Abstract
BackgroundRegulation of chromatin accessibility and transcription are tightly coordinated processes. Studies in yeast and higher eukaryotes have described accessible chromatin regions, but little work has been done in filamentous fungi.ResultsHere we present a genome-scale characterization of accessible chromatin regions in Neurospora crassa, which revealed characteristic molecular features of accessible and inaccessible chromatin. We present experimental evidence of inaccessibility within heterochromatin regions in Neurospora, and we examine features of both accessible and inaccessible chromatin, including the presence of histone modifications, types of transcription, transcription factor binding, and relative nucleosome turnover rates. Chromatin accessibility is not strictly correlated with expression level. Accessible chromatin regions in the model filamentous fungus Neurospora are characterized the presence of H3K27 acetylation and commonly associated with pervasive non-coding transcription. Conversely, methylation of H3 lysine-36 catalyzed by ASH1 is correlated with inaccessible chromatin within promoter regions. Conclusions: In N. crassa, H3K27 acetylation is the most predictive histone modification for open chromatin. Conversely, our data show that H3K36 methylation is a key marker of inaccessible chromatin in gene-rich regions of the genome. Our data are consistent with an expanded role for H3K36 methylation in intergenic regions of filamentous fungi compared to the model yeasts, S. cerevisiae and S. pombe, which lack homologs of the ASH1 methyltransferase.
Highlights
Regulation of chromatin accessibility and transcription are tightly coordinated processes
We report a diversity of promotor structures in Neurospora and we show that histone acetylation and small RNA production are highly correlated with accessible chromatin, whereas repressive modifications including H3 lysine methylation (H3K9me3), H3K27me2/ 3 and ASH1-catalyzed H3K36 methylation are correlated with inaccessible chromatin in this fungus
Characterization of accessible chromatin regions in Neurospora To characterize accessible regions in Neurospora, we performed ATAC-seq on wild type mycelial cultures. Because this assay is sensitive to contamination by mitochondria, we first performed ATAC-seq in nuclei that were sorted by flow cytometry and nuclei that were not sorted
Summary
Regulation of chromatin accessibility and transcription are tightly coordinated processes. Application of ATAC-seq in the pathogenic basidiomycete Cryptococcus neoformans has demonstrated that transcription factor ZNF2 and the Switch/Sucrose non-fermentable (SWI/SNF) complex create chromatin accessibility at filamentation genes during filamentation [27]. Another factor that may contribute to accessible chromatin is pervasive non-coding transcription [34,35,36]. While this study characterized small RNA production in the filamentous fungus Neurospora, raising the possibility that transcription may contribute to accessible chromatin, the authors did not identify accessible chromatin regions in this fungus
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