In higher plants, many stress-elicited responses are controlled at the level of transcriptional regulation, particularly through the activation of microRNA or master transcription factors. … Despite growing amounts of transcriptome data, the molecular mechanisms that govern algal lipid production have remained elusive and only a single algal transcription factor, NRR1, has been functionally implicated in lipid accumulation. NRR1 is required for lipid accumulation only during nitrogen starvation in C. reinhardtii and its role in other industrial oleaginous algae has not been recapitulated. In contrast to transcriptome profiling, distinct patterns of histone modifications can reveal active or repressed chromatin states and infer the transcriptional activity of the associated genes. … We thus hypothesized that a combination of chromatin state and transcriptome changes induced by lipid-inducing starvation conditions in C. reinhardtii may provide a sensitive and specific readout for detecting key switches controlling the lipid accumulation process.

In this study, we constructed genome-wide maps of chromatin states and their dynamics in C. reinhardtii. Compared with patterns found in metazoans and land plants, functional chromatin signatures in microalgae are a combination of both conserved and lineage-specific histone codes. We exploited chromatin signature changes to infer transcriptional regulators of lipid biosynthesis pathways and applied targeted genetic perturbation to confirm one of these transcription factor genes, PSR1, as a switch activating lipid accumulation. Our study provides insights into the regulation of TAG biosynthetic pathways and strategies for their targeted genetic engineering.

—Ngan et al.

Algal cells of Chlamydomonas reinhardtii grown under nitrogen starvation conditions to produce lipids. The red is the autofluorescence from the chlorophyll of the cells while the green indicates the lipid bodies following lipid staining with Lipidtox Green. (Image prepared by Rita Kuo.) Click to enlarge.

As part of the DOE Office of Science’s efforts to study algae for energy and environmental applications, the DOE JGI has published more than 75% of all publicly available algal genomes. One of these is the Chlamydomonas reinhardtii (“Chlamy”) reference genome, which was released back in 2007.

In their study, the team cultured Chlamy cells and starved them of nitrogen or sulfur, both of which are stress conditions to which Chlamy responds by producing lipids. They then analyzed the complex of DNA and proteins known as chromatin that define what genes are being activated, as well as the expression profiles or transcriptome, and compared these to non-stressed Chlamy cells.

Through careful analysis of genome-wide data sets, they narrowed down their search to identify two transcription factors that appeared to play a pivotal role in lipid accumulation, and then studied one of them, PSR1, in detail.

In studying the chromatin modifications, we can read out changes in the proteins bound to DNA on a genome-wide scale and then specifically target those genes whose regulation profiles are changed under lipid-producing conditions.

—Chew Yee Ngan, lead author

The study also demonstrated how cells can be tricked into producing lots of lipid without dying of starvation by overexpression of PSR1, which is a strategy that could potentially be applied in other industrial algal species better suited for large-scale biofuel production.

—co-author Axel Visel, DOE JGI Deputy for Science Programs

While the work is expected to help algal bioenergy researchers develop more targeted approaches for producing lipids for fuels, corresponding author Chia-Lin Wei, head of DOE JGI’s Sequencing Technologies Program, also pointed out that this study also successfully demonstrated an effective strategy for the integration of epigenomic and gene expression data, methods, i.e. the mapping of molecular tags that sit on top of the actual DNA sequence and affect its function, in an organism relevant to DOE missions in energy and environment.

Ngan and others at the DOE JGI are continuing this functional interrogation of the genomes in many other energy-related species Wei said.

Resources

• Chew Yee Ngan et al. (2015) “Lineage-specific chromatin signatures reveal a regulator of lipid metabolism in microalgae,” Nature Plants 1, Article number: 15107 doi: 10.1038/nplants.2015.107