The disruptive positions in human G-quadruplex motifs are less polymorphic and more conserved than their neutral counterparts
Identifieur interne : 000F44 ( Pmc/Curation ); précédent : 000F43; suivant : 000F45The disruptive positions in human G-quadruplex motifs are less polymorphic and more conserved than their neutral counterparts
Auteurs : Sigve Nakken [Norvège] ; Torbj Rn Rognes [Norvège] ; Eivind Hovig [Norvège]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2009.
Abstract
Specific guanine-rich sequence motifs in the human genome have considerable potential to form four-stranded structures known as G-quadruplexes or G4 DNA. The enrichment of these motifs in key chromosomal regions has suggested a functional role for the G-quadruplex structure in genomic regulation. In this work, we have examined the spectrum of nucleotide substitutions in G4 motifs, and related this spectrum to G4 prevalence. Data collected from the large repository of human SNPs indicates that the core feature of G-quadruplex motifs, 5′-GGG-3′, exhibits specific mutational patterns that preserve the potential for G4 formation. In particular, we find a genome-wide pattern in which sites that disrupt the guanine triplets are more conserved and less polymorphic than their neutral counterparts. This also holds when considering non-CpG sites only. However, the low level of polymorphisms in guanine tracts is not only confined to G4 motifs. A complete mapping of DNA three-mers at guanine polymorphisms indicated that short guanine tracts are the most under-represented sequence context at polymorphic sites. Furthermore, we provide evidence for a strand bias upstream of human genes. Here, a significantly lower rate of G4-disruptive SNPs on the non-template strand supports a higher relative influence of G4 formation on this strand during transcription.
Url:
DOI: 10.1093/nar/gkp590
PubMed: 19617376
PubMed Central: 2761265
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Eivind Hovig<affiliation><nlm:aff wicri:cut=" and" id="AFF1">Department of Tumor Biology, Institute for Cancer Research</nlm:aff>
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<front><div type="abstract" xml:lang="en"><p>Specific guanine-rich sequence motifs in the human genome have considerable potential to form four-stranded structures known as G-quadruplexes or G4 DNA. The enrichment of these motifs in key chromosomal regions has suggested a functional role for the G-quadruplex structure in genomic regulation. In this work, we have examined the spectrum of nucleotide substitutions in G4 motifs, and related this spectrum to G4 prevalence. Data collected from the large repository of human SNPs indicates that the core feature of G-quadruplex motifs, 5′-GGG-3′, exhibits specific mutational patterns that preserve the potential for G4 formation. In particular, we find a genome-wide pattern in which sites that disrupt the guanine triplets are more conserved and less polymorphic than their neutral counterparts. This also holds when considering non-CpG sites only. However, the low level of polymorphisms in guanine tracts is not only confined to G4 motifs. A complete mapping of DNA three-mers at guanine polymorphisms indicated that short guanine tracts are the most under-represented sequence context at polymorphic sites. Furthermore, we provide evidence for a strand bias upstream of human genes. Here, a significantly lower rate of G4-disruptive SNPs on the non-template strand supports a higher relative influence of G4 formation on this strand during transcription.</p>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Nucleic Acids Res</journal-id>
<journal-id journal-id-type="iso-abbrev">Nucleic Acids Res</journal-id>
<journal-id journal-id-type="publisher-id">nar</journal-id>
<journal-id journal-id-type="hwp">nar</journal-id>
<journal-title-group><journal-title>Nucleic Acids Research</journal-title>
</journal-title-group>
<issn pub-type="ppub">0305-1048</issn>
<issn pub-type="epub">1362-4962</issn>
<publisher><publisher-name>Oxford University Press</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">19617376</article-id>
<article-id pub-id-type="pmc">2761265</article-id>
<article-id pub-id-type="doi">10.1093/nar/gkp590</article-id>
<article-id pub-id-type="publisher-id">gkp590</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Genomics</subject>
</subj-group>
</article-categories>
<title-group><article-title>The disruptive positions in human G-quadruplex motifs are less polymorphic and more conserved than their neutral counterparts</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Nakken</surname>
<given-names>Sigve</given-names>
</name>
<xref ref-type="aff" rid="AFF1"><sup>1</sup>
</xref>
<xref ref-type="corresp" rid="COR1">*</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Rognes</surname>
<given-names>Torbjørn</given-names>
</name>
<xref ref-type="aff" rid="AFF1"><sup>1</sup>
</xref>
<xref ref-type="aff" rid="AFF1"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Hovig</surname>
<given-names>Eivind</given-names>
</name>
<xref ref-type="aff" rid="AFF1"><sup>2</sup>
</xref>
<xref ref-type="aff" rid="AFF1"><sup>3</sup>
</xref>
<xref ref-type="aff" rid="AFF1"><sup>4</sup>
</xref>
</contrib>
</contrib-group>
<aff id="AFF1"><sup>1</sup>
Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, NO-0027, Oslo,<sup>2</sup>
Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316, Oslo,<sup>3</sup>
Department of Tumor Biology, Institute for Cancer Research and<sup>4</sup>
Department of Medical Informatics, Oslo University Hospital, Norwegian Radium Hospital, Montebello, NO-0310, Oslo, Norway</aff>
<author-notes><corresp id="COR1">*To whom correspondence should be addressed. Tel: <phone>+47 22 84 47 86</phone>
; Fax: <fax>+47 22 84 47 82</fax>
; Email: <email>sigve.nakken@medisin.uio.no</email>
</corresp>
</author-notes>
<pub-date pub-type="ppub"><month>9</month>
<year>2009</year>
</pub-date>
<pub-date pub-type="epub"><day>17</day>
<month>7</month>
<year>2009</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>17</day>
<month>7</month>
<year>2009</year>
</pub-date>
<pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
. </pmc-comment>
<volume>37</volume>
<issue>17</issue>
<fpage>5749</fpage>
<lpage>5756</lpage>
<history><date date-type="received"><day>18</day>
<month>5</month>
<year>2009</year>
</date>
<date date-type="rev-recd"><day>25</day>
<month>6</month>
<year>2009</year>
</date>
<date date-type="accepted"><day>26</day>
<month>6</month>
<year>2009</year>
</date>
</history>
<permissions><copyright-statement>© 2009 The Author(s)</copyright-statement>
<copyright-year>2009</copyright-year>
<license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/2.0/uk/"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/2.0/uk/">http://creativecommons.org/licenses/by-nc/2.0/uk/</ext-link>
) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
</license>
</permissions>
<abstract><p>Specific guanine-rich sequence motifs in the human genome have considerable potential to form four-stranded structures known as G-quadruplexes or G4 DNA. The enrichment of these motifs in key chromosomal regions has suggested a functional role for the G-quadruplex structure in genomic regulation. In this work, we have examined the spectrum of nucleotide substitutions in G4 motifs, and related this spectrum to G4 prevalence. Data collected from the large repository of human SNPs indicates that the core feature of G-quadruplex motifs, 5′-GGG-3′, exhibits specific mutational patterns that preserve the potential for G4 formation. In particular, we find a genome-wide pattern in which sites that disrupt the guanine triplets are more conserved and less polymorphic than their neutral counterparts. This also holds when considering non-CpG sites only. However, the low level of polymorphisms in guanine tracts is not only confined to G4 motifs. A complete mapping of DNA three-mers at guanine polymorphisms indicated that short guanine tracts are the most under-represented sequence context at polymorphic sites. Furthermore, we provide evidence for a strand bias upstream of human genes. Here, a significantly lower rate of G4-disruptive SNPs on the non-template strand supports a higher relative influence of G4 formation on this strand during transcription.</p>
</abstract>
</article-meta>
</front>
</pmc>
</record>
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