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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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MRS distribution and AT content near genes in C. elegans (A) and C. briggsae (B). Average AT% in 50 bp (blue line) and 10 bp (red line) non-overlapping windows and number of MRS per CDS in 50 bp non-overlapping windows (black line) is displayed. The windows extend from 1000 bp upstream of the translation start site (ATG codon) through the first 400 bp of the CDS and from the last 400 bp of the CDS, through to 1000 bp downstream of the translation stop site (stop codon).
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Figure 5: MRS distribution and AT content near genes in C. elegans (A) and C. briggsae (B). Average AT% in 50 bp (blue line) and 10 bp (red line) non-overlapping windows and number of MRS per CDS in 50 bp non-overlapping windows (black line) is displayed. The windows extend from 1000 bp upstream of the translation start site (ATG codon) through the first 400 bp of the CDS and from the last 400 bp of the CDS, through to 1000 bp downstream of the translation stop site (stop codon).

Mentions: To clarify the relationship between genes, especially their 5' and 3' UTRs and MRS, the frequency of MRS in the regions surrounding gene boundaries was investigated. Using the data from MRSfinder, MRS locations were plotted on a section of sequence extending 1000 bp upstream of the translation start site (ATG codon) through the first 400 bp of the coding sequence (CDS) from each C. elegans gene. The same analysis was carried out on sequence from the last 400 bp of the CDS through to 1000 bp downstream of the stop codon (Figure 5A).


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

Anthony A, Blaxter M - BMC Genomics (2007)

MRS distribution and AT content near genes in C. elegans (A) and C. briggsae (B). Average AT% in 50 bp (blue line) and 10 bp (red line) non-overlapping windows and number of MRS per CDS in 50 bp non-overlapping windows (black line) is displayed. The windows extend from 1000 bp upstream of the translation start site (ATG codon) through the first 400 bp of the CDS and from the last 400 bp of the CDS, through to 1000 bp downstream of the translation stop site (stop codon).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: MRS distribution and AT content near genes in C. elegans (A) and C. briggsae (B). Average AT% in 50 bp (blue line) and 10 bp (red line) non-overlapping windows and number of MRS per CDS in 50 bp non-overlapping windows (black line) is displayed. The windows extend from 1000 bp upstream of the translation start site (ATG codon) through the first 400 bp of the CDS and from the last 400 bp of the CDS, through to 1000 bp downstream of the translation stop site (stop codon).
Mentions: To clarify the relationship between genes, especially their 5' and 3' UTRs and MRS, the frequency of MRS in the regions surrounding gene boundaries was investigated. Using the data from MRSfinder, MRS locations were plotted on a section of sequence extending 1000 bp upstream of the translation start site (ATG codon) through the first 400 bp of the coding sequence (CDS) from each C. elegans gene. The same analysis was carried out on sequence from the last 400 bp of the CDS through to 1000 bp downstream of the stop codon (Figure 5A).

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