Chromatin landscaping in algae reveals novel regulation pathway for biofuels production
Abstract
The diminishing reserve of fossil fuels calls for the development of biofuels. Biofuels are produced from renewable resources, including photosynthetic organisms, generating clean energy. Microalgae is one of the potential feedstock for biofuels production. It grows easily even in waste water, and poses no competition to agricultural crops for arable land. However, little is known about the algae lipid biosynthetic regulatory mechanisms. Most studies relied on the homology to other plant model organisms, in particular Arabidopsis or through low coverage expression analysis to identify key enzymes. This limits the discovery of new components in the biosynthetic pathways, particularly the genetic regulators and effort to maximize the production efficiency of algal biofuels. Here we report an unprecedented and de novo approach to dissect the algal lipid pathways through disclosing the temporal regulations of chromatin states during lipid biosynthesis. We have generated genome wide chromatin maps in chlamydomonas genome using ChIP-seq targeting 7 histone modifications and RNA polymerase II in a time-series manner throughout conditions activating lipid biosynthesis. To our surprise, the combinatory profiles of histone codes uncovered new regulatory mechanism in gene expression in algae. Coupled with matched RNA-seq data, chromatin changes revealed potential novel regulators and candidate genes involved inmore »
- Authors:
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1171822
- Report Number(s):
- LBNL-6284E-Poster
- DOE Contract Number:
- DE-AC02-05CH11231
- Resource Type:
- Conference
- Resource Relation:
- Conference: Advances in Genome Biology & Technology, Marco Island, Florida, Feb 20 - 23, 2013
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 09 BIOMASS FUELS; 99 GENERAL AND MISCELLANEOUS; Chromatin, Microalgae, biofuels, feedstock
Citation Formats
Ngan, Chew Yee, Wong, Chee-Hong, Choi, Cindy, Pratap, Abhishek, Han, James, and Wei, Chia-Lin. Chromatin landscaping in algae reveals novel regulation pathway for biofuels production. United States: N. p., 2013.
Web.
Ngan, Chew Yee, Wong, Chee-Hong, Choi, Cindy, Pratap, Abhishek, Han, James, & Wei, Chia-Lin. Chromatin landscaping in algae reveals novel regulation pathway for biofuels production. United States.
Ngan, Chew Yee, Wong, Chee-Hong, Choi, Cindy, Pratap, Abhishek, Han, James, and Wei, Chia-Lin. 2013.
"Chromatin landscaping in algae reveals novel regulation pathway for biofuels production". United States. https://www.osti.gov/servlets/purl/1171822.
@article{osti_1171822,
title = {Chromatin landscaping in algae reveals novel regulation pathway for biofuels production},
author = {Ngan, Chew Yee and Wong, Chee-Hong and Choi, Cindy and Pratap, Abhishek and Han, James and Wei, Chia-Lin},
abstractNote = {The diminishing reserve of fossil fuels calls for the development of biofuels. Biofuels are produced from renewable resources, including photosynthetic organisms, generating clean energy. Microalgae is one of the potential feedstock for biofuels production. It grows easily even in waste water, and poses no competition to agricultural crops for arable land. However, little is known about the algae lipid biosynthetic regulatory mechanisms. Most studies relied on the homology to other plant model organisms, in particular Arabidopsis or through low coverage expression analysis to identify key enzymes. This limits the discovery of new components in the biosynthetic pathways, particularly the genetic regulators and effort to maximize the production efficiency of algal biofuels. Here we report an unprecedented and de novo approach to dissect the algal lipid pathways through disclosing the temporal regulations of chromatin states during lipid biosynthesis. We have generated genome wide chromatin maps in chlamydomonas genome using ChIP-seq targeting 7 histone modifications and RNA polymerase II in a time-series manner throughout conditions activating lipid biosynthesis. To our surprise, the combinatory profiles of histone codes uncovered new regulatory mechanism in gene expression in algae. Coupled with matched RNA-seq data, chromatin changes revealed potential novel regulators and candidate genes involved in the activation of lipid accumulations. Genetic perturbation on these candidate regulators further demonstrated the potential to manipulate the regulatory cascade for lipid synthesis efficiency. Exploring epigenetic landscape in microalgae shown here provides powerful tools needed in improving biofuel production and new technology platform for renewable energy generation, global carbon management, and environmental survey.},
doi = {},
url = {https://www.osti.gov/biblio/1171822},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Tue Feb 19 00:00:00 EST 2013},
month = {Tue Feb 19 00:00:00 EST 2013}
}