Abstract

Aspergillus niger is a commercially important producer of enzymes and organic acids. In this study, I have examined the distribution of trimethylated lysine 4 of histone H3 (H3K4me3) in the A. niger genome. I performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) to determine the genomic regions enriched for nucleosomes with this histone modification. I have conducted an analysis of the resulting peaksets to determine the optimal peak finding parameters for use in the detection of H3K4me3 ChIP-enriched regions in A. niger. As H3K4me3 was previously widely reported to mark actively transcribed genes, genome-wide ChIP-seq maps for maltose and xylose growth were compared with transcriptome data generated under the same growth conditions. Almost all genes that contained H3K4me3 are actively transcribed. However, nearly a third of all actively transcribed genes are not associated with H3K4me3. In addition, H3K4me3 is not associated with the majority of genes differentially expressed on maltose or xylose growth. Chromosomal maps revealed that this histone modification is non-randomly distributed in the genome. In particular, H3K4me3 is enriched at pericentromeric regions, but absent at the centromere and at regions proximal to the telomeres. Finally, H3K4me3 occasionally localized to actively transcribed regions not predicted to contain a gene model. The results of this study suggest that H3K4me3 is positively correlated with transcriptional activity, but is not a definitive marker of active gene expression. Furthermore, this modification is highly locally organized along A. niger chromosomes. Epigenetic phenomena in A. niger warrant further study to determine their significance in genome regulation.