Best practices for methylome characterization in novel species: a case study in the microalgae Nannochloropsis
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PROVIDER: PRJNA1103682 | ENA |
REPOSITORIES: ENA
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Project description:Microalgae remain an important feedstock for the production of biofuels and bioproducts. Discovery of new species drives innovation for biotransformation, where bioengineering and other technological advances can significantly optimize performance. Production is predicated on deep knowledge of algal behavior predicted from genomic and phenotypic studies. However, prediction and manipulation of behavior, particularly for scale up, remains a challenge. Understanding the contribution of epigenetic processes to algal function provides another piece of this complex puzzle for achieving bioeconomy goals. Utilizing Nannochloropsis species as a model, we provide a methodological framework for investigating epigenetic processes, specifically DNA methylation, in new species and demonstrate best practices for discerning novel epigenetic modifications. We demonstrate specific forms of DNA methylation can be overlooked by traditional epigenetic analysis strategies. Using high-throughput, lower cost techniques, we provide evidence demonstrating Nannochloropsis gaditana and N. salina lack the most ubiquitous forms of eukaryotic DNA methylation (5mC and 5hmC) and instead employ N6-adenine methylation (6mA), commonly found in bacteria, in their genomes.
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Project description:R-loops represent an abundant class of large non-B DNA structures in genomes. Even though they form transiently and at modest frequencies, interfering with R-loop formation or dissolution significantly impacts genome stability. Addressing the mechanism(s) of R-loop-mediated genome destabilization requires a precise characterization of their distribution in genomes. A number of independent methods have been developed to visualize and map R-loops, but their results are at times discordant, leading to confusion. Here we review the main existing methodologies underlying R-loop mapping and assess their limitations and the robustness of existing datasets. We offer a set of best practices to improve the reproducibility of maps, hoping that such guidelines could be useful for authors and referees alike. Finally, we offer a possible resolution to the apparent contradictions in R-loop mapping outcomes between antibody-based and RNase H1-based mapping approaches.
2021-02-24 | GSE158480 | GEO
Project description:Best practices for the visualization, mapping, and manipulation of R-loops
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Project description:Nannochloropsis gaditana is a microalgae of the phylum eustigmatophyceae that has been reported from fresh and brackish waters. This species has been widely cultured, mainly directed to biofuel production, due to its capacity to produce and accumulates high amounts of lipids under different culturing conditions. Furthermore, nowadays N. gaditana is being used as fish and mollusc food in aquaculture facilities. Besides, microalgae are recognized protein producers, thus, are posited as an alternative protein source that could be very valuable in areas such as agri-food or biomedicine. In this sense, seas and oceans had showed their great potential for innovation, being the main focus of the initiative Blue Growth from EU. Thereby, marine biotechnology will provide of new pharmaceuticals or industrial products from marine biomass. In order to study the whole proteome of Nannochloropsis gaditana, a proteomic approach was initiated using fresh and atomized microalgae samples, as the main commercial forms. Around 7500 peptides were detected, getting 1950 protein identification hits. Qualitative and quantitative differences were analysed. The identified proteins were categorized according to gene ontology classification. In this study, it has been developed and described the first proteomic analysis of the microalgae Nannochloropsis gaditana, containing an important number of identified proteins that may have a relevant role in different agri-food and biomedical processes.
2018-11-07 | PXD008499 | Pride
Project description:Nannochloropsis oceanica CCMP1779 is a marine unicellular stramenopile and an emerging reference species for basic research on oleogenic microalgae with biotechnological relevance. We investigated its physiology and transcriptome under light/dark cycles. We observed oscillations in lipid content and a predominance of cell division in the first half of the dark phase. Globally, more than 60% of the genes cycled in N. oceanica CCMP1779, with gene expression peaking at different times of the day. Interestingly, the phase of expression of genes involved in certain biological processes was conserved across photosynthetic lineages. Furthermore, in agreement with our physiological studies we found the processes of lipid metabolism and cell division enriched in cycling genes. For example, there was tight coordination of genes involved in the lower part of glycolysis, fatty acid synthesis and lipid production at dawn preceding lipid accumulation during the day. Our results suggest that diel lipid storage plays a key role for N. oceanica CCMP1779 growth under natural conditions making this alga a promising model to gain a basic mechanistic understanding of triacylglycerol production in photosynthetic cells. Our data will help the formulation of new hypotheses on the regulation transcriptional control of cell growth and metabolism in Nannochloropsis. Nannochloropsis oceanica CCMP was entrained to 12:12 light:dark cycles and biological replicates collected every 3 hours for a cycle for a total of 16 samples.
2015-08-01 | E-GEOD-69460 | biostudies-arrayexpress
Project description:Limited systems-level understanding of oil synthesis in wild oleaginous algae has hindered the development of microalgal feedstock. Nannochloropsis is a small unicellular microalgae widely distributed in oceans and fresh water. In many large-scale and pilot-scale outdoor cultivation facilities, Nannochloropsis strains have been found to be capable of robust growth when supplied with flue gases, naturally accumulating large quantities of oils in a stationary phase, and exhibiting resistance to environmental contaminants. The rich genomic resources, compact genomes, resistance to foreign DNA invasion, wide ecological adaptation, large collections of natural strains and the demonstrated ability to grow on a large scale suggested Nannochloropsis can serve as research models and platform strains for economical and scalable photosynthetic production of fuels and chemicals. To untangle the intricate genome-wide networks underlying the robust biomass accumulation and oil production in Nannochloropsis, we applied high-throughput mRNA-sequencing and reconstructed the structure and dynamics of the genome-wide functional network underlying robust microalgal triacylglycerol (TAG) production in Nannochloropsis oceanica, by tracking the genome-wide, single-base-resolutiontranscript change for the complete time-courses of nitrogen-depletion-induced TAG synthesis. Nannochloropsis oceanica IMET1 cells were grown in liquid cultures under continuous light (approximately 50 M-BM-5mol photons m-2 s-1) at 25M-bM-^DM-^C and aerated by bubbling with a mixture of 1.5% CO2 in air. Mid-logarithmic phase algal cells were collected and washed three times with axenic seawater. Equal numbers of cells were re-inoculated in nitrogen replete medium (Control condition or C, i.e. N+) and nitrogen deprived medium (N deficiency or N, i.e. N-) with 50M-BM-5mol m-2 s-1 light intensity, respectively. Cell aliquots were collected for RNA isolation after being transferred to the designated conditions for 3h, 4h, 6h, 12h, 24h and 48h. Three biological replicates of algal cultures were established under each of the above M-bM-^@M-^\CM-bM-^@M-^] (i.e. N+) and M-bM-^@M-^\NM-bM-^@M-^] (i.e. N-) conditions, respectively. In total, 36 samples collected at six time points (3h,4h,6h,12h,24h and 48h) were used for mRNA-Seq library preparation and then submitted to Illumina HiSeq 2000 for sequencing.
2014-05-14 | E-GEOD-42508 | biostudies-arrayexpress