ABSTRACTThe University of ManchesterAndrei-Stefan LiaMaster of PhilosophyAn RNA-Seq approach to investigate light-controlled gene expression in Neurospora crassa with emphasis on red light-mediated responses14th of October 2014With increasing numbers of genomes being sequenced, many phytochrome homologues have been identified across cyanobacteria, eubacteria and filamentous fungi. In recent years, two phytochrome homologues were identified in the filamentous fungus Neurospora crassa. Although functional and phenotypic analyses have been successful in other fungal species, the functional significance of Neurospora phytochromes remains unknown.In this body of work, we aim to investigate light-regulated gene expression via an RNA-Seq approach. Bioinformatic analysis of RNA-Seq data has not only shown that there is an independent red light response, but that this response is also controlled by the two phytochrome genes. Our analysis also confirms previously established light-regulated genes. We establish differentially expressed gene sets, from which we extracted cis-regulatory elements.Finally, we also show that phytochromes are mediators of a thermal acclimation response.