Discovering sequences with potential regulatory characteristics.
Identifieur interne : 002055 ( PubMed/Corpus ); précédent : 002054; suivant : 002056Discovering sequences with potential regulatory characteristics.
Auteurs : Minou Bina ; Phillip Wyss ; Sheryl A. Lazarus ; Syed R. Shah ; Wenhui Ren ; Wojciech Szpankowski ; Gregory E. Crawford ; Sang P. Park ; Xiaohui C. SongSource :
- Genomics [ 1089-8646 ] ; 2009.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA.
- genetics : Chromosomes, Human, Pair 7, Homeodomain Proteins, Promoter Regions, Genetic, Regulatory Sequences, Nucleic Acid.
- chemical , metabolism : DNA.
- methods : Computational Biology.
- Binding Sites, Genome, Human, Humans.
Abstract
We developed a computational model to explore the hypothesis that regulatory instructions are context dependent and conveyed through specific 'codes' in human genomic DNA. We provide examples of correlation of computational predictions to reported mapped DNase I hypersensitive segments in the HOXA locus in human chromosome 7. The examples show that statistically significant 9-mers from promoter regions may occur in sequences near and upstream of transcription initiation sites, in intronic regions, and within intergenic regions. Additionally, a subset of 9-mers from coding sequences appears frequently, as clusters, in regulatory regions dispersed in noncoding regions in genomic DNA. The results suggest that the computational model has the potential of decoding regulatory instructions to discover candidate transcription factor binding sites and to discover candidate epigenetic signals that appear in both coding and regulatory regions of genes.
DOI: 10.1016/j.ygeno.2008.11.008
PubMed: 19084590
Links to Exploration step
pubmed:19084590Le document en format XML
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<author><name sortKey="Bina, Minou" sort="Bina, Minou" uniqKey="Bina M" first="Minou" last="Bina">Minou Bina</name>
<affiliation><nlm:affiliation>Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA. Bina@Purdue.edu</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Wyss, Phillip" sort="Wyss, Phillip" uniqKey="Wyss P" first="Phillip" last="Wyss">Phillip Wyss</name>
</author>
<author><name sortKey="Lazarus, Sheryl A" sort="Lazarus, Sheryl A" uniqKey="Lazarus S" first="Sheryl A" last="Lazarus">Sheryl A. Lazarus</name>
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<author><name sortKey="Shah, Syed R" sort="Shah, Syed R" uniqKey="Shah S" first="Syed R" last="Shah">Syed R. Shah</name>
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<author><name sortKey="Ren, Wenhui" sort="Ren, Wenhui" uniqKey="Ren W" first="Wenhui" last="Ren">Wenhui Ren</name>
</author>
<author><name sortKey="Szpankowski, Wojciech" sort="Szpankowski, Wojciech" uniqKey="Szpankowski W" first="Wojciech" last="Szpankowski">Wojciech Szpankowski</name>
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<author><name sortKey="Crawford, Gregory E" sort="Crawford, Gregory E" uniqKey="Crawford G" first="Gregory E" last="Crawford">Gregory E. Crawford</name>
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<author><name sortKey="Park, Sang P" sort="Park, Sang P" uniqKey="Park S" first="Sang P" last="Park">Sang P. Park</name>
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<author><name sortKey="Song, Xiaohui C" sort="Song, Xiaohui C" uniqKey="Song X" first="Xiaohui C" last="Song">Xiaohui C. Song</name>
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<author><name sortKey="Shah, Syed R" sort="Shah, Syed R" uniqKey="Shah S" first="Syed R" last="Shah">Syed R. Shah</name>
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<author><name sortKey="Szpankowski, Wojciech" sort="Szpankowski, Wojciech" uniqKey="Szpankowski W" first="Wojciech" last="Szpankowski">Wojciech Szpankowski</name>
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<series><title level="j">Genomics</title>
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<term>DNA (chemistry)</term>
<term>DNA (metabolism)</term>
<term>Genome, Human</term>
<term>Homeodomain Proteins (genetics)</term>
<term>Humans</term>
<term>Promoter Regions, Genetic (genetics)</term>
<term>Regulatory Sequences, Nucleic Acid (genetics)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term>
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<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Chromosomes, Human, Pair 7</term>
<term>Homeodomain Proteins</term>
<term>Promoter Regions, Genetic</term>
<term>Regulatory Sequences, Nucleic Acid</term>
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<front><div type="abstract" xml:lang="en">We developed a computational model to explore the hypothesis that regulatory instructions are context dependent and conveyed through specific 'codes' in human genomic DNA. We provide examples of correlation of computational predictions to reported mapped DNase I hypersensitive segments in the HOXA locus in human chromosome 7. The examples show that statistically significant 9-mers from promoter regions may occur in sequences near and upstream of transcription initiation sites, in intronic regions, and within intergenic regions. Additionally, a subset of 9-mers from coding sequences appears frequently, as clusters, in regulatory regions dispersed in noncoding regions in genomic DNA. The results suggest that the computational model has the potential of decoding regulatory instructions to discover candidate transcription factor binding sites and to discover candidate epigenetic signals that appear in both coding and regulatory regions of genes.</div>
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<Abstract><AbstractText>We developed a computational model to explore the hypothesis that regulatory instructions are context dependent and conveyed through specific 'codes' in human genomic DNA. We provide examples of correlation of computational predictions to reported mapped DNase I hypersensitive segments in the HOXA locus in human chromosome 7. The examples show that statistically significant 9-mers from promoter regions may occur in sequences near and upstream of transcription initiation sites, in intronic regions, and within intergenic regions. Additionally, a subset of 9-mers from coding sequences appears frequently, as clusters, in regulatory regions dispersed in noncoding regions in genomic DNA. The results suggest that the computational model has the potential of decoding regulatory instructions to discover candidate transcription factor binding sites and to discover candidate epigenetic signals that appear in both coding and regulatory regions of genes.</AbstractText>
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