Self-complementary DNA sequences within the BRc gene of Chironomus thummi.

The Balbiani ring c (BRc) DNA of Chironomus thummi consists of tandemly arranged 249-base pair (bp) repeats, which represent the major part of the gene (Bäumlein et al. 1982a) and are transcribed and translated in a periodic polypeptide of unusual size. To obtain further information on the DNA sequence organization of that gene a recombinant phage (lambda CthBRc-1) with a relatively long insert (containing predominantly 249-bp repeats) was studied by electron microscopy (EM). lambda CthBRc-1 was found to undergo specific sequence elimination of BRc DNA resulting in heterogeneous size distribution of insert length within the limits of the cloning capacity of the phage with a maximum around 15 kilobase pairs (kb). The EM analysis of R loops formed between recombinant molecules and poly(A)+RNA (containing the transcripts of BRc and BRb) revealed the existence of self-complementary inverted and direct repeats as further sequence elements of BRc DNA scattered throughout a long portion of the BRc transcription unit. Different intrastrand structures (stems, hairpins, complex loops) originate from the renaturation of several sets of self-complementary repeats. Most double-stranded regions fell into one main-size class with an average length of 0.1 kb. The overall data suggest that self-complementary repeats belong to the same DNA sequence family and are able to cooperate in the formation of loops of different size and complexity. The results are discussed in relation to the functional significance of self-complementary inverted repeats (palindromes) for BRc expression.