Analysis of two cosmid clones from chromosome 4 of Drosophila melanogasterreveals two new genes amid an unusual arrangement of repeated sequences

Chromosome 4 from Drosophila melanogaster has several unusual Features that distinguish it from the other chromosomes, These include a diffuse appeara nce in salivary gland polytene chromosomes, an absence of recombination, an d the variegated expression of P-element transgenes. As part of a larger pr oject to understand these properties, we are assembling a physical map of t his chromosome. Here we report the sequence of two cosmids representing sim ilar to 5% of the polytenized region. Both cosmid clones contain numerous r epeated DNA sequences, as identified by cross hybridization with labeled ge nomic DNA, BLAST searches, and dot matrix analysis, which are positioned be tween and within the transcribed sequences. The repetitive sequences includ e three copies of the mobile element Hoppel, one copy of the mobile element HE, and 18 DINE repeats. DINE is a novel, short repeated sequence disperse d throughout both cosmid sequences. One cosmid includes the previously desc ribed cubitus interruptus (ci) gene and two new genes: that a gene with a p redicted amino acid sequence similar to ribosomal protein S3a which is cons istent with the Minute(4)101 locus thought to be in the region, and a novel member of the protein family that includes plexin and met-hepatocyte growt h factor receptor. The other cosmid contains only the two short 5'-most exo ns from the zinc-finger-homology-2 (zfh-2) gene. This is the first extensiv e sequence analysis of noncoding DNA from chromosome 4. The distribution of the various repeats suggests its organization is similar to the p-heteroch romatic regions near the base of the major chromosome arms. Such a pattern may account for the diffuse banding of the polytene chromosome 4 and the va riegation of many P-element transgenes on the chromosome.