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Dynamic gene expression in fish muscle during recovery growth induced by a fasting-refeeding schedule.

Rescan PY, Montfort J, Rallière C, Le Cam A, Esquerré D, Hugot K - BMC Genomics (2007)

Bottom Line: Finally, a fourth cluster of 200 genes overexpressed only in 36-day refed trout muscle contained genes with function in carbohydrate metabolism and lipid biosynthesis.Our study is the first demonstration of a coordinated expression of functionally related genes during muscle recovery growth.Furthermore, the generation of a useful database of novel genes associated with muscle recovery growth will allow further investigations on particular genes, pathways or cellular process involved in muscle growth and regeneration.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Institute for Agricultural Research, Joint Research Unit for Fish Physiology, Biodiversity and the Environment, INRA Scribe, IFR140, Campus de Beaulieu, 35042 Rennes, France. pierre-yves.rescan@rennes.inra.fr

ABSTRACT

Background: Recovery growth is a phase of rapid growth that is triggered by adequate refeeding of animals following a period of weight loss caused by starvation. In this study, to obtain more information on the system-wide integration of recovery growth in muscle, we undertook a time-course analysis of transcript expression in trout subjected to a food deprivation-refeeding sequence. For this purpose complex targets produced from muscle of trout fasted for one month and from muscle of trout fasted for one month and then refed for 4, 7, 11 and 36 days were hybridized to cDNA microarrays containing 9023 clones.

Results: Significance analysis of microarrays (SAM) and temporal expression profiling led to the segregation of differentially expressed genes into four major clusters. One cluster comprising 1020 genes with high expression in muscle from fasted animals included a large set of genes involved in protein catabolism. A second cluster that included approximately 550 genes with transient induction 4 to 11 days post-refeeding was dominated by genes involved in transcription, ribosomal biogenesis, translation, chaperone activity, mitochondrial production of ATP and cell division. A third cluster that contained 480 genes that were up-regulated 7 to 36 days post-refeeding was enriched with genes involved in reticulum and Golgi dynamics and with genes indicative of myofiber and muscle remodelling such as genes encoding sarcomeric proteins and matrix compounds. Finally, a fourth cluster of 200 genes overexpressed only in 36-day refed trout muscle contained genes with function in carbohydrate metabolism and lipid biosynthesis. Remarkably, among the genes induced were several transcriptional regulators which might be important for the gene-specific transcriptional adaptations that underlie muscle recovery.

Conclusion: Our study is the first demonstration of a coordinated expression of functionally related genes during muscle recovery growth. Furthermore, the generation of a useful database of novel genes associated with muscle recovery growth will allow further investigations on particular genes, pathways or cellular process involved in muscle growth and regeneration.

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Supervised clustering analysis of the differentially expressed genes selected by SAM. Cluster I comprises genes up-regulated in muscle from fasted animals, cluster II includes genes with transient induction 4 to 11 days post-refeeding, cluster III contains genes whose expression began at 7 days post refeeding and was maintained up to 36 days post-refeeding and cluster IV contains genes up-regulated 36 days post-refeeding. Each row represents the temporal expression pattern of a single gene and each column corresponds to a single sample: columns 1 to 8: muscle from distinct fasted trout ; columns 9 to 17, 18 to 26, 27 to 34 and 35 to 43 : muscle from 4, 7, 11 and 36 day distinct refed trout, respectively. Expression levels are represented by a color tag, with red representing the highest levels and green the lowest levels of expression.
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Figure 2: Supervised clustering analysis of the differentially expressed genes selected by SAM. Cluster I comprises genes up-regulated in muscle from fasted animals, cluster II includes genes with transient induction 4 to 11 days post-refeeding, cluster III contains genes whose expression began at 7 days post refeeding and was maintained up to 36 days post-refeeding and cluster IV contains genes up-regulated 36 days post-refeeding. Each row represents the temporal expression pattern of a single gene and each column corresponds to a single sample: columns 1 to 8: muscle from distinct fasted trout ; columns 9 to 17, 18 to 26, 27 to 34 and 35 to 43 : muscle from 4, 7, 11 and 36 day distinct refed trout, respectively. Expression levels are represented by a color tag, with red representing the highest levels and green the lowest levels of expression.

Mentions: To screen for genes involved in muscle recovery growth, we undertook a time-course analysis of transcript expression in muscle of trout fasted for one month and then refed for 4, 7, 11 and 36 days. At each time point, eight to nine fish were sampled giving in total 43 separate complex cDNA targets that were hybridized to 43 microarrays (GEO accession number: GSE6841). Unsupervised hierarchical clustering of gene expression patterns from all samples produced a consistent grouping of the samples according to the fish feeding conditions (i.e. fasting and 4, 7, 11 and 36 days post-refeeding) (Fig 1). This validated the experimental design and allowed further analysis. To define those genes whose expression levels were significantly different in muscle from 4, 7, 11 or 36 days refed animals compared to muscle from fasted fish we used SAM analysis [10]. We therefore obtained approximately 2200 genes that were then hierarchically clustered using an average-linkage clustering [11]. This resulted in the formation of four major clusters of genes displaying distinct temporal profiles (Fig. 2). A similar clustering was obtained when using the K-means clustering (not shown). The first cluster was composed of genes with peak expression in muscle from starved fish, the second included genes overexpressed at 4, 7 and 11 days post-refeeding and down-regulated at 36 days post-refeeding (cluster II) the third was composed of genes with a later and more sustained induction (7–36 days post-refeeding) (cluster III) and the fourth (cluster IV) contained genes overexpressed only in 36 day refed trout muscle. These expression profiles and the clusters are available online as a browseable file [12]. The accession number of each spotted clones can be obtained by typing the corresponding uniq_id (clone name) in the nucleotide data base of the NCBI.


Dynamic gene expression in fish muscle during recovery growth induced by a fasting-refeeding schedule.

Rescan PY, Montfort J, Rallière C, Le Cam A, Esquerré D, Hugot K - BMC Genomics (2007)

Supervised clustering analysis of the differentially expressed genes selected by SAM. Cluster I comprises genes up-regulated in muscle from fasted animals, cluster II includes genes with transient induction 4 to 11 days post-refeeding, cluster III contains genes whose expression began at 7 days post refeeding and was maintained up to 36 days post-refeeding and cluster IV contains genes up-regulated 36 days post-refeeding. Each row represents the temporal expression pattern of a single gene and each column corresponds to a single sample: columns 1 to 8: muscle from distinct fasted trout ; columns 9 to 17, 18 to 26, 27 to 34 and 35 to 43 : muscle from 4, 7, 11 and 36 day distinct refed trout, respectively. Expression levels are represented by a color tag, with red representing the highest levels and green the lowest levels of expression.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238769&req=5

Figure 2: Supervised clustering analysis of the differentially expressed genes selected by SAM. Cluster I comprises genes up-regulated in muscle from fasted animals, cluster II includes genes with transient induction 4 to 11 days post-refeeding, cluster III contains genes whose expression began at 7 days post refeeding and was maintained up to 36 days post-refeeding and cluster IV contains genes up-regulated 36 days post-refeeding. Each row represents the temporal expression pattern of a single gene and each column corresponds to a single sample: columns 1 to 8: muscle from distinct fasted trout ; columns 9 to 17, 18 to 26, 27 to 34 and 35 to 43 : muscle from 4, 7, 11 and 36 day distinct refed trout, respectively. Expression levels are represented by a color tag, with red representing the highest levels and green the lowest levels of expression.
Mentions: To screen for genes involved in muscle recovery growth, we undertook a time-course analysis of transcript expression in muscle of trout fasted for one month and then refed for 4, 7, 11 and 36 days. At each time point, eight to nine fish were sampled giving in total 43 separate complex cDNA targets that were hybridized to 43 microarrays (GEO accession number: GSE6841). Unsupervised hierarchical clustering of gene expression patterns from all samples produced a consistent grouping of the samples according to the fish feeding conditions (i.e. fasting and 4, 7, 11 and 36 days post-refeeding) (Fig 1). This validated the experimental design and allowed further analysis. To define those genes whose expression levels were significantly different in muscle from 4, 7, 11 or 36 days refed animals compared to muscle from fasted fish we used SAM analysis [10]. We therefore obtained approximately 2200 genes that were then hierarchically clustered using an average-linkage clustering [11]. This resulted in the formation of four major clusters of genes displaying distinct temporal profiles (Fig. 2). A similar clustering was obtained when using the K-means clustering (not shown). The first cluster was composed of genes with peak expression in muscle from starved fish, the second included genes overexpressed at 4, 7 and 11 days post-refeeding and down-regulated at 36 days post-refeeding (cluster II) the third was composed of genes with a later and more sustained induction (7–36 days post-refeeding) (cluster III) and the fourth (cluster IV) contained genes overexpressed only in 36 day refed trout muscle. These expression profiles and the clusters are available online as a browseable file [12]. The accession number of each spotted clones can be obtained by typing the corresponding uniq_id (clone name) in the nucleotide data base of the NCBI.

Bottom Line: Finally, a fourth cluster of 200 genes overexpressed only in 36-day refed trout muscle contained genes with function in carbohydrate metabolism and lipid biosynthesis.Our study is the first demonstration of a coordinated expression of functionally related genes during muscle recovery growth.Furthermore, the generation of a useful database of novel genes associated with muscle recovery growth will allow further investigations on particular genes, pathways or cellular process involved in muscle growth and regeneration.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Institute for Agricultural Research, Joint Research Unit for Fish Physiology, Biodiversity and the Environment, INRA Scribe, IFR140, Campus de Beaulieu, 35042 Rennes, France. pierre-yves.rescan@rennes.inra.fr

ABSTRACT

Background: Recovery growth is a phase of rapid growth that is triggered by adequate refeeding of animals following a period of weight loss caused by starvation. In this study, to obtain more information on the system-wide integration of recovery growth in muscle, we undertook a time-course analysis of transcript expression in trout subjected to a food deprivation-refeeding sequence. For this purpose complex targets produced from muscle of trout fasted for one month and from muscle of trout fasted for one month and then refed for 4, 7, 11 and 36 days were hybridized to cDNA microarrays containing 9023 clones.

Results: Significance analysis of microarrays (SAM) and temporal expression profiling led to the segregation of differentially expressed genes into four major clusters. One cluster comprising 1020 genes with high expression in muscle from fasted animals included a large set of genes involved in protein catabolism. A second cluster that included approximately 550 genes with transient induction 4 to 11 days post-refeeding was dominated by genes involved in transcription, ribosomal biogenesis, translation, chaperone activity, mitochondrial production of ATP and cell division. A third cluster that contained 480 genes that were up-regulated 7 to 36 days post-refeeding was enriched with genes involved in reticulum and Golgi dynamics and with genes indicative of myofiber and muscle remodelling such as genes encoding sarcomeric proteins and matrix compounds. Finally, a fourth cluster of 200 genes overexpressed only in 36-day refed trout muscle contained genes with function in carbohydrate metabolism and lipid biosynthesis. Remarkably, among the genes induced were several transcriptional regulators which might be important for the gene-specific transcriptional adaptations that underlie muscle recovery.

Conclusion: Our study is the first demonstration of a coordinated expression of functionally related genes during muscle recovery growth. Furthermore, the generation of a useful database of novel genes associated with muscle recovery growth will allow further investigations on particular genes, pathways or cellular process involved in muscle growth and regeneration.

Show MeSH
Related in: MedlinePlus