Selected Transposon Papers

Transposon Annotation

Transposon detection and clustering algorithms

• Bergman CM, Quesneville H.  Discovering and detecting transposable elements in genome sequences.  Brief Bioinform. 2007 Oct 10;.
  • Review of computational methods to study transposable elements in genomes
  • An up-to-date compendium of TE bioinformatics tools from this review can be found here

• Caspi A, Pachter L.  Identification of transposable elements using multiple alignments of related genomes.  Genome Res. 2006 Feb;16(2):260-70. Epub 2005 Dec 14.
  • Transposons are identifiable as big insertions in multi-genome alignments

• Bao Z, Eddy SR.  Automated de novo identification of repeat sequence families in sequenced genomes.  Genome Res. 2002 Aug;12(8):1269-76.
  • Transposon boundaries correspond to sharp changes in the density of BLAST hits

• Bejerano G, Haussler D, Blanchette M.  Into the heart of darkness: large-scale clustering of human non-coding DNA.  Bioinformatics. 2004 Aug 4;20 Suppl 1:i40-8.
  • Start with a graph whose nodes are all putative transposons & edges correspond to BLAST matches
  • Apply the following heuristic to break up this graph:
    • Split any node whose set of neighbors can be partitioned into two dissimilar subsets
    • Iterate, reducing graph to a set of densely-connected subgraphs

• Edgar RC, Myers EW.  PILER: identification and classification of genomic repeats.  Bioinformatics. 2005 Jun;21 Suppl 1:i152-8.
  • Edgar: an "intact instance" of a transposon has multiple BLAST hits sharing exact same coords (i.e. remote homologues that are globally alignable)

• Andrieu O, Fiston AS, Anxolabehere D, Quesneville H.  Detection of transposable elements by their compositional bias.  BMC Bioinformatics. 2004 Jul 13;5:94.
  • Nucleotide composition
  • c.f. irreversible substitution models: Hamady M, Betterton MD, Knight R.  Using the nucleotide substitution rate matrix to detect horizontal gene transfer.  BMC Bioinformatics. 2006 Oct 26;7:476.

• Quesneville H, Bergman CM, Andrieu O, Autard D, Nouaud D, Ashburner M, Anxolabehere D.  Combined evidence annotation of transposable elements in genome sequences.  PLoS Comput Biol. 2005 Jul;1(2):166-75. Epub 2005 Jul 29.
  • Combining multiple lines of evidence

• Li R et al.  ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun.  PLoS Comput Biol. 2005 Sep;1(4):e43. Epub 2005 Sep 23.
  • Transposon prediction directly from shotgun reads

• Rho M, Choi JH, Kim S, Lynch M, Tang H.  De novo identification of LTR retrotransposons in eukaryotic genomes.  BMC Genomics. 2007 Apr 3;8:90.
  • LTR transposon identification

Repeats, copy languages and computational linguistics

• McCarthy EM, McDonald JF.  LTR_STRUC: a novel search and identification program for LTR retrotransposons.  Bioinformatics. 2003 Feb 12;19(3):362-7.
  • Profiling LTR transposons

• Mildly context-sensitive grammar formalisms (Kallmeyer, course notes)
  • Tree-adjoining grammars (Joshi and Schabes, 1997)
  • Context-sensitive HMMs (Yoon and Vaidyanathan)

• Conditional random fields (Hanna Wallach) (PDF)
  • Conditional Random Fields: Probabilistic Models for Segmenting and Labeling Sequence Data (Lafferty, McCallum and Pereira)
  • Sato K, Sakakibara Y.  RNA secondary structural alignment with conditional random fields.  Bioinformatics. 2005 Sep 1;21 Suppl 2:ii237-42.
  • Repetitive element segmentation and homology assignment (Anat Caspi, 2005)

Transposon Evolution

Transposons and their hosts

• Mobile DNA II book (Craig et al)

• Malik HS, Henikoff S, Eickbush TH.  Poised for contagion: evolutionary origins of the infectious abilities of invertebrate retroviruses.  Genome Res. 2000 Sep;10(9):1307-18.
  • Malik HS, Eickbush TH.  Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses.  Genome Res. 2001 Jul;11(7):1187-97.
• Sijen T, Plasterk RH.  Transposon silencing in the Caenorhabditis elegans germ line by natural RNAi.  Nature. 2003 Nov 20;426(6964):310-4.
• Smit AF.  Interspersed repeats and other mementos of transposable elements in mammalian genomes.  Curr Opin Genet Dev. 1999 Dec;9(6):657-63.

• Speculative piece in Nature: Did viruses invent DNA? (news feature, 2006)

• Abrusan G, Krambeck HJ.  Competition may determine the diversity of transposable elements.  Theor Popul Biol. 2006 Nov;70(3):364-75. Epub 2006 May 20.

Transposons catalyzing evolution

• Jones JM, Gellert M.  The taming of a transposon: V(D)J recombination and the immune system.  Immunol Rev. 2004 Aug;200:233-48.

• Bennetzen JL.  Transposable elements, gene creation and genome rearrangement in flowering plants.  Curr Opin Genet Dev. 2005 Dec;15(6):621-7. Epub 2005 Oct 10.
• Kazazian HH Jr.  Mobile elements: drivers of genome evolution.  Science. 2004 Mar 12;303(5664):1626-32.
• Ferrigno O, Virolle T, Djabari Z, Ortonne JP, White RJ, Aberdam D.  Transposable B2 SINE elements can provide mobile RNA polymerase II promoters.  Nat Genet. 2001 May;28(1):77-81.
• Bailey JA, Carrel L, Chakravarti A, Eichler EE.  Molecular evidence for a relationship between LINE-1 elements and X chromosome inactivation: the Lyon repeat hypothesis.  Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6634-9.
• Pardue ML.  Transposable elements: friends, foes, or merely fellow travelers?  Trends Genet. 2000 Apr;16(4):155-6.

Transposon Phylogeny

• Capy P, Vitalis R, Langin T, Higuet D, Bazin C.  Relationships between transposable elements based upon the integrase-transposase domains: is there a common ancestor?  J Mol Evol. 1996 Mar;42(3):359-68.

Transposon Population Genetics

Transposon population dynamics

• Charlesworth B, Langley CH.  The population genetics of Drosophila transposable elements.  Annu Rev Genet. 1989;23:251-87.
• Le Rouzic A, Deceliere G.  Models of the population genetics of transposable elements.  Genet Res. 2005 Jun;85(3):171-81.
• Le Rouzic A, Capy P.  Population genetics models of competition between transposable element subfamilies.  Genetics. 2006 Oct;174(2):785-93. Epub 2006 Aug 3.
• Weitz JS, Hartman H, Levin SA.  Coevolutionary arms races between bacteria and bacteriophage.  Proc Natl Acad Sci U S A. 2005 Jul 5;102(27):9535-40. Epub 2005 Jun 23.
• Rasgon JL, Gould F.  Transposable element insertion location bias and the dynamics of gene drive in mosquito populations.  Insect Mol Biol. 2005 Oct;14(5):493-500.

This section is clearly in dire need of some extra entries........ please feel free to add something... anything.... all you need is the pubmed ID... Ian Holmes, 26 Feb 06

Fruitfly Transposons

Transposons in Drosophila

• Bergman CM, Bensasson D.  Recent LTR retrotransposon insertion contrasts with waves of non-LTR insertion since speciation in Drosophila melanogaster.  Proc Natl Acad Sci U S A. 2007 Jul 3;104(27):11340-5. Epub 2007 Jun 25.
• Bergman CM, Quesneville H, Anxolabehere D, Ashburner M.  Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome.  Genome Biol. 2006;7(11):R112.
• Kaminker JS et al.  The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective.  Genome Biol. 2002;3(12):RESEARCH0084. Epub 2002 Dec 23.
• Vieira C, Lepetit D, Dumont S, Biemont C.  Wake up of transposable elements following Drosophila simulans worldwide colonization.  Mol Biol Evol. 1999 Sep;16(9):1251-5.
• Carareto CM, Kim W, Wojciechowski MF, O'Grady P, Prokchorova AV, Silva JC, Kidwell MG.  Testing transposable elements as genetic drive mechanisms using Drosophila P element constructs as a model system.  Genetica. 1997;101(1):13-33.

• Liao GC, Rehm EJ, Rubin GM.  Insertion site preferences of the P transposable element in Drosophila melanogaster.  Proc Natl Acad Sci U S A. 2000 Mar 28;97(7):3347-51.
• Linheiro RS, Bergman CM.  Testing the palindromic target site model for DNA transposon insertion using the Drosophila melanogaster P-element.  Nucleic Acids Res. 2008 Oct 1.

• Tc1/mariner and relatives
  • Transpositional mechanism
    • Vos JC, van Luenen HG, Plasterk RH.  Characterization of the Caenorhabditis elegans Tc1 transposase in vivo and in vitro.  Genes Dev. 1993 Jul;7(7A):1244-53.
    • Zhang L, Dawson A, Finnegan DJ.  DNA-binding activity and subunit interaction of the mariner transposase.  Nucleic Acids Res. 2001 Sep 1;29(17):3566-75.
    • Lipkow K, Buisine N, Lampe DJ, Chalmers R.  Early intermediates of mariner transposition: catalysis without synapsis of the transposon ends suggests a novel architecture of the synaptic complex.  Mol Cell Biol. 2004 Sep;24(18):8301-11.
    • Pietrokovski S, Henikoff S.  A helix-turn-helix DNA-binding motif predicted for transposases of DNA transposons.  Mol Gen Genet. 1997 May;254(6):689-95.
  • Homologues in Drosophila
    • Merriman PJ, Grimes CD, Ambroziak J, Hackett DA, Skinner P, Simmons MJ.  S elements: a family of Tc1-like transposons in the genome of Drosophila melanogaster.  Genetics. 1995 Dec;141(4):1425-38.
    • Arca B, Savakis C.  Distribution of the transposable element Minos in the genus Drosophila.  Genetica. 2000;108(3):263-7.
    • Metaxakis A, Oehler S, Klinakis A, Savakis C.  Minos as a genetic and genomic tool in Drosophila melanogaster.  Genetics. 2005 Oct;171(2):571-81. Epub 2005 Jun 21.
  • Homologues elsewhere
    • Feschotte C, Mouches C.  Evidence that a family of miniature inverted-repeat transposable elements (MITEs) from the Arabidopsis thaliana genome has arisen from a pogo-like DNA transposon.  Mol Biol Evol. 2000 May;17(5):730-7.
    • The D35E domain: Doak TG, Doerder FP, Jahn CL, Herrick G.  A proposed superfamily of transposase genes: transposon-like elements in ciliated protozoa and a common "D35E" motif.  Proc Natl Acad Sci U S A. 1994 Feb 1;91(3):942-6.
  • Historical interest
    • Brierley HL, Potter SS.  Distinct characteristics of loop sequences of two Drosophila foldback transposable elements.  Nucleic Acids Res. 1985 Jan 25;13(2):485-500.
    • Caizzi R, Caggese C, Pimpinelli S.  Bari-1, a new transposon-like family in Drosophila melanogaster with a unique heterochromatic organization.  Genetics. 1993 Feb;133(2):335-45.
  • Reviews
    • Hartl DL, Lohe AR, Lozovskaya ER.  Modern thoughts on an ancyent marinere: function, evolution, regulation.  Annu Rev Genet. 1997;31:337-58.
    • Plasterk RH, Izsvak Z, Ivics Z.  Resident aliens: the Tc1/mariner superfamily of transposable elements.  Trends Genet. 1999 Aug;15(8):326-32.

• Transposons & Piwi RNAs
  • Brennecke J, Aravin AA, Stark A, Dus M, Kellis M, Sachidanandam R, Hannon GJ.  Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila.  Cell. 2007 Mar 23;128(6):1089-103. Epub 2007 Mar 8.