Open Access Research article

Orchestrated transcription of biological processes in the marine picoeukaryote Ostreococcus exposed to light/dark cycles

Annabelle Monnier14, Silvia Liverani2, Régis Bouvet1, Béline Jesson1, Jim Q Smith2, Jean Mosser134, Florence Corellou56 and François-Yves Bouget56*

Author Affiliations

1 OUEST-genopole(R)transcriptome platform, IFR 140 GFAS, Faculté de Médecine, 2 avenue du Pr Léon Bernard, CS 34317 35043 Rennes Cedex, France

2 Department of Statistics, University of Warwick, Coventry CV4 7AL, UK

3 Medical Genomics Unit, Molecular Genetics and Biochemistry Department, Hospital Center, Rennes, France

4 CNRS UMR 6061 "Génétique et Développement", Régulation transcriptionnelle et Oncogenèse, Université de Rennes 1, IFR140 GFAS, Faculté de médecine, 2 avenue du Pr Léon Bernard, CS 34317, 35043 Rennes Cedex, France

5 UPMC University Paris 06, UMR7621 Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, F-66651, Banyuls/mer, France

6 CNRS, UMR7621 Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, F-66651, Banyuls/mer, France

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BMC Genomics 2010, 11:192  doi:10.1186/1471-2164-11-192

Published: 22 March 2010

Additional files

Additional file 1:

List of TOP50 genes with highest amplitude. TOP50 genes ranked according to their amplitude as log2(ratio).

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Additional file 2:

List of Top 50 genes with highest median expression. TOP50 genes ranked according to their median hybridization signal (absolute value).

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Additional file 3:

Coregulation of genes involved in basic transcription machinery during the night. BFC clusters from 2038 gene probes selected after PCA. Each colour corresponds to a biological process. Feature Number (Feat Num), BFC cluster number (BFC). Stars indicate two probes corresponding to two Feature Numbers associated to a single gene in the final annotation. Bottom right: The main BFC profiles and coefficients are shown. Note that clusters 61, 54, 111 and 67, clusters 29 and 92 as well as clusters 80 and 28 have almost identical profiles and for convenience only one profile (e.g. 61) is shown.

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Additional file 4:

Clusters of genes involved in protein synthesis including translation regulators, tRNA and amino acid biosynthesis around dawn. BFC clusters from 2038 gene probes selected after PCA. Each colour corresponds to a biological process. Feature Number (Feat Num), BFC cluster number (BFC). Right: The main BFC profiles are shown. Note that clusters 39 and 107 have nearly identical profiles.

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Additional file 5:

Coregulation of DNA replication and DNA repair genes at the end of the light period. S Phase BFC Clusters from 2038 gene probes selected after PCA. Each colour corresponds to a biological process. Feature Number (Feat Num), BFC cluster number (BFC). Right: The main BFC profiles and coefficients are shown. Note that clusters 41, 64 and 87 as well as clusters 57 and 116, clusters 46, 122 and 129 have nearly identical profiles.

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Additional file 6:

Cluster of genes involved in photoprotection, defence against oxidative stress and DNA repair around midday. BFC clusters from 2038 gene probes selected after PCA. Each colour corresponds to a biological process. Feature Number (Feat Num), BFC cluster number (BFC). Right: The main BFC profiles and coefficients are shown.

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Additional file 7:

Coregulation of genes involved in mitosis at dusk. Mitotic BFC clusters from 2038 gene probes selected after PCA. Each colour corresponds to a biological process. Feature Number (Feat Num), BFC cluster number (BFC). Right: The main BFC profiles and coefficients are shown. Note that clusters 71 and 49 as well as clusters 104 and 36 have nearly identical profiles.

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Additional file 8:

Late night clusters of genes involved in chloroplast biogenesis, pigment biosynthesis, lipid biosynthesis and metabolism. BFC clusters from 2038 gene probes selected after PCA. Each colour corresponds to a biological process. Feature Number (Feat Num), BFC cluster number (BFC). Right: The main BFC profiles and coefficients are shown. Note that clusters 33 and 6 have nearly identical profiles.

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Additional file 9:

Afternoon genes involved in Chlorophyll and Photosystem proteins biosynthesis. BFC clusters from 2038 gene probes selected after PCA. Each colour corresponds to a biological process. Feature Number (Feat Num), BFC cluster number (BFC). Stars indicate two probes corresponding to two Feature Numbers associated to a single gene in the final annotation. Right: The main BFC profiles and coefficients are shown.

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Additional file 10:

Transcriptional regulations of transcription factors. (A) Hierarchical clustering of 170 expressed transcription factors. (B) Transcription patterns of expression of CCAAT HAP3/HAP5 transcription factors.

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