The difficult interpretation of transcriptome data: the case of the GATC regulatory network.
Comput Biol Chem
; 28(2): 109-18, 2004 Apr.
Article
em En
| MEDLINE
| ID: mdl-15130539
ABSTRACT
Genomic analyses on part of Escherichia coli's chromosome had suggested the existence of a GATC regulated network. This has recently been confirmed through a transcriptome analysis. Two hypotheses about the molecular control mechanism have been proposed-(i) the GATC network regulation is caused by the presence of GATC clusters within the coding sequences; the regulation is the direct consequence of the clusters' hemi-methylation and therefore their elevated melting temperature, (ii) the regulation is caused by the presence of GATCs in the non-coding 500 bp upstream regions of the affected genes; it is the consequence of an interaction with a regulatory protein like Fnr or CAP. An analysis of the transcriptome data has not allowed us to decide between the two hypotheses. We have therefore taken a classic genomic approach, analyzing the statistical distribution of GATC along the chromosome, using a realistic model of the chromosome as theoretical reference. We observe no particular distribution of GATC in the non-coding upstream regions; however, we confirm the presence of GATC clusters within the genes. In order to verify that the particular distribution observed in E. coli is not a statistical artefact, but has a physiological role, we have carried out the same analysis on Salmonella, making the hypothesis that the genes containing a GATC clusters should be largely the same in the two bacteria. This has been indeed observed, showing that the genes containing a GATC cluster are part of a regulation network. The present is a case study, which demonstrates that the analysis of transcriptome data does not always permit to identify the primary cause of a phenomenon observed; on the other hand, a classic genomic approach linked with a comparative study of related genomes may allow this identification.
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Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Transcrição Gênica
/
Repetições de Microssatélites
/
Biologia Computacional
/
Genômica
Idioma:
En
Revista:
Comput Biol Chem
Assunto da revista:
BIOLOGIA
/
INFORMATICA MEDICA
/
QUIMICA
Ano de publicação:
2004
Tipo de documento:
Article
País de afiliação:
França
País de publicação:
ENGLAND
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ESCOCIA
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GB
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GREAT BRITAIN
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INGLATERRA
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REINO UNIDO
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SCOTLAND
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UK
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UNITED KINGDOM