A Moveable feast: An introduction to mobile DNA

Mobile DNA III

Volumn , Issue , 2015, Pages 3-39

  Craig, Nancy L ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Active gene assembly; Changing cell surface proteins; Homing endonucleases; Host immune defense; Mobile DNA; Moveable feast; Saccharomyces cerevisiae; Switching mating type; Targeted dna breaks lead

Indexed keywords

EID: 85103344918     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1128/9781555819217.ch1     Document Type: Chapter

References (48)

1. Stoddard B. 2014. Homing endonucleases from mobile group I introns: discovery to genome engineering. Mobile DNA 5:7.
2. Chaumeil J, Skok J. 2013. A new take on v(d)j recombination: transcription driven nuclear and chromatin reorganization in RAG-mediated cleavage. Front Immunol 4:423.
3. Kim M, Lapkouski M, Yang W, Gellert M. 2015. Crystal structure of the V(D)J recombinase RAG1-RAG2. Nature 518:507-511.
4. Jones J, Gellert M. 2004. The taming of a transposon: V(D)J recombination and the immune system. Immunol Rev 200:233-248.
5. Zhou L, Mitra R, Atkinson P, Hickman A, Dyda F, Craig NL. 2004. Transposition of hAT elements links transposable elements and V(D)J recombination. Nature 432:995-1001.
6. Hickman AB, Ewis H, Li X, Knapp J, Laver T, Doss A-L, Atkinson P, Craig NL, Dyda F. 2014. A hAT DNA transposase with an unusual subunit organization to bind long asymmetric ends. Cell 158:353-367.
7. Hencken C, Li X, Craig NL. 2012. Functional characterization a transposon with a RAG connection. Nat Struct Mol Biol 19:834-836.
8. Kapitonov V, Jurka J. 2005. RAG1 core and V(D)J recombination signal sequnces were derived from Transib transposons. PLoS Biol 3:e181.
9. Bracht J, Fang W, Goldman A, Dolzhenko E, Stein E, Landweber L. 2013. Genomes on the edge: programmed genome instability in ciliates. Cell 152:406-416.
10. Streit A. 2012. Silencing by throwing away: a role for chromatin diminution. Dev Cell 23:918-919.
11. Madireddi M, Coyne R, Smothers J, Mickey K, Yao M, Allis C. 1996. Pdd1p, a novel chromodomain-containing protein, links heterochromatin assembly and DNA elimination in Tetrahymena. Cell 87:75-84.
12. Thomas J, Phillips C, Baker R, Pritham E. 2014. Rollingcircle transposons catalyze genomic innovation in a mammalian lineage. Genome Biol Evol 6:2595-2610.
13. Ferguson A, Jiang N. 2011. Pack-MULEs: recycling and reshaping genes through GC-biased acquisition. Mob Genet Elements 1:135-138.
14. Feng X, Colloms S. 2007. In vitro transposition of ISY100, a bacterial insertion sequence belonging to the Tc1/mariner family. Mol Microbiol 65:1432-1443.
15. Krupovic M, Makarova K, Forterre P, Prangishvili D, Koonin E. 2014. Casposons: a new superfamily of selfsynthesizing DNA transposons at the origin of prokaryotic CRISPR-Cas immunity. BMC Biol 12:36.
16. van der Oost J, Westra E, Jackson R, Wiedenheft B. 2014. Unravelling the structural and mechanistic basis of CRISPR-Cas systems. Nat Rev Microbiol 12:479-492.
17. Nunez J, Lee A, Engelman A, Doudna J. 2015. Integrasemediated spacer acquisition during CRISPR-Cas adaptive immunity. Nature 159:193-198.
18. Nunez JK, Kranzusch P, Noeske J, Wright A, Davies CW, Doudna J. 2014. Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity. Nat Struct Mol Biol 21:528-534.
19. Krupovic M, Koonin EV. 2015. Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution. Nat Rev Microbiol 13:105-115.
20. Yuan Y, Wessler S. 2011. The catalytic domain of all eukaryotic cut-and-paste transposase superfamilies. Proc Natl Acad Sci U S A 108:7884-7889.
21. Syvanen M, Hopkins JD, Clements M. 1982. A new class of mutants in DNA polymerase I that affects gene transposition. J Mol Biol 158:203-212.
22. Han M, Xu H, Zhang H, Feschotte C, Zhang Z. 2014. Spy: a new group of eukaryotic DNA transposons without target site duplications. Genome Biol Evol 6:1748-1757.
23. Harshey R. 2012. The Mu story: how a maverick phage moved the field forward. Mobile DNA 3:21.
24. Montano S, Pigli Y, Rice P. 2012. The mu transpososome structure sheds light on DDE recombinase evolution. Nature 491:413-417.
25. Garcillan-Barcia M, Bernales I, Mendiola M, de la Cruz F. 2002. IS91 Rolling-Circle Transposition, p 891-904. In Craig NL, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington DC.
26. Mitra R, Li X, Kapusta A, Mayhew D, Mitra R, Feschotte C, Craig NL. 2013. Functional characterization of piggyBat from the bat Myotis lucifugus unveils the first active mammalian DNA transposon. Proc Natl Acad Sci U S A 110:234-239.
27. Nunes-Duby S, Azaro M, Landy A. 1995. Swapping DNA strands and sensing homology without branch migration in lambda site-specific recombination. Curr Biol 5:139-148.
28. Birling MC, Gofflot F, Warot X. 2009. Site-specific recombinases for manipulation of the mouse genome. Methods Mol Biol 561:245-263.
29. Rutherford K, Van Duyne G. 2014. The ins and outs of serine integrase site-specific recombination. Curr Opin Struct Biol 24:125-131.
30. Rutherford K, Yuan P, Perry K, Sharp R, Van Duyne G. 2013. Attachment site recognition and regulation of directionality by the serine integrases. Nucleic Acids Res 41:8341-8356.
31. Roberts A, Mullany P. 2011. Tn916-like genetic elements: a diverse group of modular mobile elements conferring antibiotic resistance. FEMS Microbiol Rev 35:856-871.
32. Das B, Martinez E, Midonet C, Barre F. 2013. Integrative mobile elements exploiting Xer recombination. Trends Microbiol 21:23-30.
33. Val M, Bouvier M, Campos J, Sherratt D, Cornet F, Mazel D, Barre F. 2005. The single-stranded genome of phage CTX is the form used for integration into the genome of Vibrio cholerae. Mol Cell 19:559-566.
34. Goodwin T, Butler M, Poulter R. 2003. Cryptons: a group of tyrosine-recombinase-encoding DNA transposons from pathogenic fungi. Microbiology 149:3099-3109.
35. Kojima K, Jurka J. 2011. Crypton transposons: identification of new diverse families and ancient domestication events. Mobile DNA 2:12.
36. Doak T, Witherspoon D, Jahn C, Herrick G. 2003. Selection on the genes of Euplotes crassus Tec1 and Tec2 transposons: evolutionary appearance of a programmed frameshift in a Tec2 gene encoding a tyrosine family sitespecific recombinase. Eukaryot Cell 2:95-102.
37. Jacobs M, Sanchez-Blanco A, Katz L, Klobutcher L. 2003. Tec3, a new developmentally eliminated DNA element in Euplotes crassus. Eukaryot Cell 2:103-114.
38. Kazazian H Jr. 2014. Processed pseudogene insertions in somatic cells. Mobile DNA 5:20.
39. Richardson S, Salvador-Palomeque C, Faulkner G. 2014. Diversity through duplication: whole-genome sequencing reveals novel gene retrocopies in the human population. Bioessays 36:475-481.
40. Coros C, Piazza C, Chalamcharla V, Belfort M. 2008. A mutant screen reveals RNase E as a silencer of group II intron retromobility in Escherichia coli. RNA 14:2634-2644.
41. Coros C, Piazza C, Chalamcharla V, Smith D, Belfort M. 2009. Global regulators orchestrate group II intron retromobility. Mol Cell 34:250-256.
42. Evgen'ev MB, Zelentsova H, Shostak N, Kozitsina M, Barskyi V, Lankenau DH, Corces VG. 1997. Penelope, a new family of transposable elements and its possible role in hybrid dysgenesis in Drosophila virilis. Proc Natl Acad Sci U S A 94:196-201.
43. Pyatkov K, Arkhipova I, Malkova N, Finnegan D, Evgen'ev M. 2004. Reverse transcriptase and endonuclease activities encoded by Penelope-like retroelements. Proc Natl Acad Sci U S A 101:14719-14724.
44. Cervera A, De la Pena M. 2014. Eukaryotic penelopelike retroelements encode hammerhead ribozyme motifs. Mol Biol Evol 31:2941-2947.
45. Gladyshev E, Arkhipova I. 2011. A widespread class of reverse transcriptase-related cellular genes. Proc Natl Acad Sci U S A 108:20311-20316.
46. Curcio M, Belfort M. 1996. Retrohoming: cDNAmediated mobility of group II introns requires a catalytic RNA. Cell 84:9-12.
47. Lampson B, Inouye M, Inouye S. 2005. Retrons, msDNA, and the bacterial genome. Cytogenet Genome Res 110:491-499.
48. Curcio MJ, Belfort M. 2007. The beginning of the end: links between ancient retroelements and modern telomerases. Proc Natl Acad U S A 104:9107-9108.