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Lineage-specific chromatin signatures reveal a regulator of lipid metabolism in microalgae

An Erratum to this article was published on 29 September 2015

Abstract

Alga-derived lipids represent an attractive potential source of biofuels. However, lipid accumulation in algae is a stress response tightly coupled to growth arrest, thereby imposing a major limitation on productivity. To identify transcriptional regulators of lipid accumulation, we performed an integrative chromatin signature and transcriptomic analysis to decipher the regulation of lipid biosynthesis in the alga Chlamydomonas reinhardtii. Genome-wide histone modification profiling revealed remarkable differences in functional chromatin states between the algae and higher eukaryotes and uncovered regulatory components at the core of lipid accumulation pathways. We identified the transcription factor, PSR1, as a pivotal switch that triggers cytosolic lipid accumulation. Dissection of the PSR1-induced lipid profiles corroborates its role in coordinating multiple lipid-inducing stress responses. The comprehensive maps of functional chromatin signatures in a major clade of eukaryotic life and the discovery of a transcriptional regulator of algal lipid metabolism will facilitate targeted engineering strategies to mediate high lipid production in microalgae.

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Figure 1: An integrative epigenetic and transcriptomic strategy to identify lipid regulators in C. reinhardtii.
Figure 2: Chromatin states analysis reveals unique signatures in C. reinhardtii.
Figure 3: Histone modification and transcription activities.
Figure 4: Chromatin state changes predict regulators of lipid accumulation.
Figure 5: PSR1 triggers lipid accumulation in C. reinhardtii.
Figure 6: Quantitative lipid analysis in PSR1 overexpressing cells.

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Acknowledgements

The authors thank S. Prochnik and P. Tran for their discussion and comments on the manuscript, L. Pennacchio for initiating effort in setting-up the C. reinhardtii culture, M. Kobayashi for technical advice on C. reinhardtii culture, R. Acob Agbayani and J. Chow for execution of part of the experiments, S. Deshpande for coordinating sample processing and sequencing tracking. H.C. was supported by a grant from the Laboratory Directed Research and Development program at Lawrence Berkeley National Laboratory. K.K.N. is an investigator of the Howard Hughes Medical Institute and the Gordon and Betty Moore Foundation (through Grant GBMF3070). The work is conducted by the US Department of Energy Joint Genome Institute and supported by the Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231.

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Contributions

C.Y.N., C.-H.W. and C.-L.W. designed the experiment, analysed the data and wrote the manuscript. C.Y.N., C. Choi, Y.Y., C. Chen, R.K., M.W., J.L., H.T. and C.D. performed the experiments. C.-H.W, H.C. and A.P. performed the informatics analysis. K.L., B.B., R.B. and T.N. performed the experiment for LC-MS/MS and analysed the data. J.J. and X.J. performed the TLC-GCMS experiments and analysed the data. L.L., J G.G.-C. and K.K.N. performed the enhancer assay, protein purification experiments. A.V. J.B., T.N., K.K.N. and C.-L.W contributed to the manuscript preparation.

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Correspondence to Chia-Lin Wei.

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Ngan, C., Wong, CH., Choi, C. et al. Lineage-specific chromatin signatures reveal a regulator of lipid metabolism in microalgae. Nature Plants 1, 15107 (2015). https://doi.org/10.1038/nplants.2015.107

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