An ambitious EC-funded research initiative on epigenetics advancing towards systems biology

Even though the number of sequenced plant genomes is growing rapidly, the accurate annotation of different gene types as well as regulatory elements provides a major challenge, especially for large genomes like rice (O. sativa) or corn (Z. mays). Whereas existing genome annotation tools are usually based solely on the DNA sequence information of a single species, we want to explore methods based on genome-wide epigenetic information and comparative sequence analysis to characterize complex plant genomes and identify functional elements with increased sensitivity. Currently, we are integrating different publicly available plant epigenomic –Seq datasets (e.g. histone modifications, DNase I hypersensitive sites [DHS] and DNA methylation) to identify genome-wide epigenetic states and perform, combined with cis-regulatory element analysis, detailed regulatory genome annotation. Furthermore, we are evaluating advanced unsupervised genome segmentation algorithms to improve plant genome annotations using epigenomic states. In order to increase the resolution of regulatory DNA annotation, we have developed both alignment and non-alignment-based phylogenetic footprinting methods to identify conserved non-coding sequences in both closely and more distantly related plant genomes. Combined with detailed expression clustering and condition-dependent DHS information, we want to convert these static cis-regulatory element maps to condition-dependent activity tracks. Finally, through the integration of RNA-Seq expression data, we will analyze whether specific chromatin signatures mark gene sets with specific expression patterns or functional roles.

Lab members involved:

• Jan Van de Velde (PhD student)
• Ken Heyndrickx (PhD student)
• Dries Vaneechoutte (PhD student)