Sequence comparisons of non-allelic late histone genes and their early stage counterparts: Evidence for gene conversion within the sea urchin late stage gene family

We have determined the nucleotide sequence of sea urchin ( Lytechinus pictus) late stage H3 and H4 histone genes contained on the clone pLpH3H4-21 and of the early stage H3 gene contained on the plasmid pLpA. Comparison of these differentially regulated histone genes with each other and with other L. pictus late and early stage histone H3 and H4 genes previously sequenced confirms that members of each histone gene family (early and late) are more homologous to each other than they are to members of other histone gene families. The spacer regions between two late H3–H4 gene pairs on the clones pLpH3H4-19 and pLpH3H4-21 have diverged to the point where they are no longer homologous. However, comparative analysis of the 5′ flanking DNA has identified a sequence 5′C-T-C-A-T-G-T-A-T-T3′ upstream of both late H4 genes and another, 5′A-G-A-T-T-C-A3′, upstream of both H3 genes. Except for a short conserved sequence near the initiation codon, the transcribed 5′ leaders of the late mRNAs differ in length and sequence in the two non-allelic late histone gene pairs. This divergence contrasts with the 95 to 96% conservation found between late histone gene coding sequences. The results suggest that there is intergenic exchange in the germline among members of the late histone gene family and that the unit of exchange is the individual gene rather than the heterotypic dimer which includes the common spacer DNA.