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Sequence composition similarities with the 7SL RNA are highly predictive of functional genomic features.

Paquet Y, Anderson A - Nucleic Acids Res. (2010)

Bottom Line: The results presented here show a broad spectrum of functions for genomic segments that display sequence composition similarities with the 7SL RNA gene.Transposable elements that show noticeable similarities with the 7SL sequence include Alu sequences, as expected, but also long terminal repeats and the 5'-untranslated regions of long interspersed repetitive elements.In sequences masked for repeated elements, we find, when using the 7SL RNA gene as query sequence, distinctive similarities with promoters, exons and distal gene regulatory regions.

View Article: PubMed Central - PubMed

Affiliation: Centre de recherche en cancérologie de l'Université Laval, L'Hôtel-Dieu de Québec, Centre hospitalier universitaire de Québec, Québec, Canada.

ABSTRACT
Transposable elements derived from the 7SL RNA gene, such as Alu elements in primates, have had remarkable success in several mammalian lineages. The results presented here show a broad spectrum of functions for genomic segments that display sequence composition similarities with the 7SL RNA gene. Using thoroughly documented loci, we report that DNaseI-hypersensitive sites can be singled out in large genomic sequences by an assessment of sequence composition similarities with the 7SL RNA gene. We apply a root word frequency approach to illustrate a distinctive relationship between the sequence of the 7SL RNA gene and several classes of functional genomic features that are not presumed to be of transposable origin. Transposable elements that show noticeable similarities with the 7SL sequence include Alu sequences, as expected, but also long terminal repeats and the 5'-untranslated regions of long interspersed repetitive elements. In sequences masked for repeated elements, we find, when using the 7SL RNA gene as query sequence, distinctive similarities with promoters, exons and distal gene regulatory regions. The latter being the most notoriously difficult to detect, this approach may be useful for finding genomic segments that have regulatory functions and that may have escaped detection by existing methods.

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Root word count correlation scan of a 150-kb sequence containing the human TAL1 locus using the 7SL sequence as query. Diamonds represent the center of a 300-bp sliding window. The region shown is from human chromosome 1. Coordinates are those of Follows et al. (7). Exons are in green, exons predicted by Gnomon (NCBI build 36.3) are in orange and CNEs present in the Vista enhancer browser database (10) are in blue. Exons and CNEs are annotated to scale with the graph and projected onto it in their respective transparent colors. Relevant features described by Follows et al. (7) are identified relative to the start of exon 1a of the TAL1 gene from −10 kb to +51 kb directly over the corresponding CNEs, or designated by purple arrows for elements not identified as CNEs.
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Figure 3: Root word count correlation scan of a 150-kb sequence containing the human TAL1 locus using the 7SL sequence as query. Diamonds represent the center of a 300-bp sliding window. The region shown is from human chromosome 1. Coordinates are those of Follows et al. (7). Exons are in green, exons predicted by Gnomon (NCBI build 36.3) are in orange and CNEs present in the Vista enhancer browser database (10) are in blue. Exons and CNEs are annotated to scale with the graph and projected onto it in their respective transparent colors. Relevant features described by Follows et al. (7) are identified relative to the start of exon 1a of the TAL1 gene from −10 kb to +51 kb directly over the corresponding CNEs, or designated by purple arrows for elements not identified as CNEs.

Mentions: We show here that the human TAL1 locus is rich in sequences that display both DNaseI hypersensitivity and sequence composition similarities with the 7SL sequence. Similarity peaks reflecting sequence composition resemblance with the 7SL sequence indentify promoters, exons and DHS with surprising accuracy. Our results show that sequence composition similarity with the 7SL sequence is highly predictive of DHS. The pattern of 7SL similarity peaks in and around the TAL1 gene (Figure 3) is in striking accordance with the microarray DHS mapping of Follows et al. (7) over the same genomic region (see their Figure 4). A careful side by side comparison of their results for the human TAL1 locus with our assessment of 7SL sequence similarities for the same region reveals a near perfect match with DNaseI hypersensitivity (Supplementary Figure S2). While the 65-kb STIL gene has only an isolated peak that coincides with its promoter, the region surrounding the TAL1 and PDZK1IP1 genes is densely packed with 7SL sequence similarities, from the −10-kb HS to the +51-kb HS, that faithfully reproduce the pattern of HS/enhancer regions previously described (7). Some of the latter are also documented as CNEs, as in the case of the −4, +20/21, +24 and +51 kb elements (10).Figure 3.


Sequence composition similarities with the 7SL RNA are highly predictive of functional genomic features.

Paquet Y, Anderson A - Nucleic Acids Res. (2010)

Root word count correlation scan of a 150-kb sequence containing the human TAL1 locus using the 7SL sequence as query. Diamonds represent the center of a 300-bp sliding window. The region shown is from human chromosome 1. Coordinates are those of Follows et al. (7). Exons are in green, exons predicted by Gnomon (NCBI build 36.3) are in orange and CNEs present in the Vista enhancer browser database (10) are in blue. Exons and CNEs are annotated to scale with the graph and projected onto it in their respective transparent colors. Relevant features described by Follows et al. (7) are identified relative to the start of exon 1a of the TAL1 gene from −10 kb to +51 kb directly over the corresponding CNEs, or designated by purple arrows for elements not identified as CNEs.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2926601&req=5

Figure 3: Root word count correlation scan of a 150-kb sequence containing the human TAL1 locus using the 7SL sequence as query. Diamonds represent the center of a 300-bp sliding window. The region shown is from human chromosome 1. Coordinates are those of Follows et al. (7). Exons are in green, exons predicted by Gnomon (NCBI build 36.3) are in orange and CNEs present in the Vista enhancer browser database (10) are in blue. Exons and CNEs are annotated to scale with the graph and projected onto it in their respective transparent colors. Relevant features described by Follows et al. (7) are identified relative to the start of exon 1a of the TAL1 gene from −10 kb to +51 kb directly over the corresponding CNEs, or designated by purple arrows for elements not identified as CNEs.
Mentions: We show here that the human TAL1 locus is rich in sequences that display both DNaseI hypersensitivity and sequence composition similarities with the 7SL sequence. Similarity peaks reflecting sequence composition resemblance with the 7SL sequence indentify promoters, exons and DHS with surprising accuracy. Our results show that sequence composition similarity with the 7SL sequence is highly predictive of DHS. The pattern of 7SL similarity peaks in and around the TAL1 gene (Figure 3) is in striking accordance with the microarray DHS mapping of Follows et al. (7) over the same genomic region (see their Figure 4). A careful side by side comparison of their results for the human TAL1 locus with our assessment of 7SL sequence similarities for the same region reveals a near perfect match with DNaseI hypersensitivity (Supplementary Figure S2). While the 65-kb STIL gene has only an isolated peak that coincides with its promoter, the region surrounding the TAL1 and PDZK1IP1 genes is densely packed with 7SL sequence similarities, from the −10-kb HS to the +51-kb HS, that faithfully reproduce the pattern of HS/enhancer regions previously described (7). Some of the latter are also documented as CNEs, as in the case of the −4, +20/21, +24 and +51 kb elements (10).Figure 3.

Bottom Line: The results presented here show a broad spectrum of functions for genomic segments that display sequence composition similarities with the 7SL RNA gene.Transposable elements that show noticeable similarities with the 7SL sequence include Alu sequences, as expected, but also long terminal repeats and the 5'-untranslated regions of long interspersed repetitive elements.In sequences masked for repeated elements, we find, when using the 7SL RNA gene as query sequence, distinctive similarities with promoters, exons and distal gene regulatory regions.

View Article: PubMed Central - PubMed

Affiliation: Centre de recherche en cancérologie de l'Université Laval, L'Hôtel-Dieu de Québec, Centre hospitalier universitaire de Québec, Québec, Canada.

ABSTRACT
Transposable elements derived from the 7SL RNA gene, such as Alu elements in primates, have had remarkable success in several mammalian lineages. The results presented here show a broad spectrum of functions for genomic segments that display sequence composition similarities with the 7SL RNA gene. Using thoroughly documented loci, we report that DNaseI-hypersensitive sites can be singled out in large genomic sequences by an assessment of sequence composition similarities with the 7SL RNA gene. We apply a root word frequency approach to illustrate a distinctive relationship between the sequence of the 7SL RNA gene and several classes of functional genomic features that are not presumed to be of transposable origin. Transposable elements that show noticeable similarities with the 7SL sequence include Alu sequences, as expected, but also long terminal repeats and the 5'-untranslated regions of long interspersed repetitive elements. In sequences masked for repeated elements, we find, when using the 7SL RNA gene as query sequence, distinctive similarities with promoters, exons and distal gene regulatory regions. The latter being the most notoriously difficult to detect, this approach may be useful for finding genomic segments that have regulatory functions and that may have escaped detection by existing methods.

Show MeSH
Related in: MedlinePlus