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Conserved elements associated with ribosomal genes and their trans-splice acceptor sites in Caenorhabditis elegans.

Sleumer MC, Mah AK, Baillie DL, Jones SJ - Nucleic Acids Res. (2010)

Bottom Line: We then examined the genes associated with each motif group using DAVID and Ontologizer to determine which groups are associated with genes that also have significant functional associations in the Gene Ontology and other gene annotation sources.Of the 3265 motif groups formed, 612 (19%) had significant functional associations with respect to GO terms.Eight of the first 20 motif groups based on frequent dodecamers among the cisRED motif sequences were specifically associated with ribosomal protein genes; two of these were similar to mouse EBP-45, rat HNF3-family and Drosophila Zeste transcription factor binding sites.

View Article: PubMed Central - PubMed

Affiliation: Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 570 W 7th Ave Suite 100, Vancouver, BC, Canada.

ABSTRACT
The recent publication of the Caenorhabditis elegans cisRED database has provided an extensive catalog of upstream elements that are conserved between nematode genomes. We have performed a secondary analysis to determine which subsequences of the cisRED motifs are found in multiple locations throughout the C. elegans genome. We used the word-counting motif discovery algorithm DME to form the motifs into groups based on sequence similarity. We then examined the genes associated with each motif group using DAVID and Ontologizer to determine which groups are associated with genes that also have significant functional associations in the Gene Ontology and other gene annotation sources. Of the 3265 motif groups formed, 612 (19%) had significant functional associations with respect to GO terms. Eight of the first 20 motif groups based on frequent dodecamers among the cisRED motif sequences were specifically associated with ribosomal protein genes; two of these were similar to mouse EBP-45, rat HNF3-family and Drosophila Zeste transcription factor binding sites. Additionally, seven motif groups were extensions of the canonical C. elegans trans-splice acceptor site. One motif group was tested for regulatory function in a series of green fluorescent protein expression experiments and was shown to be involved in pharyngeal expression.

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Ribosomal instances of the motif group 12-0. The motif group 12-0 was found upstream of 28 ribosomal transcripts, of which two pairs were on bidirectional promoters: lsm-1 (F40F8.9; a small nuclear ribonucleoprotein splicing factor) and rps-9 (F40F8.10) and rps-30 (C26F1.4) and rpl-39 (C26F1.9). Shown here are the 26 ribosomal upstream regions; instances of motif group 12-0 are shown in red. Instances of motif groups 12-1, 12-5, 12-8, 12-11 and 12-18 are shown in cyan, magenta, gray, blue and green, respectively. The motif logo for all instances of motif group 12-0 in these regions is also shown.
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Figure 1: Ribosomal instances of the motif group 12-0. The motif group 12-0 was found upstream of 28 ribosomal transcripts, of which two pairs were on bidirectional promoters: lsm-1 (F40F8.9; a small nuclear ribonucleoprotein splicing factor) and rps-9 (F40F8.10) and rps-30 (C26F1.4) and rpl-39 (C26F1.9). Shown here are the 26 ribosomal upstream regions; instances of motif group 12-0 are shown in red. Instances of motif groups 12-1, 12-5, 12-8, 12-11 and 12-18 are shown in cyan, magenta, gray, blue and green, respectively. The motif logo for all instances of motif group 12-0 in these regions is also shown.

Mentions: The first dodecameric motif group, 12-0, had the most significant P-value with respect to ribosomal genes of the eight motif groups and also had the most members. We observed that it was GC-rich (75% GC) and very strongly conserved—the IC of all 120 instances of the group was 1.7 and the IC of the 28 instances near ribosomal genes was 1.8. It tended to appear ∼300 bp upstream of the translation start site (ATG) of the gene and was not strand-biased (Figure 1). It also tended to occur about 30 bp upstream or downstream of one of the other ribosomal motifs such as 12-5, 12-11 or 12-18. It was not found to co-occur in an upstream region with motif group 12-3 or 12-4. Group 12-0 was found upstream of 28 ribosomal genes, of which two pairs of genes were on bidirectional promoters and therefore had the same upstream regions: lsm-1 (F40F8.9; a small nuclear ribonucleoprotein splicing factor) and rps-9 (F40F8.10), and rps-30 (C26F1.4) and rpl-39 (C26F1.9).Figure 1.


Conserved elements associated with ribosomal genes and their trans-splice acceptor sites in Caenorhabditis elegans.

Sleumer MC, Mah AK, Baillie DL, Jones SJ - Nucleic Acids Res. (2010)

Ribosomal instances of the motif group 12-0. The motif group 12-0 was found upstream of 28 ribosomal transcripts, of which two pairs were on bidirectional promoters: lsm-1 (F40F8.9; a small nuclear ribonucleoprotein splicing factor) and rps-9 (F40F8.10) and rps-30 (C26F1.4) and rpl-39 (C26F1.9). Shown here are the 26 ribosomal upstream regions; instances of motif group 12-0 are shown in red. Instances of motif groups 12-1, 12-5, 12-8, 12-11 and 12-18 are shown in cyan, magenta, gray, blue and green, respectively. The motif logo for all instances of motif group 12-0 in these regions is also shown.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2875031&req=5

Figure 1: Ribosomal instances of the motif group 12-0. The motif group 12-0 was found upstream of 28 ribosomal transcripts, of which two pairs were on bidirectional promoters: lsm-1 (F40F8.9; a small nuclear ribonucleoprotein splicing factor) and rps-9 (F40F8.10) and rps-30 (C26F1.4) and rpl-39 (C26F1.9). Shown here are the 26 ribosomal upstream regions; instances of motif group 12-0 are shown in red. Instances of motif groups 12-1, 12-5, 12-8, 12-11 and 12-18 are shown in cyan, magenta, gray, blue and green, respectively. The motif logo for all instances of motif group 12-0 in these regions is also shown.
Mentions: The first dodecameric motif group, 12-0, had the most significant P-value with respect to ribosomal genes of the eight motif groups and also had the most members. We observed that it was GC-rich (75% GC) and very strongly conserved—the IC of all 120 instances of the group was 1.7 and the IC of the 28 instances near ribosomal genes was 1.8. It tended to appear ∼300 bp upstream of the translation start site (ATG) of the gene and was not strand-biased (Figure 1). It also tended to occur about 30 bp upstream or downstream of one of the other ribosomal motifs such as 12-5, 12-11 or 12-18. It was not found to co-occur in an upstream region with motif group 12-3 or 12-4. Group 12-0 was found upstream of 28 ribosomal genes, of which two pairs of genes were on bidirectional promoters and therefore had the same upstream regions: lsm-1 (F40F8.9; a small nuclear ribonucleoprotein splicing factor) and rps-9 (F40F8.10), and rps-30 (C26F1.4) and rpl-39 (C26F1.9).Figure 1.

Bottom Line: We then examined the genes associated with each motif group using DAVID and Ontologizer to determine which groups are associated with genes that also have significant functional associations in the Gene Ontology and other gene annotation sources.Of the 3265 motif groups formed, 612 (19%) had significant functional associations with respect to GO terms.Eight of the first 20 motif groups based on frequent dodecamers among the cisRED motif sequences were specifically associated with ribosomal protein genes; two of these were similar to mouse EBP-45, rat HNF3-family and Drosophila Zeste transcription factor binding sites.

View Article: PubMed Central - PubMed

Affiliation: Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, 570 W 7th Ave Suite 100, Vancouver, BC, Canada.

ABSTRACT
The recent publication of the Caenorhabditis elegans cisRED database has provided an extensive catalog of upstream elements that are conserved between nematode genomes. We have performed a secondary analysis to determine which subsequences of the cisRED motifs are found in multiple locations throughout the C. elegans genome. We used the word-counting motif discovery algorithm DME to form the motifs into groups based on sequence similarity. We then examined the genes associated with each motif group using DAVID and Ontologizer to determine which groups are associated with genes that also have significant functional associations in the Gene Ontology and other gene annotation sources. Of the 3265 motif groups formed, 612 (19%) had significant functional associations with respect to GO terms. Eight of the first 20 motif groups based on frequent dodecamers among the cisRED motif sequences were specifically associated with ribosomal protein genes; two of these were similar to mouse EBP-45, rat HNF3-family and Drosophila Zeste transcription factor binding sites. Additionally, seven motif groups were extensions of the canonical C. elegans trans-splice acceptor site. One motif group was tested for regulatory function in a series of green fluorescent protein expression experiments and was shown to be involved in pharyngeal expression.

Show MeSH