Talk Abstract

Epigenetic regulation in plants is a mystic yet excellent complement to genetic controls in their developmental programs and stress responses.  The advances in sequencing technologies in the past decades opened up possibilities to profile and analyze multiple epigenetic factors, including DNA methylation, histone modifications, and chromatin accessibility, to present a more complete picture of plant genomics that has never been revealed.  The technologies brought in new biological insights but also generate multiple data analysis challenges.

My lab has been devising bioinformatic strategies based on biological hypotheses, followed by computational implementation supported by statistical modeling.  In the past few years, we were privileged to work with many excellent bioinformaticians and plant biologists; together, we have dissected the epigenome impacts of callus transformation in rice and the synergistic regulation in Arabidopsis.  As a focus of our research programme, we developed a series of bioinformatic tools specific for epigenome analysis, including profiling DNA methylation landscapes, identifying epialleles highly correlated with transcription, and visualizing and analyzing genomewide chromatin accessibility.  Lastly, we are leveling up to turn epigenomes from attributes of genomes to predictors of gene regulation.  Altogether, we are excited to be able to unveil small pieces of the mystery in epigenomes.

KEYWORDS: Epigenome, Bioinformatics, Gene regulation, Rice, DNA methylation, Histone Modifications

Speaker Biography

Dr. Pao-Yang Chen received his Ph.D. degree in Statistics (computational biology) from Oxford University, where he studied statistical modeling of protein interaction networks.  He joined Prof. Matteo Pellegrini’s laboratory at the University of California, Los Angeles, where he expanded his research interests to the genomic and epigenomic data analysis in plants, animals, and human.  Dr. Chen is now associate research fellow at Institute of Plant and Microbial Biology, Academia Sinica, Taiwan.

His group is interested in developing bioinformatic strategies to interpret genomic and epigenomic data.  By integrating data produce from the massively parallel sequencing technologies, his group implements novel analytical strategies to solve problems in genetics and molecular biology.  The Chen lab has been developing bioinformatic platforms and pipelines for computationally processing and analyzing the epigenomes of plants (such as rice, maize, Arabidopsis), animal and fungi.  The lab research goes beyond DNA methylation to really consider all layers of epigenomes together.  With what they have learned from plants, animals and fungi, the Chen lab also contributed to rice epigenome research, hopefully, advance our current sciences in epigenomics from multiple aspects.