 Mitochondrial DNA repairs double-strand breaks in yeast chromosomes. Nature 402 96 100

6. van der GiezenM

2009 Hydrogenosomes and mitosomes: conservation and evolution of functions. J Eukaryot Microbiol 56 221 231

7. LeisterD

2005 Origin, evolution and genetic effects of nuclear insertions of organelle DNA. Trends Genet 21 655 663

8. TovarJ

Leon-AvilaG

SanchezLB

SutakR

TachezyJ

2003 Mitochondrial remnant organelles of Giardia function in iron-sulphur protein maturation. Nature 426 172 176

9. van den BoogaartP

SamalloJ

AgsteribbeE

1982 Similar genes for a mitochondrial ATPase subunit in the nuclear and mitochondrial genomes of Neurospora crassa. Nature 298 187 189

10. EllisJ

1982 Promiscuous DNA–chloroplast genes inside plant mitochondria. Nature 299 678 679

11. LopezJV

YuhkiN

MasudaR

ModiW

O'BrienSJ

1994 Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat. J Mol Evol 39 174 190

12. GiampieriC

CenturelliM

BonafeM

OlivieriF

CardelliM

2004 A novel mitochondrial DNA-like sequence insertion polymorphism in Intron I of the FOXO1A gene. Gene 327 215 219

13. WilliamsST

KnowltonN

2001 Mitochondrial pseudogenes are pervasive and often insidious in the snapping shrimp genus Alpheus. Mol Biol Evol 18 1484 1493

14. YuanJD

ShiJX

MengGX

AnLG

HuGX

1999 Nuclear pseudogenes of mitochondrial DNA as a variable part of the human genome. Cell Res 9 281 290

15. BlanchardJL

SchmidtGW

1995 Pervasive migration of organellar DNA to the nucleus in plants. J Mol Evol 41 397 406

16. BlanchardJL

SchmidtGW

1996 Mitochondrial DNA migration events in yeast and humans: integration by a common end-joining mechanism and alternative perspectives on nucleotide substitution patterns. Mol Biol Evol 13 893

17. BensassonD

ZhangD

HartlDL

HewittGM

2001 Mitochondrial pseudogenes: evolution's misplaced witnesses. Trends Ecol Evol 16 314 321

18. MourierT

HansenAJ

WillerslevE

ArctanderP

2001 The Human Genome Project reveals a continuous transfer of large mitochondrial fragments to the nucleus. Mol Biol Evol 18 1833 1837

19. TourmenY

BarisO

DessenP

JacquesC

MalthieryY

2002 Structure and chromosomal distribution of human mitochondrial pseudogenes. Genomics 80 71 77

20. WoischnikM

MoraesCT

2002 Pattern of organization of human mitochondrial pseudogenes in the nuclear genome. Genome Res 12 885 893

21. Hazkani-CovoE

GraurD

2007 A comparative analysis of numt evolution in human and chimpanzee. Mol Biol Evol 24 13 18

22. Hazkani-CovoE

SorekR

GraurD

2003 Evolutionary dynamics of large numts in the human genome: rarity of independent insertions and abundance of post-insertion duplications. J Mol Evol 56 169 174

23. BensassonD

FeldmanMW

PetrovDA

2003 Rates of DNA duplication and mitochondrial DNA insertion in the human genome. J Mol Evol 57 343 354

24. BrownWM

GeorgeMJr

WilsonAC

1979 Rapid evolution of animal mitochondrial DNA. Proc Natl Acad Sci USA 76 1967 1971

25. BrownWM

PragerEM

WangA

WilsonAC

1982 Mitochondrial DNA sequences of primates: tempo and mode of evolution. J Mol Evol 18 225 239

26. Haag-LiautardC

CoffeyN

HouleD

LynchM

CharlesworthB

2008 Direct estimation of the mitochondrial DNA mutation rate in Drosophila melanogaster. PLoS Biol 6 e204

27. PernaNT

KocherTD

1996 Mitochondrial DNA: molecular fossils in the nucleus. Curr Biol 6 128 129

28. ZhangDX

HewittGM

1996 Nuclear integrations: Challenges for mitochondrial DNA markers. Trends Ecol Evol 11 247 251

29. LeisterD

2005 Origin, evolution and genetic effects of nuclear insertions of organelle DNA. Trends Genet 21 655 663

30. RicchettiM

TekaiaF

DujonB

2004 Continued colonization of the human genome by mitochondrial DNA. PLoS Biol 2 E273

31. Hazkani-CovoE

2009 Mitochondrial insertions into primate nuclear genomes suggest the use of numts as a tool for phylogeny. Mol Biol Evol 26 2175 2179

32. ChenJM

ChuzhanovaN

StensonPD

FerecC

CooperDN

2005 Meta-analysis of gross insertions causing human genetic disease: novel mutational mechanisms and the role of replication slippage. Hum Mutat 25 207 221

33. Willett-BrozickJE

SavulSA

RicheyLE

BaysalBE

2001 Germ line insertion of mtDNA at the breakpoint junction of a reciprocal constitutional translocation. Hum Genet 109 216 223

34. BorensztajnK

ChafaO

Alhenc-GelasM

SalhaS

ReghisA

2002 Characterization of two novel splice site mutations in human factor VII gene causing severe plasma factor VII deficiency and bleeding diathesis. Br J Haematol 117 168 171

35. TurnerC

KilloranC

ThomasNS

RosenbergM

ChuzhanovaNA

2003 Human genetic disease caused by de novo mitochondrial-nuclear DNA transfer. Hum Genet 112 303 309

36. GoldinE

StahlS

CooneyAM

KaneskiCR

GuptaS

2004 Transfer of a mitochondrial DNA fragment to MCOLN1 causes an inherited case of mucolipidosis IV. Hum Mutat 24 460 465

37. AhmedZM

SmithTN

RiazuddinS

MakishimaT

GhoshM

2002 Nonsyndromic recessive deafness DFNB18 and Usher syndrome type IC are allelic mutations of USHIC. Hum Genet 110 527 531

38. SacerdotC

CasaregolaS

LafontaineI

TekaiaF

DujonB

2008 Promiscuous DNA in the nuclear genomes of hemiascomycetous yeasts. FEMS Yeast Res 8 846 857

39. TriantDA

DeWoodyJA

2008 Molecular analyses of mitochondrial pseudogenes within the nuclear genome of arvicoline rodents. Genetica 132 21 33

40. NoutsosC

RichlyE

LeisterD

2005 Generation and evolutionary fate of insertions of organelle DNA in the nuclear genomes of flowering plants. Genome Res 15 616 628

41. PamiloP

ViljakainenL

VihavainenA

2007 Exceptionally high density of NUMTs in the honeybee genome. Mol Biol Evol 24 1340 1346

42. BehuraSK

2007 Analysis of nuclear copies of mitochondrial sequences in honeybee (Apis mellifera) genome. Mol Biol Evol 24 1492 1505

43. BensassonD

PetrovDA

ZhangDX

HartlDL

HewittGM

2001 Genomic gigantism: DNA loss is slow in mountain grasshoppers. Mol Biol Evol 18 246 253

44. RichlyE

LeisterD

2004 NUMTs in sequenced eukaryotic genomes. Mol Biol Evol 21 1081 1084

45. StuparRM

LillyJW

TownCD

ChengZ

KaulS

2001 Complex mtDNA constitutes an approximate 620-kb insertion on Arabidopsis thaliana chromosome 2: implication of potential sequencing errors caused by large-unit repeats. Proc Natl Acad Sci USA 98 5099 5103

46. MartinW

2003 Gene transfer from organelles to the nucleus: frequent and in big chunks. Proc Natl Acad Sci USA 100 8612 8614

47. AntunesA

PontiusJ

RamosMJ

O'BrienSJ

JohnsonWE

2007 Mitochondrial introgressions into the nuclear genome of the domestic cat. J Hered 98 414 420

48. ThorsnessPE

FoxTD

1990 Escape of DNA from mitochondria to the nucleus in Saccharomyces cerevisiae. Nature 346 376 379

49. SchiestlRH

DominskaM

PetesTD

1993 Transformation of Saccharomyces cerevisiae with nonhomologous DNA: illegitimate integration of transforming DNA into yeast chromosomes and in vivo ligation of transforming DNA to mitochondrial DNA sequences. Mol Cell Biol 13 2697 2705

50. ThorsnessPE

WeberER

1996 Escape and migration of nucleic acids between chloroplasts, mitochondria, and the nucleus. Int Rev Cytol 165 207 234

51. ShaferKS

HanekampT

WhiteKH

ThorsnessPE

1999 Mechanisms of mitochondrial DNA escape to the nucleus in the yeast Saccharomyces cerevisiae. Curr Genet 36 183 194

52. ParkS

HanekampT

ThorsnessMK

ThorsnessPE

2006 Yme2p is a mediator of nucleoid structure and number in mitochondria of the yeast Saccharomyces cerevisiae. Curr Genet 50 173 182

53. CampbellCL

ThorsnessPE

1998 Escape of mitochondrial DNA to the nucleus in yme1 yeast is mediated by vacuolar-dependent turnover of abnormal mitochondrial compartments. J Cell Sci 111 2455 2464

54. PriaultM

SalinB

SchaefferJ

ValletteFM

di RagoJP

2005 Impairing the bioenergetic status and the biogenesis of mitochondria triggers mitophagy in yeast. Cell Death Differ 12 1613 1621

55. AbeliovichH

2007 Mitophagy: the life-or-death dichotomy includes yeast. Autophagy 3 275 277

56. MotaM

1963 Electron microscope study of relationship between nucleus and mitochondria in Chlorophytum capense (L.) Kuntze. Cytologia (Tokyo) 28 409 416

57. JensenH

EngedalH

SaetersdalTS

1976 Ultrastructure of mitochondria-containing nuclei in human myocardial cells. Virchows Archiv B Cell Pathology Zell-pathologie 21 1 12

58. ListerDL

BatemanJM

PurtonS

HoweCJ

2003 DNA transfer from chloroplast to nucleus is much rarer in Chlamydomonas than in tobacco. Gene 316 33 38

59. HuangCY

GrunheitN

AhmadinejadN

TimmisJN

MartinW

2005 Mutational decay and age of chloroplast and mitochondrial genomes transferred recently to angiosperm nuclear chromosomes. Plant Physiol 138 1723 1733

60. HenzeK

MartinW

2001 How do mitochondrial genes get into the nucleus? Trends Genet 17 383 387

61. Hazkani-CovoE

CovoS

2008 Numt-mediated double-strand break repair mitigates deletions during primate genome evolution. PLoS Genet 4 e1000237

62. LinY

WaldmanAS

2001 Capture of DNA sequences at double-strand breaks in mammalian chromosomes. Genetics 158 1665 1674

63. RamadanK

MagaG

ShevelevIV

VillaniG

BlancoL

2003 Human DNA polymerase lambda possesses terminal deoxyribonucleotidyl transferase activity and can elongate RNA primers: implications for novel functions. J Mol Biol 328 63 72

64. AllenJF

1993 Control of gene expression by redox potential and the requirement for chloroplast and mitochondrial genomes. J Theor Biol 165 609 631

65. PuthiyaveetilS

KavanaghTA

CainP

SullivanJA

NewellCA

2008 The ancestral symbiont sensor kinase CSK links photosynthesis with gene expression in chloroplasts. Proc Natl Acad Sci USA 105 10061 10066

66. LakeJA

2007 Disappearing act. Nature 446 983

67. MartinW

KooninEV

2006 Introns and the origin of nucleus-cytosol compartmentalization. Nature 440 41 45

68. CoxCJ

FosterPG

HirtRP

HarrisSR

EmbleyTM

2008 The archaebacterial origin of eukaryotes. Proc Natl Acad Sci USA 105 20356 20361

69. RichlyE

LeisterD

2004 NUPTs in sequenced eukaryotes and their genomic organization in relation to NUMTs. Mol Biol Evol 21 1972 1980

70. KellerI

BensassonD

NicholsRA

2007 Transition-transversion bias is not universal: a counter example from grasshopper pseudogenes. PLoS Genet 3 e22

71. TriantDA

DeWoodyJA

2007 Extensive mitochondrial DNA transfer in a rapidly evolving rodent has been mediated by independent insertion events and by duplications. Gene 401 61 70

72. SheppardAE

TimmisJN

2009 Instability of plastid DNA in the nuclear genome. PLoS Genet 5 e1000323

73. KaranjawalaZE

MurphyN

HintonDR

HsiehCL

LieberMR

2002 Oxygen metabolism causes chromosome breaks and is associated with the neuronal apoptosis observed in DNA double-strand break repair mutants. Curr Biol 12 397 402

74. KarthikeyanG

ResnickMA

2005 Impact of mitochondria on nuclear genome stability. DNA Repair (Amst) 4 141 148

75. StorchovaZ

BrenemanA

CandeJ

DunnJ

BurbankK

2006 Genome-wide genetic analysis of polyploidy in yeast. Nature 443 541 547

76. AguileraA

2002 The connection between transcription and genomic instability. EMBO J 21 195 201

77. PetrovDA

SangsterTA

JohnstonJS

HartlDL

ShawKL

2000 Evidence for DNA loss as a determinant of genome size. Science 287 1060 1062

78. PetrovDA

HartlDL

1998 High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups. Mol Biol Evol 15 293 302

79. KidwellMG

2002 Transposable elements and the evolution of genome size in eukaryotes. Genetica 115 49 63

80. KirikA

SalomonS

PuchtaH

2000 Species-specific double-strand break repair and genome evolution in plants. EMBO J 19 5562 5566

81. AllenJF

2003 The function of genomes in bioenergetic organelles. Philos Trans R Soc Lond B Biol Sci 358 19 37

82. YaoYG

KongQP

SalasA

BandeltHJ

2008 Pseudomitochondrial genome haunts disease studies. J Med Genet 45 769 772

83. WallaceDC

StugardC

MurdockD

SchurrT

BrownMD

1997 Ancient mtDNA sequences in the human nuclear genome: a potential source of errors in identifying pathogenic mutations. Proc Natl Acad Sci USA 94 14900 14905

84. ThangarajK

JoshiMB

ReddyAG

RasalkarAA

SinghL

2003 Sperm mitochondrial mutations as a cause of low sperm motility. J Androl 24 388 392

85. BiswasNK

DeyB

MajumderPP

2007 Using HapMap data: a cautionary note. Eur J Hum Genet 15 246 249

86. BlaxterML

2004 The promise of a DNA taxonomy. Philos Trans R Soc Lond B Biol Sci 359 669 679

87. LorenzJG

JacksonWE

BeckJC

HannerR

2005 The problems and promise of DNA barcodes for species diagnosis of primate biomaterials. Philos Trans R Soc Lond B Biol Sci 360 1869 1877

88. SorensonMD

QuinnTW

1998 Numts: a challenge for avian systematics and population biology. Auk 115 214 221

89. van der KuylAC

KuikenCL

DekkerJT

PerizoniusWR

GoudsmitJ

1995 Nuclear counterparts of the cytoplasmic mitochondrial 12S rRNA gene: a problem of ancient DNA and molecular phylogenies. J Mol Evol 40 652 657

90. ThalmannO

HeblerJ

PoinarHN

PaaboS

VigilantL

2004 Unreliable mtDNA data due to nuclear insertions: a cautionary tale from analysis of humans and other great apes. Mol Ecol 13 321 335

91. SongH

BuhayJE

WhitingMF

CrandallKA

2008 Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified. Proc Natl Acad Sci USA 105 13486 13491

92. WoodwardSR

WeyandNJ

BunnellM

1994 DNA sequence from Cretaceous period bone fragments. Science 266 1229 1232

93. ColluraRV

StewartCB

1995 Insertions and duplications of mtDNA in the nuclear genomes of Old World monkeys and hominoids. Nature 378 485 489

94. ZischlerH

HossM

HandtO

von HaeselerA

van der KuylAC

1995 Detecting dinosaur DNA. Science 268 1192 1193

95. GoremykinVV

SalaminiF

VelascoR

ViolaR

2009 Mitochondrial DNA of Vitis vinifera and the issue of rampant horizontal gene transfer. Mol Biol Evol 26 99 110