Genome-wide Map of Nucleosome Acetylation and Methylation in Yeast

Abstract

Eukaryotic genomes are packaged into nucleosomes whose position and chemical modification state can profoundly influence regulation of gene expression. We profiled nucleosome modifications across the yeast genome using chromatin immunoprecipitation coupled with DNA microarrays to produce high-resolution genome-wide maps of histone acetylation and methylation. These maps take into account changes in nucleosome occupancy at actively transcribed genes and, in doing so, revise previous assessments of the modifications associated with gene expression. Both acetylation and methylation of histones are associated with transcriptional activity, but the former occurs predominantly at the beginning of genes, whereas the latter can occur throughout transcribed regions. Most notably, specific methylation events are associated with the beginning, middle, and end of actively transcribed genes. These maps provide the foundation for further understanding the roles of chromatin in gene expression and genome maintenance.

The histone methylase Set2p and the histone deacetylase Rpd3p repress meiotic recombination at the HIS4 meiotic recombination hotspot in Saccharomyces cerevisiae

“…We also examined the effects of eliminating Dot1p, an H3K79 histone methyltransferase (38,39). H3K79 methylation is at low levels at yeast telomeres (40), but occurs at high levels at activelytranscribed genes (41). As described below, we found that deletion of SET2 or RPD3 strongly stimulated HIS4 hotspot activity, whereas deletion of HDA1 had a more subtle stimulatory effect.…”

DNA microarray technologies for measuring protein–DNA interactions

“…In another study using such arrays, the nuclear pore associated protein Mlp1 was found to associate with alpha-factor-induced genes in an RNA-dependent manner, suggesting a mechanism for chromosome conformational changes in response to the alpha factor mating pheromone [·25]. A separate study used an Agilent DNA microarray containing ∼44,000 60-mer oligonucleotides covering most of the yeast genome at an average probe density of 266 bp to map histone acetylation and methylation at high resolution [26]. In another study, histone methylations in mouse embryonic stem cells were mapped using Affymetrix arrays customdesigned to tile noncoding regions that are highly conserved over mammalian genomes and may be important for gene regulation during development [27].…”

Conditional Random Fields for Predicting and Analyzing Histone Occupancy, Acetylation and Methylation Areas in DNA Sequences

“…There have been recently many studies of mapping histone occupancies together with their modifications in DNA sequences and of relationship between them and various genetic activities concerning DNAs [1,2,5,7,16,18,19]. But most of these studies were experimentally conducted by the combination of chromatin immunoprecipitation and whole-genome DNA microarrays, or ChIP-Chip protocol.…”

“…The majority of acetylation and methylation occurs at specific highly conserved residues in the histone components of nucleosomes: acetylation sites include at least nine lysines in histone H3 and H4 (H3K9, H3K14, H3K18, H3K23, H3K27, H4K5, H4K8, H4K12, and H4K16); methylation sites include H3K4, H3K9, H3K27, H3K36, H3K79, H3R17, H4K20, H4K59, H4R3 [14]. When a nucleosome appears in a specific DNA sequence area, these potentially sites can have a certain acetylation or methylation level [5,16].…”

“…The histone components of nucleosomes and their modification state (of which acetylation and methylation are the most important ones) can profoundly influence many genetic activities, including transcription [2,4,5,16], DNA repair, and DNA remodeling [13].…”