Cin 1 is a dispersed repetitive DNA element in both Zea mays and Zea mexicana (teosinte). The element is approximately 700 bp in size and was first recognized due to its presence on a 5.7 kb EcoR1 fragment of a Northern Flint maize line and its absence on the homologous 5 kb, unique fragment in the midwestern maize, Line C (Wienand et al., 1982, Mol. Gen. Genet. 187:195-201). Cloning of these maize fragments (Shepherd et al., 1982, Mol. Gen. Genet. 188:266-271) and subsequent DNA sequence analysis of the ends of the Cin 1 element show a short inverted repeat structure with the terminal 5 bases being identical to that of the Copia transposable element of Drosophila (5' TGTTG 3') (Levis et al., 1980, Cell 21:581). DNA sequence analysis of the "target" site in the 5 kb recombinant clone from Line C does not reveal a duplication of target site sequences immediately flanking the element.
In order to analyze the conservation of the element and to confirm the lack of a target site duplication, several other Cin containing clones were isolated from the Zea mays Line C genome and from Zea mexicana, Teosinte Guerrero. The Zea mays recombinant clones contain maize fragments ranging from 2.5 - 10 kb.
All clones were found to contain Cin surrounded by repetitive DNA sequences. Thus, it has not yet been possible to screen other maize lines for the absence of the Cin element at these various loci in order to obtain target site information. However, the DNA sequence of one Cin containing clone, LC102, does show a 5 bp direct repeat in the sequence immediately flanking the element. Comparison of the Cin 102 and Cin1 sequences shows 87% conservation of the element. Although sequence analysis of the other clones is still in progress, it is clear that the Cin element has diverged significantly and represents more of a repetitive DNA family rather than a highly conserved element.
N. S. Shepherd, M. Gupta, Zs. Schwarz-Sommer, U. Wienand, B. Deumling and H. Saedler
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