Abstract
BackgroundAlthough Caenorhabditis elegans was the first multicellular organism with a completely sequenced genome, how this genome is arranged within the nucleus is not known.ResultsWe 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.ConclusionsLocal 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.
Highlights
Caenorhabditis elegans was the first multicellular organism with a completely sequenced genome, how this genome is arranged within the nucleus is not known
We identify genomic regions associated with an inner nuclear membrane protein in Caenorhabditis elegans utilizing a different approach, chromatin immunoprecipitation (ChIP) of the LEM-2 protein coupled with detection by tiling microarray (ChIP-chip) and next-generation sequencing (ChIP-seq)
The integral membrane protein LEM-2 is localized to the nuclear membrane in every cell of C. elegans embryos We generated two rabbit polyclonal antibodies directed against the amino terminus of the C. elegans LEM-2 protein
Summary
Caenorhabditis elegans was the first multicellular organism with a completely sequenced genome, how this genome is arranged within the nucleus is not known. The nuclear envelope, which consists of nuclear membranes, nuclear pore complexes and the nuclear lamina, primarily functions to separate the nuclear contents from the cytoplasm, and to maintain the structural integrity of the nucleus This barrier is physically associated with chromatin, which has led to the hypothesis that the nuclear envelope helps to control the spatial arrangement of the genome within the nucleus [1,2,3,4]. B-type lamins are one of the two major types of lamins in animal cells, and emerin is an inner nuclear transmembrane protein [9] All of these studies inferred regions of DNA interaction with B-type lamins or emerin using the DamID (DNA adenine methyltransferase identification) technique, in which the proteins are fused with bacterial adenine methyltransferase [6,7,8,10]. The common finding among human, mouse, and fly is that nuclear envelopeassociated regions possess heterochromatic characteristics, such as high levels of histone H3K9 dimethylation and H3K27 trimethylation, low gene density, and low gene expression
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