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The segment polarity gene cubitus interruptus (ci) is required to maintain expression of the wingless gene and to specify naked cuticle within each epidermal segment. Antibodies were generated against the ci protein and used to analyze its pattern of expression. By stage 11, post-transcriptional regulation of ci is observed. ci transcript levels are uniform across the anterior compartment, but protein levels are higher next to the compartment boundaries. The distribution of the ci protein is altered in fused, hedgehog and wingless mutants suggesting cell-cell signaling may regulate ci protein levels. The role of ci in cell-cell signaling and pattern formation was examined in double mutants of ci with patched and zeste-white3/shaggy.

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The proteasome degrades some proteins, such as transcription factors Cubitus interruptus (Ci) and NF-kappaB, to generate biologically active protein fragments. Here we have identified and characterized the signals in the substrate proteins that cause this processing. The minimum signal consists of a simple sequence preceding a tightly folded domain in the direction of proteasome movement. The strength of the processing signal depends primarily on the complexity of the simple sequence rather than on amino acid identity, the resistance of the folded domain to unraveling by the proteasome and the spacing between the simple sequence and folded domain. We show that two unrelated transcription factors, Ci and NF-kappaB, use this mechanism to undergo partial degradation by the proteasome in vivo. These findings suggest that the mechanism is conserved evolutionarily and that processing signals may be widespread in regulatory proteins.

Using a recently developed chemical approach, we have generated a genome-wide map of nucleosomes in vivo in Schizosaccharomyces pombe (S. pombe) at base pair resolution. The shorter linker length previously identified in S. pombe is due to a preponderance of nucleosomes separated by ∼4/5 bp, placing nucleosomes on opposite faces of the DNA. The periodic dinucleotide feature thought to position nucleosomes is equally strong in exons as in introns, demonstrating that nucleosome positioning information can be superimposed on coding information. Unlike the case in Saccharomyces cerevisiae, A/T-rich sequences are enriched in S. pombe nucleosomes, particularly at ±20 bp around the dyad. This difference in nucleosome binding preference gives rise to a major distinction downstream of the transcription start site, where nucleosome phasing is highly predictable by A/T frequency in S. pombe but not in S. cerevisiae, suggesting that the genomes and DNA binding preferences of nucleosomes have coevolved in different species. The poly (dA-dT) tracts affect but do not deplete nucleosomes in S. pombe, and they prefer special rotational positions within the nucleosome, with longer tracts enriched in the 10-to 30-bp region from the dyad. S. pombe does not have a welldefined nucleosome-depleted region immediately upstream of most transcription start sites; instead, the −1 nucleosome is positioned with the expected spacing relative to the +1 nucleosome, and its occupancy is negatively correlated with gene expression. Although there is generally very good agreement between nucleosome maps generated by chemical cleavage and micrococcal nuclease digestion, the chemical map shows consistently higher nucleosome occupancy on DNA with high A/T content.chromatin structure | heterochromatin | gene regulation E ukaryotic DNA is organized into nucleosome arrays that facilitate proper genome compaction and regulation of the genetic information. Genome-wide nucleosome maps from different organisms have provided important insights into how nucleosome positioning regulates chromosome functions (1-6). It is commonly accepted that the DNA sequence itself plays a major role in the exact positions where histone octamers bind DNA to form nucleosomes (7-9). Most remarkably, nucleosomes prefer special dinucleotide motifs at specific rotational angles within the nucleosome core (10, 11) and disfavor poly (dA-dT) tracts (12-15). Although the ability of DNA to interact with the histone core is important, nucleosome occupancy is influenced by additional extrinsic factors, including species-specific DNA binding proteins (16), ATP-dependent remodeling complexes (17,18), and the transcription machinery (19)(20)(21)(22).The underlying mechanisms for the species-or cell typespecific nucleosome positioning features have not been well understood. The fission yeast Schizosaccharomyces pombe and the budding yeast Saccharomyces cerevisiae are two highly diverged model organisms widely used to study basic biological processes in eukaryotes (23). Although similar in siz...