Comparative genomic hybridization of Ectocarpus - different strains
ABSTRACT: Comparative Genome Hybridization of Ectocarpus siliculosus strains 371 (freshwater ecotype), 524 (copper-tolerant strain), and 568 (female strain), as well as E. fasciculatus strain 395 against the sequenced genome strain (32).
BACKGROUND: Brown algae of the genus Ectocarpus exhibit high levels of genetic diversity and variability in morphological and physiological characteristics. With the establishment of E. siliculosus as a model and the availability of a complete genome sequence, it is now of interest to analyze variability among different species, ecotypes, and strains of the genus Ectocarpus both at the genome and the transcriptome level. RESULTS: We used an E. siliculosus gene expression microarray based on EST ...[more]
Project description:Four cultures (four biological replicates) of each of two strains, wild type H37Rv and a deletion mutant for mce3R gene, were grown in in Middlebrook 7H9 medium supplemented with 0.05% Tween 80, or Middlebrook 7H11, supplemented with albumin 0.5%, dextrose 0.4%, and 0.5% glycerol (M7H9-AD-G). <br>Total RNA was extracted from each culture, dyed with Cy5 and hybridised onto two separated microarrays (technical duplicates). <br>In the second channel a mix of genomic DNA from strains H37Rv and AF2122 was dyed with CY3 and used as a common control in all the microarrays.<br>An statistical analysis of microarray data was performed to detect genes with differential expression between genotypes.
Project description:Leukemias are characterized by bone marrow failure due to oncogenic mutations of hematopoietic stem cells (HSC) or blood precursor cells. HSC differentiation and self-renewal properties are tightly regulated by Polycomb group (PcG) proteins, a well-characterized family of transcriptional epigenetic regulators. PcG proteins form two canonical complexes: Polycomb repressive complex 1 (PRC1), and Polycomb repressive complex 2 (PRC2).CBX proteins link the activity of PRC1 with PRC2, serving as critical regulators of PcG-mediating activity. While the functional role of some CBX proteins in cancer has been largely explored, recent reports support the specific role of CBX2 in human tumors, thus it represent a promising new target for anti-cancer strategies. To date, chromodomain inhibitors have been identified for CBX7 , but no molecules inhibiting CBX2 have been described. Nevertheless, different chromatin-modulating drugs such as histone deacetylase inhibitors (HDACi) are reported to regulate CBX2 targets on chromatin, suggesting that HDACi might be used to indirectly modulate aberrant effects of CBX2 in cancer. We describe a novel SAHA-mediated mechanism of CBX2 post-translational regulation. We found that CBX2 undergoes SAHA-induced SUMO2/3 modification and that CBX2 SUMOylation promotes its ubiquitination and proteasome-dependent degradation. We also identified the specific molecular pathway and key players regulating CBX2 stability, demonstrating that CBX4 and RNF4 act as the E3 SUMO and E3 ubiquitin ligase, respectively. Additionally, CBX2-depleted leukemic cells display impaired proliferation, showing that CBX2 is required for leukemia cell clonogenicity. Our study provides the first evidence of a non-canonical SAHA-mediated anti-tumorigenic activity via CBX2 SUMOylation and degradation
Project description:The aim of the experiment is to identify Ectocarpus siliculosus (strain Ec32) genes which are up- or down-regulated by auxin. RNAs were extracted from sporophytes treated with auxin NAA 5.10-6M for 30min or 3h, and labelled either with Cy3 or Cy5. Biological triplicates were performed.
Project description:Transformants either containing pCS1 (strain CCS1) or pNIM as control (strain CCS2) were induced by doxycycline (40 ﾵg/ml) for the indicated times (T0-T10, 0 to 10 min) in aerated hypha-inducing medium (10 % serum, 37 ﾰC). For each time point, cDNA of CCS1 and CCS2 were co-hybridised to microarrays and ratios of expression were calculated for each gene. Each gene is represented by duplicate spots on the DNA microarrays.