Project description:Nickel is an essential component of many eukaryotic and prokaryotic metallo-enzymes. Due to its employment in many industrial applications, wastewaters from industrial plants often contain millimolar concentrations of Ni2+ that are toxic and life-threatening for many organism. Several lines of preliminary evidence suggest that members of the genus Sphingobium are able to grow in the presence of high concentrations of metal ions. We have isolated a novel Sphingobium strain (sp. ba1) able to grow in the presence of high concentrations (up to 20 mM) of NiCl2. Sequencing of its genome allowed the identification of several genes coding for proteins potentially involved in efflux-mediated resistance mechanisms. Here we use the RNA-seq approach to analyze the response of the Sphingobium sp. ba1 strain to high concentrations (10 mM) of Ni ions. Transcriptomic data show the differential expression of about one-hundred and twenty genes, most of which are up-regulated and encode proteins such as membrane proteins and components of metal efflux systems, enzymes involved in oxidative stress responses (catalases, peroxidases) and signal transduction systems.
Project description:We conducted genome-wide bisulfite sequencing analysis of the follicular lymphoma cell line RL and found that a large amount of methylated genes are polycomb target genes in ES cells. We therefore conducted a ChIP-chip experiment to determine the methylated genes that are bound by the polycomb protein Suz12. Although 28% of MRIs are PRC2 target genes in ES cells, our ChIP-on-Chip analysis showed that only 13% of MRIs are associated with H3K27Me3 marks and only 5% of the MRIs are bound by Suz12 in RL cells in vivo.
Project description:We conducted genome-wide bisulfite sequencing analysis of the follicular lymphoma cell line RL and found that a large amount of methylated genes are polycomb target genes in ES cells. We therefore conducted a ChIP-chip experiment to determine the methylated genes that are bound by the polycomb protein Suz12. Although 28% of MRIs are PRC2 target genes in ES cells, our ChIP-on-Chip analysis showed that only 13% of MRIs are associated with H3K27Me3 marks and only 5% of the MRIs are bound by Suz12 in RL cells in vivo. Comparison of DNA methylation with histone modifications in RL cells.