Pack-Mutator-like transposable elements (Pack-MULEs) induce directional modification of genes through biased insertion and DNA acquisition

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue 4, 2011, Pages 1537-1542

  Jiang, Ning ^a   Ferguson, Ann A ^a   Slotkin, R Keith ^b   Lisch, Damon ^c  

^a MICHIGAN STATE UNIVERSITY   (United States)

^b OHIO STATE UNIVERSITY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Gene duplication; Gene modification

Indexed keywords

ARTICLE; DNA MODIFICATION; EXON; GC RICH SEQUENCE; GENE INSERTION; GENE STRUCTURE; GRASS; MAIZE; NONHUMAN; NUCLEOTIDE SEQUENCE; PACK MUTATOR LIKE TRANSPOSABLE ELEMENT GENE; PRIORITY JOURNAL; RICE; TRANSPOSON;

ARABIDOPSIS; BASE SEQUENCE; CHROMOSOMES, PLANT; DNA TRANSPOSABLE ELEMENTS; DNA, PLANT; GC RICH SEQUENCE; GENES, PLANT; GENOME, PLANT; MUTAGENESIS, INSERTIONAL; ORYZA SATIVA; PLANT PROTEINS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; ZEA MAYS;

ARABIDOPSIS; DICOTYLEDONEAE; LILIOPSIDA; POACEAE;

EID: 79952152599     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1010814108     Document Type: Article

References (46)

1. Bennetzen JL, Kellogg EA (1997) Do plants have a one-way ticket to genomic obesity? Plant Cell 9:1509-1514.
2. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815.
3. Schnable PS, et al. (2009) The B73 maize genome: Complexity, diversity, and dynamics. Science 326:1112-1115.
4. Jiang N, Bao Z, Zhang X, Eddy SR, Wessler SR (2004) Pack-MULE transposable elements mediate gene evolution in plants. Nature 431:569-573. (Pubitemid 39336337)
5. Talbert LE, Chandler VL (1988) Characterization of a highly conserved sequence related to Mutator transposable elements in maize. Mol Biol Evol 5:519-529.
6. Walbot V, Rudenko GN (2002) MuDR/Mu Transposons of Maize Mobile DNA II, eds Craig N, Craigie R, Gellert M, Lambowitz A (America Society of Microbiology Press, Washington, DC), pp 533-564.
7. Lisch D (2005) Pack-MULEs: Theft on a massive scale. Bioessays 27:353-355.
8. Juretic N, Hoen DR, Huynh ML, Harrison PM, Bureau TE (2005) The evolutionary fate of MULE-mediated duplications of host gene fragments in rice. Genome Res 15:1292-1297. (Pubitemid 41247920)
9. Holligan D, Zhang X, Jiang N, Pritham EJ, Wessler SR (2006) The transposable element landscape of the model legume Lotus japonicus. Genetics 174:2215-2228.
10. Hanada K, et al. (2009) The functional role of pack-MULEs in rice inferred from purifying selection and expression profile. Plant Cell 21:25-38.
11. Carels N, Bernardi G (2000) Two classes of genes in plants. Genetics 154:1819-1825. (Pubitemid 30211260)
12. Wong GK, et al. (2002) Compositional gradients in Gramineae genes. Genome Res 12:851-856. (Pubitemid 34662279)
13. Glémin S, Bazin E, Charlesworth D (2006) Impact of mating systems on patterns of sequence polymorphism in flowering plants. Proc Biol Sci 273:3011-3019. (Pubitemid 46622432)
14. Tatarinova TV, Alexandrov NN, Bouck JB, Feldmann KA (2010) GC3 biology in corn, rice, sorghum and other grasses. BMC Genomics 11:308.
15. Gouy M, Gautier C (1982) Codon usage in bacteria: Correlation with gene expressivity. Nucleic Acids Res 10:7055-7074.
16. Yu Z, Wright SI, Bureau TE (2000) Mutator-like elements in Arabidopsis thaliana: Structure, diversity and evolution. Genetics 156:2019-2031. (Pubitemid 32001260)
17. Dietrich CR, et al. (2002) Maize Mu transposons are targeted to the 5′ untranslated region of the gl8 gene and sequences flanking Mu target-site duplications exhibit nonrandom nucleotide composition throughout the genome. Genetics 160:697-716. (Pubitemid 34194541)
18. Lisch D (2002) Mutator transposons. Trends Plant Sci 7:498-504.
19. Slotkin RK, et al. (2009) Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136:461-472.
20. Robbins ML, Sekhon RS, Meeley R, Chopra SA (2008) A Mutator transposon insertion is associated with ectopic expression of a tandemly repeated multicopy Myb gene pericarp color1 of maize. Genetics 178:1859-1874.
21. Liu S, et al. (2009) Mu transposon insertion sites and meiotic recombination events colocalize with epigenetic marks for open chromatin across the maize genome. PLoS Genet 5:e1000733.
22. Rice Chromosomes 11 and 12 Sequencing Consortia (2005) The sequence of rice chromosome 11 and 12, rich in disease resistance genes and recent gene duplication. BMC Biol 3:20.
23. Bennetzen JL, Springer PS, Cresse AD, Hendrickx M (1993) Specificity and regulation of the Mutator transposable element system in maize. Crit Rev Plant Sci 12:57-95.
24. Ohno S (1970) Evolution by Gene Duplication (Springer-Verlag, New York).
25. Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155.
26. Zhang J (2003) Evolution by gene duplication: An update. Trends Ecol Evol 18:292-298.
27. Kazazian HH, Jr. (2004) Mobile elements: Drivers of genome evolution. Science 303:1626-1632.
28. Bennetzen JL (2005) Transposable elements, gene creation and genome rearrangement in flowering plants. Curr Opin Genet Dev 15:621-627.
29. Feschotte C, Pritham EJ (2007) DNA transposons and the evolution of eukaryotic genomes. Annu Rev Genet 41:331-368.
30. Moran JV, DeBerardinis RJ, Kazazian HH, Jr. (1999) Exon shuffling by L1 retrotransposition. Science 283:1530-1534.
31. Pickeral OK, Makałowski W, Boguski MS, Boeke JD (2000) Frequent human genomic DNA transduction driven by LINE-1 retrotransposition. Genome Res 10:411-415. (Pubitemid 30259072)
32. Morgante M, et al. (2005) Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat Genet 37:997-1002. (Pubitemid 43086159)
33. Yang L, Bennetzen JL (2009) Distribution, diversity, evolution, and survival of Helitrons in the maize genome. Proc Natl Acad Sci USA 106:19922-19927.
34. Du C, Fefelova N, Caronna J, He L, Dooner HK (2009) The polychromatic Helitron landscape of the maize genome. Proc Natl Acad Sci USA 106:19916-19921.
35. Bennetzen JL, Springer PS (1994) The generation of Mutator transposable element subfamilies in maize. Theor Appl Genet 87:657-667.
36. Engels WR, Johnson-Schlitz DM, Eggleston WB, Sved J (1990) High-frequency P element loss in Drosophila is homolog dependent. Cell 62:515-525.
37. Yamashita S, Takano-Shimizu T, Kitamura K, Mikami T, Kishima Y (1999) Resistance to gap repair of the transposon Tam3 in Antirrhinum majus: A role of the end regions. Genetics 153:1899-1908.
38. Wang HC, Hickey DA (2007) Rapid divergence of codon usage patterns within the rice genome. BMC Evol Biol 7 (Suppl 1):S6.
39. Duret L, Galtier N (2009) Biased gene conversion and the evolution of mammalian genomic landscapes. Annu Rev Genomics Hum Genet 10:285-311.
40. Fullerton SM, Bernardo Carvalho A, Clark AG (2001) Local rates of recombination are positively correlated with GC content in the humangenome. Mol Biol Evol 18:1139-1142. (Pubitemid 32520487)
41. Birdsell JA (2002) Integrating genomics, bioinformatics, and classical genetics to study the effects of recombination on genome evolution. Mol Biol Evol 19:1181-1197.
42. Kudla G, Lipinski L, Caffin F, Helwak A, Zylicz M (2006) High guanine and cytosine content increases mRNA levels in mammalian cells. PLoS Biol 4:e180.
43. Kalisz S, Purugganan MD (2004) Epialleles via DNA methylation: Consequences for plant evolution. Trends Ecol Evol 19:309-314. (Pubitemid 38729832)
44. Chan SW, et al. (2006) RNAi, DRD1, and histone methylation actively target developmentally important non-CG DNA methylation in Arabidopsis. PLoS Genet 2:e83.
45. Law JA, Jacobsen SE (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11:204-220.
46. Vinogradov AE (2003) DNA helix: The importance of being GC-rich. Nucleic Acids Res 31:1838-1844.