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Alternative Ac/Ds Transposition and Chromosomal Rearrangements in Maize

This material is based upon work supported by the National Science Foundation under Awards 0110170, 0450243, and 0923826.

Background

Ac/Ds transposition: The maize Ac (Activator) and Ds (Dissociation) elements comprise a classical two component transposable element system of the hAT transposon family. The autonomous Ac element is 4565 bp in length, whereas the non-autonomous Ds elements vary in length and internal sequence composition. Ac and Ds elements share 11 bp terminal inverted repeat sequences (TIRs), and they also contain multiple copies of hexamer motifs (AAACGG or similar) located within 250 bp of the element termini. The Ac element produces a single predominant spliced mRNA which encodes a 102 kD transposase protein that could bind to the AAACGG hexamer motifs in the Ac/Ds subterminal regions. Although the exact mechanism of Ac/Ds transposition is unclear, evidence to date indicates that Ac/Ds elements transpose by a cut-and-paste mechanism; excision of Ac/Ds elements leaves a characteristic footprint (minor sequence changes) at the donor site, and reinsertion of the element generates a short sequence duplications flanking the element (target site duplication). The following animation shows the normal Ac element transposition process.

The maize p1 gene: The maize p1 gene regulates the synthesis of a red phlobaphene pigment in maize floral organs, including the pericarp (outermost layer of the kernel derived from the ovary wall) and the cob. The two-letter suffix of p1 indicates its expression in pericarp and cob; i.e., P1-rr specifies red pericarp and red cob, P1-wr specifies white pericarp and red cob, and p1-ww specifies white pericarp and white cob. The standard p1-vv allele described by Emerson conditions variegated pericarp and variegated cob. This p1-vv allele contains an Ac transposable element inserted in intron 2 of a P1-rr gene. Two p1 alleles are used here: The p1-vv9D9A allele contains an Ac element and a terminally deleted Ac element termed fAc (fractured Ac, 2039 bp of the Ac 3' end) inserted in intron 2 of P1-rr (see Sister chromatid transposition for structure); The P1-rr11 allele has similar structure to that of p1-vv9D9A except that the Ac element inserts upstream the p1 locus (see Reversed Ac ends transposition for structure). The numerals placed after the two-letter suffix indicate the culture number of origin of each allele, and alleles with the same phenotype but different culture numbers may have different gene structures.

Rationale

Transposition is essentially a biochemical reaction. The enzyme that catalyzes the reaction is transposase, and the substrates of transposase are the 5' and 3' termini of the transposon. Theoretically, noncontiguous 5' and 3' transposon termini could serve as transposase substrates, and transposition could involve transposon termini located on different chromosomes. Such alternative transposition events involving dispersed transposon ends could lead to major chromosomal rearrangements, whereas ordinary transposition of a contiguous element changes only the location of the transposon in the genome. A pair of the 5' transposon end and a 3' transposon end could have three different configurations:
  1. The 5' end and the 3' end are in the direct orientation (one of the transposon end is reversed);
  2. The 5' end and the 3' end are in reversed orientation (both transposon ends are reversed);
  3. The 5' end and the 3' end are in different chromosomes.
Using maize p1 and r1 alleles carrying Ac/Ds and/or fAc, three kinds of alternative transposition events are tested here.

Sister chromatid transposition

The 5' end of Ac and the 3' end of fAc in p1-vv9D9A are in direct orientation. The p1-vv9D9A allele is very unstable; many deletion and inverted duplication alleles have been isolated from it. The origins of these deletions and inverted duplications could be explained by the following animation: In the above animation, Ac transposase binds to the 5' terminus of Ac in one sister chromatid and the 3' terminus of fAc in the other sister chromatid; A chromatid bridge is formed following the excision the the Ac/fAc ends; Insertion of the excised Ac/fAc ends into a site in the chromatid bridge generates a proximal deletion and a reciprocal inverted duplication. This transposition event is termed sister chromatid transposition (SCT) since the involved Ac/fAc ends are from different sister chromatids. A deletion and its reciprocal inverted duplication have been isolated from a twin sector resulting from a single SCT event, and the characteristic footprint and target site duplication have been identified from these twinned alleles.

Reversed Ac ends transposition

The 5' end of Ac and the 3' end of fAc in P1-rr11 are in reversed orientation. From P1-rr11, many p1-ww, p1-vv, and Pf-oo alleles have been isolated. Around twenty of these alleles have been analyzed: Two are local rearrangements, seven are proximal deletions, two are distal deletions, and the rest should be inversions (both proximal and distal).

The structure of the mutants indicate that they are generate by transposition events involving the pair of reversed Ac ends in the same sister chromatid (note: only one sister chromatid is shown in the animations below): Ac transposase binds to the 5' end of the Ac element and the 3' end of the fAc element in P1-rr11; The sequences flanking the Ac/fAc ends will join together to form a circle following the Ac/fAc ends excision; Depending on the insertion sites of excised Ac/fAc ends, a variety of chromosomal rearrangements could be generated.

Local rearrangement

If the reinsertion site of the excised Ac/fAc ends is in the circle, a local rearrangement could be generated. Both footprint and target site duplication, the hallmark of transposition, have been identified in these local rearrangements. In most cases, Local rearrangement would destroy p1 gene function, but the Ac 5' end and the fAc 3' end in the rearrangement are still competent for transposition. In further reversed-ends transposition events, the transposon ends could reinsert into the p1 intron 2 sequences in the correct orientation so as to restore p1 function. Consistent with this idea, both local rearrangement alleles are distinctive in exhibiting occasional red sectors (phenotype of p1-vv) that are not observed with the p1-ww alleles.

Distal inversion and distal deletion

If the excised Ac/fAc ends reinsert into a site distal to p1, a distal deletion or inversion could be generated depending on the way the transposon ends join to the insertion site. If the Ac 5' end joins to the proximal side of the insertion site (the 3' fAc end joins to the distal side of the insertion site), an inversion will be formed.

If the Ac 5' end joins to the distal side of the insertion site (the 3' fAc end joins to the proximal side of the insertion site), a deletion will be formed. Both the distal deletion and inversion should have p1-ww phenotype because the circle containing exons 1 and 2 of p1 would be lost.

Reciprocal translocation

If the excised Ac/fAc ends reinsert into a site in other chromosomes, reciprocal translocation will be generated.

Inter-chromosome transposition

The P1-rr617 allele carries a fAc element insertion in intron 2 on chromosome 1, the r1-navajo allele carries an Ac insertion in the r1 locus on chromosome 10. Transposition reaction involving the 5' end of Ac on chromosome 10 and the 3' end of fAc on chromosome 1 would destroy both p1 function and r1 function. We screened ~4000 ears, no mutants resulting from such transposition event has been ever isolated. So the frequency of inter-chromosome transposition should be very low.

Consequences of alternative transposition

Alternative Ac/Ds transposition produces a variety of chromosomal rearrangements such as deletions, duplications (inverted and direct), inversions, ring chromosomes, and reciprocal translocations. Since Ac/Ds and other DNA transposons tend to insert preferentially into genic regions, the chromosomal rearrangements caused by alternative transposition greatly enhances their potential role in mediating coding and/or regulatory sequences shuffling reactions, which could generate new gene or change gene expression pattern. Indeed, four cases of exon shuffling have be identified; In each case, joining the fAc element to a site in intron 2 of p2 gene (a p1 homologous gene, ~60 kb upstream the p1 locus) generates a functional chimerical gene containing the promoter, exon 1, and exon 2 of p2 and exon 3 of p1. The new genes specify orange pericarp and orange cob, so they are named Pf-oo (f indicates fusion).

The above transposition events are summarized in either Flash or QuickTime format here:
Flash format
QuickTime fromat (The newer version (>7.1?) QuickTime doesn't support the movie anymore)

Publications

  1. Zhang J, Zuo T, Peterson T. 2013 Generation of tandem direct duplications by reversed-ends transposition of maize ac elements. PLoS Genet. 9(8):e1003691 Link
  2. Zhang, J., Yu, C., Pulletikurti, V., Lamb, J., Tatiana Danilova, T., David F. Weber, D. F., Birchler, J. and Peterson, T. 2009 Alternative Ac/Ds transposition induces major chromosomal rearrangements in maize. Gene & Development 23(6):755-765. Link
  3. Zhang, J., Zhang, F., and Peterson, T. 2006 Transposition of reversed Ac element ends generates novel chimeric genes in maize. PLoS Genetics 2(10):1535-1540. Link
  4. Zhang, J. and Peterson, T. 2005 A segmental deletion series generated by sister-chromatid transposition of Ac transposable elements in maize. Genetics. 171(1):333-344. Link
  5. Zhang, J. and Peterson, T. 2004 Transposition of reversed Ac element ends generates chromosome rearrangements in maize. Genetics. 167(4):1929-1937. Link
  6. Zhang, J. and Peterson, T. 1999 Genome rearrangements by nonlinear transposons in maize. Genetics. 153(3):1403-1410. Link
  7. Yu, C., Zhang, J., Weber, D., Pulletikurti, V., and Peterson, T. 2010 Spatial configuration of transposable element Ac termini affects their ability to induce chromosomal breakage in maize. Plant Cell 22(3):744-54. Link
  8. Krishnaswamy, L., Zhang, J. and Peterson, T. 2008 Reversed end Ds element: a novel tool for chromosome engineering in Arabidopsis. Plant Mol Biol 68, 399-411. Link
  9. Xuan YH, Zhang J, Peterson T, Han CD. 2012 Ac/Ds-induced chromosomal rearrangements in rice genomes. Mob Genet Elements. 2(2):67-71. Link
  10. Yu C, Han F, Zhang J, Birchler J, Peterson T. 2012 A transgenic system for generation of transposon Ac/Ds-induced chromosome rearrangements in rice. Theor Appl Genet. 125(7):1449-62 Link
  11. Xuan YH, Piao HL, Je BI, Park SJ, Park SH, Huang J, Zhang JB, Peterson T, Han CD. 2011 Transposon Ac/Ds-induced chromosomal rearrangements at the rice OsRLG5 locus. Nucleic Acids Res. 39(22):e149 Link

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