Targeting determinants of dosage compensation in Drosophila

The dosage compensation complex (DCC) in Drosophila melanogaster is
responsible for up-regulating transcription from the single male X
chromosome to equal the transcription from the two X chromosomes in
females. Visualization of the DCC, a large ribonucleoprotein
complex, on male larval polytene chromosomes reveals that the
complex binds selectively to many interbands on the X chromosome.
The targeting of the DCC is thought to be in part determined by DNA
sequences that are enriched on the X. So far, lack of knowledge
about DCC binding sites has prevented the identification of
sequence determinants. Only three binding sites have been
identified to date, but analysis of their DNA sequence did not
allow the prediction of further binding sites. We have used
chromatin immunoprecipitation to identify a number of new DCC
binding fragments and characterized them in vivo by visualizing DCC
binding to autosomal insertions of these fragments, and we have
demonstrated that they possess a wide range of potential to recruit
the DCC. By varying the in vivo concentration of the DCC, we
provide evidence that this range of recruitment potential is due to
differences in affinity of the complex to these sites. We were also
able to establish that DCC binding to ectopic high-affinity sites
can allow nearby low-affinity sites to recruit the complex. Using
the sequences of the newly identified and previously characterized
binding fragments, we have uncovered a number of short sequence
motifs, which in combination may contribute to DCC recruitment. Our
findings suggest that the DCC is recruited to the X via a number of
binding sites of decreasing affinities, and that the presence of
high-and moderate-affinity sites on the X may ensure that
lower-affinity sites are occupied in a context-dependent manner.
Our bioinformatics analysis suggests that DCC binding sites may be
composed of variable combinations of degenerate motifs.