Unknown,Transcriptomics,Genomics,Proteomics

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Cyanothece 51142 grown under high CO2 conditions: 0.03% CO2 vs. 8% CO2

ABSTRACT: Cyanobacteria are oxygenic photoautotrophs notable for their ability to utilize atmospheric CO2 as the major source of carbon. The prospect of using cyanobacteria in converting solar energy and high concentrations of CO2 (e.g. flue gas from coal power plants) efficiently into biomass and renewable energy sources is of interest to many research fields. In order to guide further advances in this area, a better understanding about the metabolic changes that occur under conditions of high CO2 is important. The objective of this study is to utilize genome-wide microarray expression profiling in the unicellular diazotrophic cyanobacterium Cyanothece 51142 grown in 8% CO2-enriched air and to determined the impact of high CO2 on cyanobacterial cell physiology and growth. Study of metabolic and cellular adaptations to high CO2 conditions in the unicellular diazotrophic cyanobacterium Cyanothece 51142. Two-condition experiment: 0.03% CO2 vs. 8% CO2. Biological replicates: 2; technical replicates: 3; Spots/ORF: 3 per Chip. Samples were collected at 7 time points over a period of two days, namely, Day1_30minLight (30min), Day1_2hrsLight (2hr), Day1_6hrsLight (6hr), Day1_1hrsDark (13hr), Day1-6hrsDark (18hr), Day2_6hrsLight (30hr) and Day2_6hrsDark (42hr).

ORGANISM(S): Cyanothece sp. ATCC 51142

SUBMITTER: Thanura Elvitigala

PROVIDER: E-GEOD-37621 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The local protein composition of chromatin is important for the regulation of transcription and other functions. By integrative analysis of genome-wide binding maps of 53 broadly selected chromatin components in Drosophila cells, we show that the genome is segmented into five principal chromatin types that are defined by unique, yet overlapping combinations of proteins, and form domains that can extend over >100 kb. We identify a novel repressive chromatin type that covers about half of the genome and lacks classic heterochromatin markers. Furthermore, transcriptionally active euchromatin consists of two distinct types that differ in molecular organization and H3K36 methylation, and regulate distinct classes of genes. Finally, we provide evidence that the different chromatin types act as guides that help to target DNA-binding factors to specific subsets of their recognition motifs. These results uncover basic principles of chromatin organization in a higher eukaryote. For this study, we generated whole-genome DamID binding profiles of 45 chromatin proteins in Drosophila Kc167 cells. Additionally, we perused published binding data of 8 chromatin proteins and generated a binding profile of one exogenous (yeast) DNA binding factor in Kc167 cells. On the same array platform, we obtained ChIP-on-chip profiles of histone H3, H1, H3K9me2, H3K27me3, H3K4me2, and H3K79me3. See supplementary files below. Gene expression was measured by RNA tag profiling. See GeneCounts supplementary file below. [1] RNA tag sequences were optained on an Illumina GAII with the digital gene expression (DGE) module from duplicate RNA samples. [2] All DamID and ChIP experiments were done in Drosophila Kc167 cells in duplicate. Samples were hybridized to 380k NimbleGen arrays with 300 bp probe spacing. Every experiment was done in duplicate in the reverse dye orientation, where Dam-fusion material was hybridized over Dam-only material. For ChIP, immunoprecipitated material was hybridized over ChIP input material. 18 previously-submitted Samples were included in this study. 10 of 18 Samples have been renormalized for the GSE22069 study: GSM509087, GSM509088, GSM509089, GSM509090, GSM509091, GSM509092, GSM509093, GSM509094, GSM509095, GSM509096 New GSM accession numbers have been issued for these 10 samples. 8 of 18 Samples are identical in the original studies and in GSE22069: GSM423290, GSM423291, GSM423298, GSM423299, GSM493592, GSM493593, GSM509085, GSM509086 [3] The genomic locations in files GSE22069_norm_aggregated_discretized_tiling_arrays.txt and GSE22069_norm_aggregated_tiling_arrays.txt are relative to FlyBase release 5 (BDGP R5/dm3).

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Cyanothece 51142 grown under high CO2 conditions: 0.03% CO2 vs. 8% CO2

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