Over-represented sequences located on 3' UTRs are potentially involved in regulatory functions.
Identifieur interne : 005392 ( Main/Exploration ); précédent : 005391; suivant : 005393Over-represented sequences located on 3' UTRs are potentially involved in regulatory functions.
Auteurs : Kihoon Yoon [États-Unis] ; Daijin Ko ; Mark Doderer ; Carolina B. Livi ; Luiz O F. PenalvaSource :
- RNA biology [ 1555-8584 ]
Descripteurs français
- KwdFr :
- Analyse de regroupements, Données de séquences moléculaires, Humains, Opéron (génétique), Régions 3' non traduites (génétique), Régulation de l'expression des gènes, Réseaux de régulation génique, Sites de fixation, Séquence nucléotidique, Séquences d'acides nucléiques régulatrices (génétique), Transcription génétique, microARN (génétique).
- MESH :
- génétique : Opéron, Régions 3' non traduites, Séquences d'acides nucléiques régulatrices, microARN.
- Analyse de regroupements, Données de séquences moléculaires, Humains, Régulation de l'expression des gènes, Réseaux de régulation génique, Sites de fixation, Séquence nucléotidique, Transcription génétique.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : 3' Untranslated Regions, MicroRNAs.
- genetics : Operon, Regulatory Sequences, Nucleic Acid.
- Base Sequence, Binding Sites, Cluster Analysis, Gene Expression Regulation, Gene Regulatory Networks, Humans, Molecular Sequence Data, Transcription, Genetic.
Abstract
Eukaryotic gene expression must be coordinated for the proper functioning of biological processes. This coordination can be achieved both at the transcriptional and post-transcriptional levels. In both cases, regulatory sequences placed at either promoter regions or on UTRs function as markers recognized by regulators that can then activate or repress different groups of genes according to necessity. While regulatory sequences involved in transcription are quite well documented, there is a lack of information on sequence elements involved in post-transcriptional regulation. We used a statistical over-representation method to identify novel regulatory elements located on UTRs. An exhaustive search approach was used to calculate the frequency of all possible n-mers (short nucleotide sequences) in 16,160 human genes of NCBI RefSeq sequences and to identify any peculiar usage of n-mers on UTRs. After a stringent filtering process, we identified 2,772 highly over-represented n-mers on 3' UTRs. We provide evidence that these n-mers are potentially involved in regulatory functions. Identified n-mers overlap with previously identified binding sites for HuR and TIA-1 and, ARE and GRE sequences. We determine also that n-mers overlap with predicted miRNA target sites. Finally, a method to cluster n-mer groups allowed the identification of putative gene networks.
DOI: 10.4161/rna.7116
PubMed: 18971640
Affiliations:
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Le document en format XML
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Livi</name></author><author><name sortKey="Penalva, Luiz O F" sort="Penalva, Luiz O F" uniqKey="Penalva L" first="Luiz O F" last="Penalva">Luiz O F. Penalva</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="????"><PubDate><MedlineDate>2008 Oct-Dec</MedlineDate></PubDate></date><idno type="RBID">pubmed:18971640</idno><idno type="pmid">18971640</idno><idno type="doi">10.4161/rna.7116</idno><idno type="wicri:Area/PubMed/Corpus">002062</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002062</idno><idno type="wicri:Area/PubMed/Curation">002062</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002062</idno><idno type="wicri:Area/PubMed/Checkpoint">002A80</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">002A80</idno><idno type="wicri:Area/Ncbi/Merge">000648</idno><idno type="wicri:Area/Ncbi/Curation">000648</idno><idno type="wicri:Area/Ncbi/Checkpoint">000648</idno><idno type="wicri:Area/Main/Merge">005472</idno><idno type="wicri:Area/Main/Curation">005392</idno><idno type="wicri:Area/Main/Exploration">005392</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Over-represented sequences located on 3' UTRs are potentially involved in regulatory functions.</title><author><name sortKey="Yoon, Kihoon" sort="Yoon, Kihoon" uniqKey="Yoon K" first="Kihoon" last="Yoon">Kihoon Yoon</name><affiliation wicri:level="1"><nlm:affiliation>Department of Epidemiology and Biostatistics, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229-3900, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Epidemiology and Biostatistics, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229-3900</wicri:regionArea><wicri:noRegion>Texas 78229-3900</wicri:noRegion></affiliation></author><author><name sortKey="Ko, Daijin" sort="Ko, Daijin" uniqKey="Ko D" first="Daijin" last="Ko">Daijin Ko</name></author><author><name sortKey="Doderer, Mark" sort="Doderer, Mark" uniqKey="Doderer M" first="Mark" last="Doderer">Mark Doderer</name></author><author><name sortKey="Livi, Carolina B" sort="Livi, Carolina B" uniqKey="Livi C" first="Carolina B" last="Livi">Carolina B. Livi</name></author><author><name sortKey="Penalva, Luiz O F" sort="Penalva, Luiz O F" uniqKey="Penalva L" first="Luiz O F" last="Penalva">Luiz O F. Penalva</name></author></analytic><series><title level="j">RNA biology</title><idno type="eISSN">1555-8584</idno></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>3' Untranslated Regions (genetics)</term><term>Base Sequence</term><term>Binding Sites</term><term>Cluster Analysis</term><term>Gene Expression Regulation</term><term>Gene Regulatory Networks</term><term>Humans</term><term>MicroRNAs (genetics)</term><term>Molecular Sequence Data</term><term>Operon (genetics)</term><term>Regulatory Sequences, Nucleic Acid (genetics)</term><term>Transcription, Genetic</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de regroupements</term><term>Données de séquences moléculaires</term><term>Humains</term><term>Opéron (génétique)</term><term>Régions 3' non traduites (génétique)</term><term>Régulation de l'expression des gènes</term><term>Réseaux de régulation génique</term><term>Sites de fixation</term><term>Séquence nucléotidique</term><term>Séquences d'acides nucléiques régulatrices (génétique)</term><term>Transcription génétique</term><term>microARN (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>3' Untranslated Regions</term><term>MicroRNAs</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Operon</term><term>Regulatory Sequences, Nucleic Acid</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Opéron</term><term>Régions 3' non traduites</term><term>Séquences d'acides nucléiques régulatrices</term><term>microARN</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Binding Sites</term><term>Cluster Analysis</term><term>Gene Expression Regulation</term><term>Gene Regulatory Networks</term><term>Humans</term><term>Molecular Sequence Data</term><term>Transcription, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de regroupements</term><term>Données de séquences moléculaires</term><term>Humains</term><term>Régulation de l'expression des gènes</term><term>Réseaux de régulation génique</term><term>Sites de fixation</term><term>Séquence nucléotidique</term><term>Transcription génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Eukaryotic gene expression must be coordinated for the proper functioning of biological processes. This coordination can be achieved both at the transcriptional and post-transcriptional levels. In both cases, regulatory sequences placed at either promoter regions or on UTRs function as markers recognized by regulators that can then activate or repress different groups of genes according to necessity. While regulatory sequences involved in transcription are quite well documented, there is a lack of information on sequence elements involved in post-transcriptional regulation. We used a statistical over-representation method to identify novel regulatory elements located on UTRs. An exhaustive search approach was used to calculate the frequency of all possible n-mers (short nucleotide sequences) in 16,160 human genes of NCBI RefSeq sequences and to identify any peculiar usage of n-mers on UTRs. After a stringent filtering process, we identified 2,772 highly over-represented n-mers on 3' UTRs. We provide evidence that these n-mers are potentially involved in regulatory functions. Identified n-mers overlap with previously identified binding sites for HuR and TIA-1 and, ARE and GRE sequences. We determine also that n-mers overlap with predicted miRNA target sites. Finally, a method to cluster n-mer groups allowed the identification of putative gene networks.</div></front></TEI><affiliations><list><country><li>États-Unis</li></country></list><tree><noCountry><name sortKey="Doderer, Mark" sort="Doderer, Mark" uniqKey="Doderer M" first="Mark" last="Doderer">Mark Doderer</name><name sortKey="Ko, Daijin" sort="Ko, Daijin" uniqKey="Ko D" first="Daijin" last="Ko">Daijin Ko</name><name sortKey="Livi, Carolina B" sort="Livi, Carolina B" uniqKey="Livi C" first="Carolina B" last="Livi">Carolina B. Livi</name><name sortKey="Penalva, Luiz O F" sort="Penalva, Luiz O F" uniqKey="Penalva L" first="Luiz O F" last="Penalva">Luiz O F. Penalva</name></noCountry><country name="États-Unis"><noRegion><name sortKey="Yoon, Kihoon" sort="Yoon, Kihoon" uniqKey="Yoon K" first="Kihoon" last="Yoon">Kihoon Yoon</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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