Covalent modifications of the amino-termini of the core histones in nucleosomes have been shown to be one of the key regulatory mechanisms in transcription regulation. Recently, new roles for histone modifications have been uncovered for the efficient functioning of RNA Pol II. Besides acetylation, which is the most characterized to date these modifications comprise phosphorylation, methylation, and ubiquitination. This review gives comprehensive view of all the major histone modifications and their effect on transcriptional regulation, in Saccharomyces cerevisiae.