Abstract
Well-organized chromatin is involved in a number of various transcriptional regulation and gene expression. We used genome-wide mapping of nucleosomes in response to different nitrogen conditions to determine both nucleosome profiles and gene expression events in Saccharomyces cerevisiae. Nitrogen conditions influence general nucleosome profiles and the expression of nitrogen catabolite repression (NCR) sensitive genes. The nucleosome occupancy of TATA-containing genes was higher compared to TATA-less genes. TATA-less genes in high or low nucleosome occupancy, showed a significant change in gene coding regions when shifting cells from glutamine to proline as the sole nitrogen resource. Furthermore, a correlation between the expression of nucleosome occupancy induced NCR sensitive genes or TATA containing genes in NCR sensitive genes, and nucleosome prediction were found when cells were cultured in proline or shifting from glutamine to proline as the sole nitrogen source compared to glutamine. These results also showed that variation of nucleosome occupancy accompany with chromatin-dependent transcription factor could influence the expression of a series of genes involved in the specific regulation of nitrogen utilization.
Highlights
Nucleosomes form the basic repeating unit of eukaryotic chromatin, consisting of ~147 bp DNA wrapped around a histone octamer core[1,2,3]
Much experimental work has focused on determining the relationship between genome-wide nucleosome positioning and the regulation of gene expression and how these changes of nucleosome positioning influence gene expression[27]
Dynamic remodeling of nucleosomes in the S. cerevisiae S288C genome was mapped under different nitrogen conditions using a combination of micrococcal nuclease digestion, mononucleosome DNA isolation and the Illumina high-throughput sequencing technologies
Summary
Nucleosomes form the basic repeating unit of eukaryotic chromatin, consisting of ~147 bp DNA wrapped around a histone octamer core[1,2,3]. Dynamic changes of genome-wide maps of nucleosome positions reflect a set of molecular processes, including DNA replication, gene expression and transcription regulation[4,5]. More than 392 genes are involved in the response to changes of nitrogen source type and quality and about 90 genes are regulated directly by the four GATA regulators[9,14,15] A 3′ NFR present in >95% of all genes might be important in transcription termination;[23] the dynamic change of nucleosome positions in response to different nitrogen conditions has not been examined on a genome-wide scale in S. cerevisiae. To map the location of individual nucleosomes on a genomic scale in response to different nitrogen conditions, we used a MNase-seq method to sequence the ends of nucleosome-associated DNA. The expression of NCR-sensitive genes was calculated to investigate their relationship under different nitrogen conditions
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