Data from Price et al. 2019

Chromatin profiling of the repetitive and non-repetitive genome of the human fungal pathogen Candida albicans

Our study provides the first epigenomic maps of histone modifications throughout the C. albicans genome. We have generated genome-wide profiles of histone modifications (H3K4me3, H3K9Ac, H4K16Ac and H2AS129p) and investigated their relationship to gene expression, using ChIP-seq and RNA-seq. We have also investigated the roles of two chromatin modifiers, SIR2 and SET1.

Here, we provide the coverage tracks for the ChIP-seq data, as well as the genome assembly and annotation files used in our analyses. All genome-wide experiments were carried out in duplicate.

Instructions for Use

The coverage tracks provided can be opened with IGV, which can be obtained from the Broad Institute website below:

Integrative Genomics Viewer (IGV)

 

Our analyses were performed using a custom haploid version of assembly 22 of the C. albicans genome, as well as a custom annotation file consisting of the A22 features combined with a large number of non-coding RNAs.

A22_Chromosomes.fasta
A22_All_Features.gff3

 

Our custom C. albicans A22 assembly and associated features can be loaded into IGV following the instructions at the link below:

How to Load a Custom Genome into IGV

Wild Type Coverage Tracks

The following coverage tracks were all obtained from wild type (BWP17) cells grown under normal laboratory conditions (YPD, 30C). The histone modification tracks are normalised to unmodified histone H4, and the RNAPII track is normalised to the corresponding input sample.

 

WT_H2AS129p.bigwig
WT_H3.bigwig
WT_H3K4me3.bigwig
WT_H3K9Ac.bigwig
WT_H4K16Ac.bigwig

WT_RNAPII.bigwig

 

Mutant Coverage Tracks

The following coverage tracks were obtained from either sir2Δ/Δ (H3K9ac and H4K16ac) or set1 Δ/Δ (H3K4me3) mutant cells grown under normal laboratory conditions (YPD, 30C). The tracks are normalised to the corresponding wild type sample.

sir2_H3K9Ac.bigwig
sir2_H4K16Ac.bigwig
set1_H3K4me3.bigwig

Wild Type Significant Regions

The following BED files can be used to indicate which peaks show a statistically significant enrichment or depletion compared to histone H4 occupancy. The score indicates the average log2 fold change across that region.

 

For each interval, biological duplicate counts were compared between each histone modification and unmodified histone H4 samples using DESeq2, with an adjusted p-value threshold of <0.05 being used to identify significant differences.

 

Significant_WT_H2AS129p_Regions.bed
Significant_WT_H3_Regions.bed
Significant_WT_H3K4me3_Regions.bed
Significant_WT_H3K9Ac_Regions.bed
Significant_WT_H4K16Ac_Regions.bed

 

 

Mutant Significant Regions

The following BED files can be used to indicate which peaks in the mutant strains show a statistically significant enrichment or depletion compared to occupancy in the wild type strain. The score indicates the average log2 fold change across that region.

 

For each interval, reference reads per million (RRPM) values were compared between the mutant and WT samples using a two-sample t-test, with a p-value threshold of <0.05 being used to identify significant differences.

 

Significant_sir2_H3K9Ac_Regions.bed
Significant_sir2_H4K16Ac_Regions.bed
Significant_set1_H3K4me3_Regions.bed

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