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Association of the matrix attachment region recognition signature with coding regions in Caenorhabditis elegans.

Anthony A, Blaxter M - BMC Genomics (2007)

Bottom Line: 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.Genes associated with MRS were significantly enriched for receptor activity annotations, but not for expression level or other features.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK. al.anthony@ed.ac.uk

ABSTRACT

Background: 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. 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.

Results: Using 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.

Conclusion: Through 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.

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Distribution of genes and MRS in C. elegans chromosomes. Number of gene (black) and MRS (red) start positions in non-overlapping 2 Mb windows. To account for short sequence length in the end window, the number of genes and MRS in the last window has been scaled to 2 Mb.
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Figure 1: Distribution of genes and MRS in C. elegans chromosomes. Number of gene (black) and MRS (red) start positions in non-overlapping 2 Mb windows. To account for short sequence length in the end window, the number of genes and MRS in the last window has been scaled to 2 Mb.

Mentions: However, at a chromosomal level distinct patterns emerged. Analyses of non-overlapping 2 Mb windows along the chromosomes showed that MRS were significantly more abundant in the centres than in the arms of all chromosomes except chromosome IV (Figure 1 and Additional File 2). The division between chromosome arms and centres is characteristic of several genomic features in C. elegans. Centres tend to be gene rich, with a high concentration of essential, well conserved and highly expressed genes [27,28]. By comparison, the chromosome arms exhibit a higher meiotic recombination rate, and are enriched for transposons and repeats [27]. Thus, at the chromosome level, MRS are more likely to be found in the vicinity of highly expressed and essential genes.


Association of the matrix attachment region recognition signature with coding regions in Caenorhabditis elegans.

Anthony A, Blaxter M - BMC Genomics (2007)

Distribution of genes and MRS in C. elegans chromosomes. Number of gene (black) and MRS (red) start positions in non-overlapping 2 Mb windows. To account for short sequence length in the end window, the number of genes and MRS in the last window has been scaled to 2 Mb.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2234258&req=5

Figure 1: Distribution of genes and MRS in C. elegans chromosomes. Number of gene (black) and MRS (red) start positions in non-overlapping 2 Mb windows. To account for short sequence length in the end window, the number of genes and MRS in the last window has been scaled to 2 Mb.
Mentions: However, at a chromosomal level distinct patterns emerged. Analyses of non-overlapping 2 Mb windows along the chromosomes showed that MRS were significantly more abundant in the centres than in the arms of all chromosomes except chromosome IV (Figure 1 and Additional File 2). The division between chromosome arms and centres is characteristic of several genomic features in C. elegans. Centres tend to be gene rich, with a high concentration of essential, well conserved and highly expressed genes [27,28]. By comparison, the chromosome arms exhibit a higher meiotic recombination rate, and are enriched for transposons and repeats [27]. Thus, at the chromosome level, MRS are more likely to be found in the vicinity of highly expressed and essential genes.

Bottom Line: 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.Genes associated with MRS were significantly enriched for receptor activity annotations, but not for expression level or other features.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK. al.anthony@ed.ac.uk

ABSTRACT

Background: 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. 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.

Results: Using 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.

Conclusion: Through 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.

Show MeSH