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Series GSE154497 Query DataSets for GSE154497
Status Public on Nov 12, 2020
Title Chromatin accessibility profiling in Neurospora crassa reveals features associated with accessible and inaccessible chromatin
Organism Neurospora crassa
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Background: Regulation of chromatin accessibility and transcription are tightly coordinated processes. Studies in yeast and higher eukaryotes has described accessible chromatin regions, but little work has been done in filamentous fungi. Results: Here 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. of accessible chromatin in Neurospora
Overall design Mycelial cultures collected at 18 hours. Cells lysed and subjected to ATAC-seq or chromatin immunoprecipitation. 18 total samples, replicates vary by sample.
Contributor(s) Ferraro AR, Lu Z, Courtney AJ, Kamei M, Schmitz RJ, Lewis ZA
Citation(s) 34147068
Submission date Jul 15, 2020
Last update date Jul 02, 2021
Contact name Zachary A Lewis
Organization name University of Georgia
Department Microbiology
Lab Lewis
Street address 1000 Cedar St. Biosciences Bldg
City Athens
State/province GA
ZIP/Postal code 30602
Country USA
Platforms (1)
GPL20660 Illumina NextSeq 500 (Neurospora crassa)
Samples (18)
GSM4672236 WT_ATACseq_unsortedNuclei
GSM4672237 WT_ATACseq_sortedNuclei
GSM4672238 WT_ ATACseq_Rep1
BioProject PRJNA646493
SRA SRP272099

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Supplementary file Size Download File type/resource
GSE154497_RAW.tar 703.2 Mb (http)(custom) TAR (of BW)
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Raw data are available in SRA
Processed data provided as supplementary file

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