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Open Access Research

Caenorhabditis elegans chromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2

Kohta Ikegami1, Thea A Egelhofer2, Susan Strome2 and Jason D Lieb1*

Author affiliations

1 Department of Biology, Carolina Center for Genome Sciences and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, 407 Fordham Hall, Chapel Hill, North Carolina 27599, USA

2 Department of MCD Biology, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, USA

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Citation and License

Genome Biology 2010, 11:R120  doi:10.1186/gb-2010-11-12-r120

Published: 23 December 2010

Abstract

Background

Although Caenorhabditis elegans was the first multicellular organism with a completely sequenced genome, how this genome is arranged within the nucleus is not known.

Results

We determined the genomic regions associated with the nuclear transmembrane protein LEM-2 in mixed-stage C. elegans embryos via chromatin immunoprecipitation. Large regions of several megabases on the arms of each autosome were associated with LEM-2. The center of each autosome was mostly free of such interactions, suggesting that they are largely looped out from the nuclear membrane. Only the left end of the X chromosome was associated with the nuclear membrane. At a finer scale, the large membrane-associated domains consisted of smaller subdomains of LEM-2 associations. These subdomains were characterized by high repeat density, low gene density, high levels of H3K27 trimethylation, and silent genes. The subdomains were punctuated by gaps harboring highly active genes. A chromosome arm translocated to a chromosome center retained its association with LEM-2, although there was a slight decrease in association near the fusion point.

Conclusions

Local DNA or chromatin properties are the main determinant of interaction with the nuclear membrane, with position along the chromosome making a minor contribution. Genes in small gaps between LEM-2 associated regions tend to be highly expressed, suggesting that these small gaps are especially amenable to highly efficient transcription. Although our data are derived from an amalgamation of cell types in mixed-stage embryos, the results suggest a model for the spatial arrangement of C. elegans chromosomes within the nucleus.