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

Nature Plants

Volumn 1, Issue , 2015, Pages

  Ngan, Chew Yee ^a   Wong, Chee Hong ^a   Choi, Cindy ^a   Yoshinaga, Yuko ^a   Louie, Katherine ^a,b   Jia, Jing ^c   Chen, Cindy ^a   Bowen, Benjamin ^a,b   Cheng, Haoyu ^a   Leonelli, Lauriebeth ^c   Kuo, Rita ^a,b   Baran, Richard ^c   Garciá Cerdán, José G ^a   Pratap, Abhishek ^a   Wang, Mei ^a   Lim, Joanne ^a   Tice, Hope ^a   Daum, Chris ^c   Xu, Jian ^a,b   Northen, Trent ^a,d,e   Visel, Axel ^a   Bristow, James ^a   Niyogi, Krishna K ^b,c   Wei, Chia Lin ^a   more..

^a DOE JOINT GENOME INSTITUTE   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^d QINGDAO INSTITUTE OF BIOENERGY AND BIOPROCESS TECHNOLOGY   (China)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84959270999     PISSN: None     EISSN: 20550278     Source Type: Journal    
DOI: 10.1038/nplants.2015.107     Document Type: Article

References (48)

1. Wijffels, R. H., Barbosa, M. J. An outlook on microalgal biofuels. Science 329, 796-799 (2010).
2. Merchant, S. S., Kropat, J., Liu, B., Shaw, J., Warakanont, J. TAG, you're it! Chlamydomonas as a reference organism for understanding algal triacylglycerol accumulation. Curr. Opin. Biotechnol. 23, 352-363 (2012).
3. Ferrell, J., Sarisky-Reed, V. National Algal Biofuels Technology Roadmap (eds Fishman, D. et al.) (US DOE, 2010).
4. Liu, B., Benning, C. Lipid metabolism in microalgae distinguishes itself. Curr. Opin. Biotechnol. 24, 300-309 (2013).
5. Blatti, J. L., Michaud, J., Burkart, M. D. Engineering fatty acid biosynthesis in microalgae for sustainable biodiesel. Curr. Opin. Chem. Boil. 17, 496-505 (2013).
6. Cagnon, C. et al. Development of a forward genetic screen to isolate oil mutants in the green microalga Chlamydomonas reinhardtii. Biotechnol. Biofuels 6, 178 (2013).
7. Csavina, J. L., Stuart, B. J., Riefler, R. G., Vis, M. L. Growth optimization of algae for biodiesel production. J. Appl. Microbiol. 111, 312-318 (2011).
8. Courchesne, N. M., Parisien, A., Wang, B., Lan, C. Q. Enhancement of lipid production using biochemical, genetic and transcription factor engineering approaches. J. Biotechnol. 141, 31-41 (2009).
9. Hu, Q. et al. Microalgal triacylglycerols as feedstocks for biofuel production: perspectives and advances. Plant J. 54, 621-639 (2008).
10. Harris, E. H. The Chlamydomonas Sourcebook 2nd edn (Academic Press, 2009).
11. Radakovits, R., Jinkerson, R. E., Darzins, A., Posewitz, M. C. Genetic engineering of algae for enhanced biofuel production. Eukaryot. Cell 9, 486-501 (2010).
12. Merchant, S. S. et al. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318, 245-250 (2007).
13. Boyle, N. R. et al. Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas. J. Biol. Chem. 287, 15811-15825 (2012).
14. Hemschemeier, A. et al. Copper response regulator1-dependent and-independent responses of the Chlamydomonas reinhardtii transcriptome to dark anoxia. Plant Cell 25, 3186-3211 (2013).
15. Lauressergues, D. et al. Primary transcripts of microRNAs encode regulatory peptides. Nature 520, 90-93 (2015).
16. Nuruzzaman, M., Sharoni, A. M., Kikuchi, S. Roles of NAC transcription factors in the regulation of biotic and abiotic stress responses in plants. Front. Microbiol. 4, 248 (2013).
17. Borevitz, J. O., Xia, Y., Blount, J., Dixon, R. A., Lamb, C. Activation tagging identifies a conserved MYB regulator of phenylpropanoid biosynthesis. Plant Cell 12, 2383-2394 (2000).
18. Gonzalez-Ballester, D. et al. RNA-seq analysis of sulfur-deprived Chlamydomonas cells reveals aspects of acclimation critical for cell survival. Plant Cell 22, 2058-2084 (2010).
19. Castruita, M. et al. Systems biology approach in Chlamydomonas reveals connections between copper nutrition and multiple metabolic steps. Plant Cell 23, 1273-1292 (2011).
20. Kouzarides, T. Chromatin modifications and their function. Cell 128, 693-705 (2007).
21. Li, X. et al. High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression. Plant Cell 20, 259-276 (2008).
22. Wang, X. et al. Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell 21, 1053-1069 (2009).
23. Ay, N. et al. Epigenetic programming via histone methylation at WRKY53 controls leaf senescence in Arabidopsis thaliana. Plant J. 58, 333-346 (2009).
24. Consortium, E. P. et al. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
25. Celniker, S. E. et al. Unlocking the secrets of the genome. Nature 459, 927-930 (2009).
26. Roudier, F. et al. Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. EMBO J. 30, 1928-1938 (2011).
27. Casas-Mollano, J. A., van Dijk, K., Eisenhart, J., Cerutti, H. SET3p monomethylates histone H3 on lysine 9 and is required for the silencing of tandemly repeated transgenes in Chlamydomonas. Nucleic Acids Res. 35, 939-950 (2007).
28. Miller, R. et al. Changes in transcript abundance in Chlamydomonas reinhardtii following nitrogen deprivation predict diversion of metabolism. Plant Physiol. 154, 1737-1752 (2010).
29. Schmollinger, S. et al. Nitrogen-sparing mechanisms in Chlamydomonas affect the transcriptome, the proteome, and photosynthetic metabolism. Plant Cell 26, 1410-1435 (2014).
30. Peters, A. H. et al. Histone H3 lysine 9 methylation is an epigenetic imprint of facultative heterochromatin. Nature Genet. 30, 77-80 (2002).
31. Guenther, M. G., Levine, S. S., Boyer, L. A., Jaenisch, R., Young, R. A. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130, 77-88 (2007).
32. Ernst, J., Kellis, M. ChromHMM: automating chromatin-state discovery and characterization. Nature Methods 9, 215-216 (2012).
33. Luo, C. et al. Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production. Plant J. 73, 77-90 (2013).
34. Creyghton, M. P. et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl Acad. Sci. USA 107, 21931-21936 (2010).
35. Chepelev, I., Wei, G., Wangsa, D., Tang, Q., Zhao, K. Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization. Cell Res. 22, 490-503 (2012).
36. Shlyueva, D., Stampfel, G., Stark, A. Transcriptional enhancers: from properties to genome-wide predictions. Nature Rev. Genet. 15, 272-286 (2014).
37. Moseley, J. L., Gonzalez-Ballester, D., Pootakham, W., Bailey, S., Grossman, A. R. Genetic interactions between regulators of Chlamydomonas phosphorus and sulfur deprivation responses. Genetics 181, 889-905 (2009).
38. Moseley, J. L., Chang, C. W., Grossman, A. R. Genome-based approaches to understanding phosphorus deprivation responses and PSR1 control in Chlamydomonas reinhardtii. Eukaryot. Cell 5, 26-44 (2006).
39. Wykoff, D. D., Grossman, A. R., Weeks, D. P., Usuda, H., Shimogawara, K. Psr1, a nuclear localized protein that regulates phosphorus metabolism in Chlamydomonas. Proc. Natl Acad. Sci. USA 96, 15336-15341 (1999).
40. Iwai, M., Ikeda, K., Shimojima, M., Ohta, H. Enhancement of extraplastidic oil synthesis in Chlamydomonas reinhardtii using a type-2 diacylglycerol acyltransferase with a phosphorus starvation-inducible promoter. Plant Biotechnol. J. 12, 808-819 (2014).
41. Chen,W., Zhang, C., Song, L., Sommerfeld, M., Hu, Q. A high throughput Nile red method for quantitative measurement of neutral lipids in microalgae. J. Microbiol. Methods 77, 41-47 (2009).
42. Liu, J. et al. Production potential of Chlorella zofingienesis as a feedstock for biodiesel. Bioresour Technol. 101, 8658-8663 (2010).
43. Moser, B. Biodiesel production, properties, and feedstocks. In Vitro Cell. Dev. Biol. Plant 45, 229-266 (2009).
44. Pinzi, S. et al. The ideal vegetable oil-based biodiesel composition: a review of social, economical and technical implications. Energy Fuels 23, 2325-2341 (2009).
45. Rubio, V. et al. A conserved MYB transcription factor involved in phosphate starvation signaling both in vascular plants and in unicellular algae. Genes Dev. 15, 2122-2133 (2001).
46. Chen, X. et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133, 1106-1117 (2008).
47. Parkhomchuk, D. et al. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res. 37, e123 (2009).
48. Rasala, B. A. et al. Robust expression and secretion of Xylanase1 in Chlamydomonas reinhardtii by fusion to a selection gene and processing with the FMDV 2A peptide. PLoS ONE 7, e43349 (2012).