MersV1, Main, Exploration, bibRecord, 003075

Clustering of DNA sequences in human promoters.

Identifieur interne : 003075 ( Main/Exploration ); précédent : 003074; suivant : 003076

Clustering of DNA sequences in human promoters.

Auteurs : Peter C. Fitzgerald [États-Unis] ; Andrey Shlyakhtenko ; Alain A. Mir ; Charles Vinson

Source :

Genome research [ 1088-9051 ] ; 2004.

RBID : pubmed:15256515

Descripteurs français

KwdFr :
- Analyse de regroupements, Biologie informatique (), Données de séquences moléculaires, Humains, Modèles génétiques, Régions promotrices (génétique), Site d'initiation de la transcription, Séquence consensus, Séquence nucléotidique.
MESH :
- Analyse de regroupements, Biologie informatique, Données de séquences moléculaires, Humains, Modèles génétiques, Régions promotrices (génétique), Site d'initiation de la transcription, Séquence consensus, Séquence nucléotidique.

English descriptors

KwdEn :
- Base Sequence, Cluster Analysis, Computational Biology (methods), Consensus Sequence, Humans, Models, Genetic, Molecular Sequence Data, Promoter Regions, Genetic, Transcription Initiation Site.
MESH :
- methods : Computational Biology.
- Base Sequence, Cluster Analysis, Consensus Sequence, Humans, Models, Genetic, Molecular Sequence Data, Promoter Regions, Genetic, Transcription Initiation Site.

Abstract

We have determined the distribution of each of the 65,536 DNA sequences that are eight bases long (8-mer) in a set of 13,010 human genomic promoter sequences aligned relative to the putative transcription start site (TSS). A limited number of 8-mers have peaks in their distribution (cluster), and most cluster within 100 bp of the TSS. The 156 DNA sequences exhibiting the greatest statistically significant clustering near the TSS can be placed into nine groups of related sequences. Each group is defined by a consensus sequence, and seven of these consensus sequences are known binding sites for the transcription factors (TFs) SP1, NF-Y, ETS, CREB, TBP, USF, and NRF-1. One sequence, which we named Clus1, is not a known TF binding site. The ninth sequence group is composed of the strand-specific Kozak sequence that clusters downstream of the TSS. An examination of the co-occurrence of these TF consensus sequences indicates a positive correlation for most of them except for sequences bound by TBP (the TATA box). Human mRNA expression data from 29 tissues indicate that the ETS, NRF-1, and Clus1 sequences that cluster are predominantly found in the promoters of housekeeping genes (e.g., ribosomal genes). In contrast, TATA is more abundant in the promoters of tissue-specific genes. This analysis identified eight DNA sequences in 5082 promoters that we suggest are important for regulating gene expression.

DOI: 10.1101/gr.1953904
PubMed: 15256515

Affiliations:

États-Unis

Le document en format XML

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<term>Cluster Analysis</term>
<term>Consensus Sequence</term>
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<term>Molecular Sequence Data</term>
<term>Promoter Regions, Genetic</term>
<term>Transcription Initiation Site</term>
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<term>Modèles génétiques</term>
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<front><div type="abstract" xml:lang="en">We have determined the distribution of each of the 65,536 DNA sequences that are eight bases long (8-mer) in a set of 13,010 human genomic promoter sequences aligned relative to the putative transcription start site (TSS). A limited number of 8-mers have peaks in their distribution (cluster), and most cluster within 100 bp of the TSS. The 156 DNA sequences exhibiting the greatest statistically significant clustering near the TSS can be placed into nine groups of related sequences. Each group is defined by a consensus sequence, and seven of these consensus sequences are known binding sites for the transcription factors (TFs) SP1, NF-Y, ETS, CREB, TBP, USF, and NRF-1. One sequence, which we named Clus1, is not a known TF binding site. The ninth sequence group is composed of the strand-specific Kozak sequence that clusters downstream of the TSS. An examination of the co-occurrence of these TF consensus sequences indicates a positive correlation for most of them except for sequences bound by TBP (the TATA box). Human mRNA expression data from 29 tissues indicate that the ETS, NRF-1, and Clus1 sequences that cluster are predominantly found in the promoters of housekeeping genes (e.g., ribosomal genes). In contrast, TATA is more abundant in the promoters of tissue-specific genes. This analysis identified eight DNA sequences in 5082 promoters that we suggest are important for regulating gene expression.</div>
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Serveur d'exploration MERS

Clustering of DNA sequences in human promoters.

Clustering of DNA sequences in human promoters.

Source :

Descripteurs français

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki

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