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modENCODE_submission_3168 Although C. elegans was the first multicellular organism with a completely sequenced genome, how this genome is arranged within the nucleus is not known. By chromatin immunoprecipitation of the nuclear transmembrane protein LEM-2, we determined the regions of the C. elegans genome associated with the nuclear membrane. We found that large regions of several megabases on the left and right arms of each autosome were associated with the nuclear membrane. The center of each autosome was free of such interactions, suggesting these regions are largely looped out from the nuclear membrane. The X chromosome, unlike the autosomes, was associated with the nuclear membrane only at its left end. At a finer scale, these large membrane-associated domains consist of smaller subdomains of LEM-2 associations. These subdomains are characterized by a high density of repetitive sequences, a low density of genes, and high levels of H3K27 trimethylation. The subdomains were punctuated by gaps containing genes with high transcriptional activity. Finally, we found that a chromosome arm translocated to the center of a chromosome retained its association with the nuclear membrane, although there was a decrease of association up to 400 kb from the fusion point. This indicates that local chromatin properties are the main determinant of interaction with the nuclear membrane, but the degree of association can be modulated by position along the chromosome. Our data provide the foundation for a model of the spatial arrangement of C.elegans chromosomes within the nucleus. Supplemental materials are available online at http://www.genome.org . Microarray and high-throughput sequencing data are available online at modENCODE Data Coordinating Center website, http://206.108.121.120/submit/public/list . These dataset are designed to confirm ChIP-chip experiments. The three experiments listed consist of: (1) LEM-2 ChIP-seq (seq-SDQ3891_LEM2_N2_MXemb_1_A_EE8_KI021); (2) control IgG ChIP-seq (seq-AB46540_NIgG_N2_MXemb_2_A_EE1432); and (3)Input-seq (seq-NA_N2_MXemb_3_A_EE1432) For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

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