Arabidopsis Phytochrome A Directly Targets Numerous Promoters for Individualized Modulation of Genes in a Wide Range of Pathways

Author Profile

Fang Chen and Bosheng Li

Fang Chen

Current Position: Associate Research Scientist, Department of Molecular, Cellular, and Developmental Biology, Yale University, USA.

Education: PhD, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences.

Non-scientific Interests: Reading, cooking, sewing, jogging and travelling.

The birth announcement of Dolly the cloned sheep in 1997 dragged my interests to biology and made me choose biology as my major in college. After I learned the basic knowledge of molecular and cellular biology and got my B.S. degree at Shanghai University, I pursued my Ph.D. degree in SIPPE under the supervision of Dr. Zuhua He. As a Ph.D. student, I studied how rice fights pathogen attack on the cellular and proteomic level and further gained expertise on plant interaction with external environmental stimuli. After my Ph.D. graduation, I was fortunate to get an opportunity to work with Dr. Xing-Wang Deng, an expert in plant responses to the most important environmental cue--light signals. In his lab at Yale University, I found that the far-red light photoreceptor phytochrome A is able to directly associate with chromatin for gene regulation upon far-red light irradiation (Chen et al., The Plant Cell, 2012). Thanks to the availability of bioinformatics support in our lab, it is feasible to thoroughly analyze the high-throughput sequencing data of phytochrome A-associated DNA at a genome-wide level and further reveal how the photoreceptor transduces far-red light to downstream genes in coordination with other signaling pathways in the cell.

Bosheng Li

Current Position: Postdoc Associate, Molecular Cellular and Developmental Biology, Yale University.

Education: PhD, Silviculture, Beijing Forestry University.

Non-scientific Interests:: Badminton, swimming, ski, opera and travel.

I got my Bachelor's degree in biological technology at Beijing Forestry University (BJFU) in 2006. During my subsequent PhD study at BJFU, I focused on research in plant microRNAs and bioinformatics. Before I received my PhD degree in 2012, I had a great opportunity to join Professor Xing-Wang Deng's lab as a visiting student in 2010 and again became a postdoctoral associate in 2013. Professor Deng had a great idea to systematically identify the targets of photomorphogenesis essential transcript factors by chromatin immunoprecipitation and sequencing (ChIP-seq). Using his idea, I previously worked with Dr. Ouyang Xinhao and other colleagues explored the target genes of Far-Red Elongated Hypocotyl3 (FHY3) and revealed its new function in controlling chloroplast development (Ouyang et al., the Plant Cell 2011). In this study, our scope was expanded to include the far-red light photoreceptor phytochrome A (phyA). Dr. Fang Chen and I identified the phyA associated chromatin sites genome-wide, in which I contributed the bioinformatics analysis.