Abstract
BackgroundMatrix attachment regions (MAR) are the sites on genomic DNA that interact with the nuclear matrix. There is increasing evidence for the involvement of MAR in regulation of gene expression. The unsuitability of experimental detection of MAR for genome-wide analyses has led to the development of computational methods of detecting MAR. The MAR recognition signature (MRS) has been reported to be associated with a significant fraction of MAR in C. elegans and has also been found in MAR from a wide range of other eukaryotes. However the effectiveness of the MRS in specifically and sensitively identifying MAR remains unresolved.ResultsUsing custom software, we have mapped the occurrence of MRS across the entire C. elegans genome. We find that MRS have a distinctive chromosomal distribution, in which they appear more frequently in the gene-rich chromosome centres than in arms. Comparison to distributions of MRS estimated from chromosomal sequences randomised using mono-, di- tri- and tetra-nucleotide frequency patterns showed that, while MRS are less common in real sequence than would be expected from nucleotide content alone, they are more frequent than would be predicted from short-range nucleotide structure. In comparison to the rest of the genome, MRS frequency was elevated in 5' and 3' UTRs, and striking peaks of average MRS frequency flanked C. elegans coding sequence (CDS). Genes associated with MRS were significantly enriched for receptor activity annotations, but not for expression level or other features.ConclusionThrough a genome-wide analysis of the distribution of MRS in C. elegans we have shown that they have a distinctive distribution, particularly in relation to genes. Due to their association with untranslated regions, it is possible that MRS could have a post-transcriptional role in the control of gene expression. A role for MRS in nuclear scaffold attachment is not supported by these analyses.
Highlights
Matrix attachment regions (MAR) are the sites on genomic DNA that interact with the nuclear matrix
We investigated whether the distribution of OFivgeurr-ere6presented Gene Ontology (GO) terms for C. elegans genes with an MAR recognition signature (MRS) within 200 bp of coding sequence (CDS) stop codon Over-represented GO terms for C. elegans genes with an MRS within 200 bp of CDS stop codon
We have carried out a genome-wide analysis of the distribution of MRS in C. elegans
Summary
Matrix attachment regions (MAR) are the sites on genomic DNA that interact with the nuclear matrix. There is increasing evidence for the involvement of MAR in regulation of gene expression. As genome sequencing and annotation has progressed, it has become clear that even relatively compact eukaryotic genomes have large amounts of non-coding DNA. This DNA harbours elements that control genomic activity such as gene regulators, non-coding RNAs and less well characterised elements that position the chromosomes on the nuclear matrix. Localisation of genes in this way is likely to involve control of higher order chromosome structure and there is evidence that some chromatin loop attachments are under developmental control [9]
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