We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor–binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs. We constructed hierarchical networks of transcription factor–binding and microRNA interactions and discovered chromosomal locations bound by an unusually large number of transcription factors. Different patterns of chromatin composition and histone modification were revealed between chromosome arms and centers, with similarly prominent differences between autosomes and the X chromosome. Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome.

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Introductory paragraphAmong organisms with chromosome-based mechanisms of sex determination, failure to equalize expression of X-linked genes between the sexes is typically lethal. In C. elegans, XX hermaphrodites halve transcription from each X chromosome to match the output of XO males 1 . Here, we mapped the binding location of the condensin homolog DPY-27 and the zinc finger protein SDC-3, two components of the C. elegans dosage compensation complex (DCC) 2,3 . Strong foci of DCC binding were observed on X, around which broader regions of localization were centered. Binding foci, but not adjacent regions of localization, were distinguished by clusters of a stereotypic 10-bp DNA sequence, suggesting a recruitment-andspreading mechanism for X recognition. In contrast to the Drosophila DCC, the C. elegans DCC was bound preferentially upstream of genes, suggesting modulation of transcriptional initiation and polymerase-coupled spreading. A mechanism for tuning DCC activity at specific loci was indicated by stronger DCC binding upstream of genes with high transcriptional activity. These data provide a basis for understanding how proteins involved in higher-order chromosome dynamics can regulate transcription at individual loci. Main TextTo compensate for differences in X-linked gene dosage between XY males and XX females, mammals inactivate most genes on one of the two female X chromosomes 4 . In contrast, C. elegans XX hermaphrodites dosage compensate by reducing transcription from each X chromosome by a factor of two to match the expression of XO males 1 . This mechanism is remarkable in that the subtle two-fold downregulation is imposed upon X-linked genes expressed over a large dynamic range 5,6 . The dosage compensation complex (DCC) required for C. elegans X-repression is composed of proteins encoded by the genes sdc-1, sdc-2, sdc-3, dpy-21, dpy-26, dpy-27, dpy-28, dpy-30 and mix-1 7 . DPY-26, DPY-27, DPY-28 and MIX-1 are homologous to members of the condensin complex, which is required for chromosome condensation and segregation in organisms ranging from bacteria to humans 8 . While the *Correspondence should be addressed to: Jason D. Lieb jlieb@bio.unc.edu (919) 843-3228. AUTHOR CONTRIBUTIONS This study was designed by SE and JDL. SE conducted the experiments. SE, PGG, CMW, and JDL conducted the data analysis. XZ and RDG designed, manufactured, and hybridized the DNA microarrays. SE and JDL wrote the paper. COMPETING INTERESTS STATEMENTThe authors declare that they have no competing financial interests. NIH Public Access NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript molecular parallels to mitotic chromosome condensation broadly suggest a mechanism for reducing X-linked transcription 9,10 , the features of X that control DCC binding have proven more difficult to investigate. Four loci on X (rex-1-4) sufficient for DCC recruitment were identified recently by using confocal microscopy to detect DCC binding to multiple-copy extrachromosomal transgenic DNA 11,12 . Here, we take an ...

In all eukaryotes, histone variants are incorporated into a subset of nucleosomes to create functionally specialized regions of chromatin. One such variant, H2A.Z, replaces histone H2A and is required for development and viability in all animals tested to date. However, the function of H2A.Z in development remains unclear. Here, we use ChIP-chip, genetic mutation, RNAi, and immunofluorescence microscopy to interrogate the function of H2A.Z (HTZ-1) during embryogenesis in Caenorhabditis elegans, a key model of metazoan development. We find that HTZ-1 is expressed in every cell of the developing embryo and is essential for normal development. The sites of HTZ-1 incorporation during embryogenesis reveal a genome wrought by developmental processes. HTZ-1 is incorporated upstream of 23% of C. elegans genes. While these genes tend to be required for development and occupied by RNA polymerase II, HTZ-1 incorporation does not specify a stereotypic transcription program. The data also provide evidence for unexpectedly widespread independent regulation of genes within operons during development; in 37% of operons, HTZ-1 is incorporated upstream of internally encoded genes. Fewer sites of HTZ-1 incorporation occur on the X chromosome relative to autosomes, which our data suggest is due to a paucity of developmentally important genes on X, rather than a direct function for HTZ-1 in dosage compensation. Our experiments indicate that HTZ-1 functions in establishing or maintaining an essential chromatin state at promoters regulated dynamically during C. elegans embryogenesis.