A knob-associated tandem repeat in maize capable of forming fold-back DNA segments: are chromosome knobs megatransposons? - PubMed (original) (raw)

A knob-associated tandem repeat in maize capable of forming fold-back DNA segments: are chromosome knobs megatransposons?

E V Ananiev et al. Proc Natl Acad Sci U S A. 1998.

Abstract

A class of tandemly repeated DNA sequences (TR-1) of 350-bp unit length was isolated from the knob DNA of chromosome 9 of Zea mays L. Comparative fluorescence in situ hybridization revealed that TR-1 elements are also present in cytologically detectable knobs on other maize chromosomes in different proportions relative to the previously described 180-bp repeats. At least one knob on chromosome 4 is composed predominantly of the TR-1 repeat. In addition, several small clusters of the TR-1 and 180-bp repeats have been found in different chromosomes, some not located in obvious knob heterochromatin. Variation in restriction fragment fingerprints and copy number of the TR-1 elements was found among maize lines and among maize chromosomes. TR-1 tandem arrays up to 70 kilobases in length can be interspersed with stretches of 180-bp tandem repeat arrays. DNA sequence analysis and restriction mapping of one particular stretch of tandemly arranged TR-1 units indicate that these elements may be organized in the form of fold-back DNA segments. The TR-1 repeat shares two short segments of homology with the 180-bp repeat. The longest of these segments (31 bp; 64% identity) corresponds to the conserved region among 180-bp repeats. The polymorphism and complex structure of knob DNA suggest that, similar to the fold-back DNA-containing giant transposons in Drosophila, maize knob DNA may have some properties of transposable elements.

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Figures

Figure 1

Figure 1

Nucleotide sequence of a TR-1 element associated with the knob region of maize chromosome 9. The DNA segment between nucleotides 26 and 56 in the TR-1 element shares 64% homology with the conserved segment between nucleotides 122 and 157 of a 180-bp repeat.

Figure 2

Figure 2

A molecular map of the knob DNA segment with 180-bp and TR-1 tandem repeats from cosmid 9. The FB-1 element is composed of two inverted arrays of TR-1 elements (indicated by two black arrows) and is flanked by 180-bp repeats. Dashed boxes with clear arrows represent blocks of tandem arrays of TR-1 elements, and clear boxes with black short arrows represent blocks of tandem arrays of 180-bp repeats with arrowheads indicating individual repeats and their orientation. E, _Eco_RI site; N, _Nde_I site.

Figure 3

Figure 3

The integration sites of TR-1 elements into 180-bp repeats. All junctures in TR-1 as well as in 180-bp (bold) repeats are different. In three cases, A, C, and D, there are short stretches of unrelated DNA sequences (underlined) that separate the TR-1 from 180-bp repeats.

Figure 4

Figure 4

Hybridization of the TR-1 element to a blot panel of maize genomic DNA (Seneca 60) digested with different restriction enzymes. A typical ladder-like pattern of bands hybridizing to TR-1 is seen in lanes with DNA cut by _Eco_RI, _Alu_I, _Rsa_I, and _Sau_3A, the restriction enzymes that have a recognition site within TR-1. DNA samples cut with _Hae_III, _Taq_I, and _Nde_I, which have no recognition sites within TR-1, reveal maximum hybridization signal with DNA fragments larger than 10–20 kb. _Sty_I produced an intermediate ladder-like pattern of hybridization.

Figure 5

Figure 5

Hybridization of the TR-1 element to a DNA blot panel of oat–maize chromosome addition lines revealed a high level of polymorphism in copy number and restriction DNA fragment pattern among maize chromosomes and also between two maize lines, Seneca 60 and A188. Plant genomic DNA was cut by _Hae_III restriction enzyme. 1kb, molecular weight 1-kb marker ladder; 2, 3, 4, 7, 8, and 9, oat–maize addition lines with corresponding maize chromosomes; M1, mixture of λ DNA cut with _Hin_dIII and _Pst_I; M2, λ monomer (50 kb and dimer 100 kb); Oat, oat DNA from parental line Starter 1; S60 and A188, DNA of two maize lines (Seneca 60 and A188).

Figure 6

Figure 6

In situ hybridization of the TR-1 and 180-bp repeats to pachytene chromosomes of maize (Seneca 60). (A) The overall view of pachytene chromosomes stained with 4′,6-diamino-2-phenylindole (DAPI), the 180-bp repeat (green), and the TR-1 repeat (red) fluorescent images. The 180-bp repeats reveal strong hybridization signal to large knobs on chromosomes 5, 6, and 9, and the TR-1 elements reveal strong hybridization to the large knob on chromosome 4. Several additional small clusters of 180-bp repeats and TR-1 elements may be found in different sites on the chromosomes. (B) Distribution of hybridization signals over chromosomes 4 and 5. Overall view of 4′,6-diamino-2-phenylindole-stained chromosomes 4 and 5 (DAPI), the 180-bp repeat (green), and the TR-1 element (red) fluorescent images. The 180-bp repeat is detected in the large knob of chromosome 5 but not in the large knob of chromosome 4. However, there is a small cluster of 180-bp repeats at the terminus of chromosome 4. The TR-1 repeat is detected in both large knobs and in the small cluster at the terminus of chromosome 4. (C) Distribution of hybridization signals over chromosome 6. The overall view of 4′,6-diamino-2-phenylindole-stained chromosome 6 (DAPI), the 180-bp repeat (green), and the TR-1 element (red) fluorescent images. The 180-bp repeat and TR-1 element form two clusters: a big one in the knob at the terminus of the short arm and a small one probably in the first chromomere of the satellite of chromosome 6.

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References

    1. McClintock B. Science. 1929;69:629. - PubMed
    1. McClintock B. Proc Natl Acad Sci USA. 1930;16:791–796. - PMC - PubMed
    1. Reeves R G. Genetica (The Hague) 1944;29:141–147. - PubMed
    1. Longley A A. Bot Rev. 1952;18:399–412.
    1. McClintock B, Kato Y, Bluemenshein A. Chromosome Constitution of Races of Maize. Chapingo, Mexico: Colegio de Postgraduados; 1981.

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