Chromatin profiling of the human fungal pathogen Candida albicans

In this study, we have used ChIP-seq to establish the first comprehensive genome-wide map of histone modifications (H3K9Ac, H4K16Ac, H3K4me3, H2AS129p) in C. albicans. To understand the link between histone modification states and transcriptional activity, we have performed genome-wide mapping of RNA Polymerase II (RNAPII), in addition to transcriptome expression profiling. We demonstrate that specific chromatin states associate with the repetitive and non-repetitive C. albicans genome. While gene-rich regions are associated with active chromatin marks mirroring their transcriptional state, different types of repetitive elements are assembled into distinct chromatin types. Finally, we developed the first C. albicans quantitative ChIP-seq (q-ChIP-seq) methodology that, coupled to genome-wide expression profiling, allowed us to determine the roles the HDAC Sir2 and the HMT Set1 play in shaping the chromatin state of C. albicans genome and regulating gene expression.