In many species, a dosage compensation complex (DCC) is targeted to X chromosomes of one sex to equalize levels of X-gene products between males (1X) and females (2X). Here we identify cis-acting regulatory elements that target the Caenorhabditis elegans X chromosome for repression by the DCC. The DCC binds to discrete, dispersed sites on X of two types. rex sites (recruitment elements on X) recruit the DCC in an autonomous, DNA sequence-dependent manner using a 12-base-pair (bp) consensus motif that is enriched on X. This motif is critical for DCC binding, is clustered in rex sites, and confers much of X-chromosome specificity. Motif variants enriched on X by 3.8-fold or more are highly predictive (95%) for rex sites. In contrast, dox sites (dependent on X) lack the X-enriched variants and cannot bind the DCC when detached from X. dox sites are more prevalent than rex sites and, unlike rex sites, reside preferentially in promoters of some expressed genes. These findings fulfill predictions for a targeting model in which the DCC binds to recruitment sites on X and disperses to discrete sites lacking autonomous recruitment ability. To relate DCC binding to function, we identified dosage-compensated and noncompensated genes on X. Unexpectedly, many genes of both types have bound DCC, but many do not, suggesting the DCC acts over long distances to repress X-gene expression. Remarkably, the DCC binds to autosomes, but at far fewer sites and rarely at consensus motifs. DCC disruption causes opposite effects on expression of X and autosomal genes. The DCC thus acts at a distance to impact expression throughout the genome.[Keywords: Dosage compensation; condensin; X chromosome; gene expression; epigenetics; C. elegans] Supplemental material is available at http://www.genesdev.org.

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pecies in the genus Aspergillus are of broad interest to medical 1 , applied 2,3 , and basic research 4. Members of Aspergillus section Nigri ('black aspergilli') are prolific producers of native and heterologous proteins 5,6 , organic acids (in particular citric acid 2,7,8), and secondary metabolites (including biopharmaceuticals and mycotoxins like ochratoxin A). Furthermore, the section members are generally very efficient producers of extracellular enzymes 9,10 ; they are the production organisms for 49 out of 260 industrial enzymes 11,12. Among the most important of these, in addition to A. niger, are A. tubingensis, A. aculeatus, and A. luchuensis (previously A. acidus, A. kawachii, and A. awamori 13-15 , respectively). Members of Aspergillus section Nigri are also known as destructive degraders of foods and feeds, and some isolates produce the potent mycotoxins ochratoxin A 16 and fumonisins 17-19. In addition, some species in this section have been proposed to be pathogenic to humans and other animals 20. It is thus of interest to further examine section Nigri for industrial exploitation, as well as prevention of food spoilage, toxin production, and pathogenicity caused by these fungi. A combined phylogenetic and phenotypic approach has shown that section Nigri contains at least 27 species 21-25. Recent results have shown that the section contains species with high diversity and may consist of two separate clades: the biseriate species and the uniseriate species 26 , which show differences in sexual states 27 , sclerotium formation 28 , and secondary metabolite production 29. In the section, only six species have had their genome sequenced: A. niger 2,8 , A. luchuensis 15,30 , A. carbonarius 31 , A. aculeatus 31 , A. tubingensis 31 , and A. brasiliensis 31. This section, with its combination of species richness and fungal species with a diverse impact on humanity, is thus particularly interesting for studying the diversification of fungi into species. In this study, we have de novo-sequenced the genomes of 20 species of section Nigri, thus completing a genome compendium of 26 described species in the section. Further, we have genome-sequenced three