An inverted sea urchin histone gene sequence with breakpoints between TATA boxes and mRNA cap sites.

A sea urchin histone gene fragment containing inverted regions of the normal repeat has been cloned in pBR322. Restriction enzyme mapping and homoduplex analysis of this fragment indicate that the H1-H4 spacer of one repeat is situated alongside the inverted H2A-H1 spacer of another repeat. The site of the breakpoint has been sequenced and compared with homologous stretches of the normal repeat. The breakpoints in the original duplexes were found to be within 4-6 bp of the H4 mRNA cap site and 8-10 bp of the H1 mRNA cap site in the standard repeat. The breakpoints in both original duplexes contain short direct repeats and an overlap of 3 bases. As this is the first breakpoint resulting in the apposition of inverted sequence to be analyzed at the level of DNA sequence, we speculate whether structural features described here are typical of such rearrangements. The structure observed is consistent with, but does not prove, that the sequence is the endpoint of a true inversion since only one junction has been isolated and characterized.