Abstract

Post-translational modifications of histones (e.g. acetylation, methylation, phosphorylation and ubiquitination) play crucial roles in regulating gene expression by altering chromatin structures and creating docking sites for histone/chromatin regulators. However, the combination patterns of histone modifications, regulatory proteins and their corresponding target genes remain incompletely understood. Therefore, it is advantageous to have a tool for the enrichment/depletion analysis of histone modifications and histone/chromatin regulators from a gene list. Many ChIP-chip/ChIP-seq datasets of histone modifications and histone/chromatin regulators in yeast can be found in the literature. Knowing the needs and having the data motivate us to develop a web tool, called Yeast Histone Modifications Identifier (YHMI), which can identify the enriched/depleted histone modifications and the enriched histone/chromatin regulators from a list of yeast genes. Both tables and figures are provided to visualize the identification results. Finally, the high-quality and biological insight of the identification results are demonstrated by two case studies. We believe that YHMI is a valuable tool for yeast biologists to do epigenetics research.

Introduction

Histone modification and chromatin remodelling play an important role in DNA replication, transcription and DNA repair (1–3). The N-terminal and C-terminal tails of histones are subject to post-translational modifications, including acetylation, methylation, phosphorylation and ubiquitination (4, 5). Several lines of evidence have shown that these modified histones provide the binding sites for effector proteins to elicit specific and selective effects on these biological processes (1, 6). To date, a large number of domains within these effector proteins that can be associated with acetylated, methylated and phosphorylated histones have been characterized. For example, the bromodomain binds to acetylated histones (7); the BRCA1 C Terminus (BRCT) domain binds to the phosphorylated histones (8); and the plant homeodomain (PHD), chromodomain and tudor domains associate with methylated histones (9–14). A recent study further revealed that tandem PHD fingers of MORF/MOZ acetyltransferases display selectivity for acetylated histone H3 (15). Many chromatin-associated proteins themselves contain these domains or are partnered with effector proteins containing these domains. Therefore, multivalent and combinatorial interactions are likely to be an important aspect of how these chromatin-associated proteins work—a concept known as the histone code hypothesis (1, 6). However, how these multivalent and combinatorial interactions contribute to various biological processes in response to environmental stimuli remains incompletely understood.

In yeast Saccharomyces cerevisiae, histones are modified by various histone modification complexes, including Spt-Ada-Gcn5-Acetyltransferase (SAGA), NuA4, COMPASS, Set2 and Dot1 (3, 4). SAGA and NuA4 complexes are able to acetylate histone H3 and histone H4 (H4ac), respectively (3, 16, 17). The COMPASS complex, Set2 and Dot1 are able to methylate lysine 4 of histone H3 (H3K4me), lysine 36 of histone H3 (H3K36me) and lysine 79 of histone H3 (H3K79me), respectively (3). Information about the other histone modifications and their related enzymes is listed in Table 1. The chromatin remodelling complexes include SWI/SNF, RSC, ISWI, CHD, INO80 and SWR1 that are able to slide, displace and exchange histones (3). The histone modification and chromatin remodelling complexes often form a large complex with many subunits containing bromodomain, chromodomain or PHD domain. Therefore, it is likely that the combination of these domains plays an important role in selectivity and specificity of these complexes to their target genes. There are about 400 proteins that regulate gene transcription (18). Therefore, many open questions remain. How many regulators and specific histone modifications are needed to transcribe a subset of genes in response to environmental stimuli? Are there combination patterns of these domains and their corresponding modified histones in order to transcribe a subset of genes?

Table 1

Many known histone modifications in S. cerevisiae are provided. Most of the information in this table came from Rando and Winston (3)

HistoneResidueModificationModification enzyme
H2AK5AcEsa1, Rpd3
S129PhMec1, Tel1, Pph3
H2BK123UbRad6, Ubp8
H3R2Me
K4Me, AcSet1, Jhd2, Rtt109, Gcn5
K9AcGcn5, Rpd3, Hos2, Hda1
S10PhSnf1
K14AcGcn5, Rpd3, Hos2, Hda1
K18AcGcn5, Rpd3, Hos2, Hda1
K23AcGcn5, Rpd3, Hos2, Hda1
K27Ac
K36MeSet2, Rph1, Jhd1
K56AcRtt109, Hst3, Hst4
K79MeDot1
H4R3Me
K5AcEsa1, Rpd3, Hos2
K8AcEsa1, Rpd3, Hos2
K12AcEsa1, Rpd3, Hos2
K16AcEsa1, Sas2, Sir2, Hos2, Hst1
K20Me
HistoneResidueModificationModification enzyme
H2AK5AcEsa1, Rpd3
S129PhMec1, Tel1, Pph3
H2BK123UbRad6, Ubp8
H3R2Me
K4Me, AcSet1, Jhd2, Rtt109, Gcn5
K9AcGcn5, Rpd3, Hos2, Hda1
S10PhSnf1
K14AcGcn5, Rpd3, Hos2, Hda1
K18AcGcn5, Rpd3, Hos2, Hda1
K23AcGcn5, Rpd3, Hos2, Hda1
K27Ac
K36MeSet2, Rph1, Jhd1
K56AcRtt109, Hst3, Hst4
K79MeDot1
H4R3Me
K5AcEsa1, Rpd3, Hos2
K8AcEsa1, Rpd3, Hos2
K12AcEsa1, Rpd3, Hos2
K16AcEsa1, Sas2, Sir2, Hos2, Hst1
K20Me
Table 1

Many known histone modifications in S. cerevisiae are provided. Most of the information in this table came from Rando and Winston (3)

HistoneResidueModificationModification enzyme
H2AK5AcEsa1, Rpd3
S129PhMec1, Tel1, Pph3
H2BK123UbRad6, Ubp8
H3R2Me
K4Me, AcSet1, Jhd2, Rtt109, Gcn5
K9AcGcn5, Rpd3, Hos2, Hda1
S10PhSnf1
K14AcGcn5, Rpd3, Hos2, Hda1
K18AcGcn5, Rpd3, Hos2, Hda1
K23AcGcn5, Rpd3, Hos2, Hda1
K27Ac
K36MeSet2, Rph1, Jhd1
K56AcRtt109, Hst3, Hst4
K79MeDot1
H4R3Me
K5AcEsa1, Rpd3, Hos2
K8AcEsa1, Rpd3, Hos2
K12AcEsa1, Rpd3, Hos2
K16AcEsa1, Sas2, Sir2, Hos2, Hst1
K20Me
HistoneResidueModificationModification enzyme
H2AK5AcEsa1, Rpd3
S129PhMec1, Tel1, Pph3
H2BK123UbRad6, Ubp8
H3R2Me
K4Me, AcSet1, Jhd2, Rtt109, Gcn5
K9AcGcn5, Rpd3, Hos2, Hda1
S10PhSnf1
K14AcGcn5, Rpd3, Hos2, Hda1
K18AcGcn5, Rpd3, Hos2, Hda1
K23AcGcn5, Rpd3, Hos2, Hda1
K27Ac
K36MeSet2, Rph1, Jhd1
K56AcRtt109, Hst3, Hst4
K79MeDot1
H4R3Me
K5AcEsa1, Rpd3, Hos2
K8AcEsa1, Rpd3, Hos2
K12AcEsa1, Rpd3, Hos2
K16AcEsa1, Sas2, Sir2, Hos2, Hst1
K20Me
YHMI includes the ChIP-chip/ChIP-seq datasets of 32 histone marks and 83 histone/chromatin regulators.
Figure 1

YHMI includes the ChIP-chip/ChIP-seq datasets of 32 histone marks and 83 histone/chromatin regulators.

Table 2

The information about the collected ChIP-chip/ChIP-seq datasets of histone modifications (15 histone acetylation, 13 histone methylation, 2 histone phosphorylation, 1 histone ubiquitination and 1 histone variant). See Supplementary Table 1 for details

Type of histone modificationData valueType of histone modificationData value
Acetylation (H2AK5ac)alog2(H2AK5ac/Inputb)Methylation (H3R2me2a)clog2(H3R2me2a/H3)
Acetylation (H3K4ac)log2(H3K4ac/H3)Methylation (H3K4me)log2(H3K4me/H3)
Acetylation (H3K9ac)log2(H3K9ac/H3)Methylation (H3K4me2)log2(H3K4me2/H3)
Acetylation (H3K14ac)log2(H3K14ac/H3)Methylation (H3K4me3)log2(H3K4me3/H3)
Acetylation (H3K14ac [H2O2]d)log2(H3K14ac/H3)Methylation (H3K36me)alog2(H3K36me/Input)
Acetylation (H3K18ac)alog2(H3K18ac/Input)Methylation (H3K36me2)alog2(H3K36me2/Input)
Acetylation (H3K23ac)alog2(H3K23ac/Input)Methylation (H3K36me3)log2(H3K36me3/H3)
Acetylation (H3K27ac)alog2(H3K27ac/Input)Methylation (H3K79me)alog2(H3K79me/Input)
Acetylation (H3K56ac)alog2(H3K56ac/Input)Methylation (H3K79me2)MATe score (H3K79me2/Input)
Acetylation (H4ac)log2(H4ac/H3)Methylation (H3K79me3)MAT score (H3K79me3/Input)
Acetylation (H4ac [H2O2]d)log2(H4ac/H3)Methylation (H4R3me)alog2(H4R3me/Input)
Acetylation (H4K5ac)alog2(H4K5ac/Input)Methylation (H4R3me2s)alog2(H4R3me2s/Input)
Acetylation (H4K8ac)alog2(H4K8ac/Input)Methylation (H4K20me)alog2(H4K20me/Input)
Acetylation (H4K12ac)alog2(H4K12ac/Input)Phosphorylation (H2AS129ph)alog2(H2AS129ph/Input)
Acetylation (H4K16ac)alog2(H4K16ac/Input)Phosphorylation (H3S10ph)alog2(H3S10ph/Input)
Histone Variant (H2AZ)log2(H2AZ/H2B)Ubiquitination (H2BK123ub)MAT score (H2BK123ub/Input)
Type of histone modificationData valueType of histone modificationData value
Acetylation (H2AK5ac)alog2(H2AK5ac/Inputb)Methylation (H3R2me2a)clog2(H3R2me2a/H3)
Acetylation (H3K4ac)log2(H3K4ac/H3)Methylation (H3K4me)log2(H3K4me/H3)
Acetylation (H3K9ac)log2(H3K9ac/H3)Methylation (H3K4me2)log2(H3K4me2/H3)
Acetylation (H3K14ac)log2(H3K14ac/H3)Methylation (H3K4me3)log2(H3K4me3/H3)
Acetylation (H3K14ac [H2O2]d)log2(H3K14ac/H3)Methylation (H3K36me)alog2(H3K36me/Input)
Acetylation (H3K18ac)alog2(H3K18ac/Input)Methylation (H3K36me2)alog2(H3K36me2/Input)
Acetylation (H3K23ac)alog2(H3K23ac/Input)Methylation (H3K36me3)log2(H3K36me3/H3)
Acetylation (H3K27ac)alog2(H3K27ac/Input)Methylation (H3K79me)alog2(H3K79me/Input)
Acetylation (H3K56ac)alog2(H3K56ac/Input)Methylation (H3K79me2)MATe score (H3K79me2/Input)
Acetylation (H4ac)log2(H4ac/H3)Methylation (H3K79me3)MAT score (H3K79me3/Input)
Acetylation (H4ac [H2O2]d)log2(H4ac/H3)Methylation (H4R3me)alog2(H4R3me/Input)
Acetylation (H4K5ac)alog2(H4K5ac/Input)Methylation (H4R3me2s)alog2(H4R3me2s/Input)
Acetylation (H4K8ac)alog2(H4K8ac/Input)Methylation (H4K20me)alog2(H4K20me/Input)
Acetylation (H4K12ac)alog2(H4K12ac/Input)Phosphorylation (H2AS129ph)alog2(H2AS129ph/Input)
Acetylation (H4K16ac)alog2(H4K16ac/Input)Phosphorylation (H3S10ph)alog2(H3S10ph/Input)
Histone Variant (H2AZ)log2(H2AZ/H2B)Ubiquitination (H2BK123ub)MAT score (H2BK123ub/Input)
a

aThis is a ChIP-seq dataset.

b

b`Input’ means the control experiment, which is the ChIP-chip/ChIP-seq experiment without using any anti-histone modification (e.g. anti-H3K79me2) antibody.

c

cWe used the ChIP-chip dataset mapped to the plus strand.

d

dThe yeast cells are grown in the rich medium adding H2O2.

e

eMAT stands for Model-based Analysis of Tiling-arrays (48), which is an algorithm for reliably detecting enriched regions. The higher the MAT score, the higher the enrichment.

Table 2

The information about the collected ChIP-chip/ChIP-seq datasets of histone modifications (15 histone acetylation, 13 histone methylation, 2 histone phosphorylation, 1 histone ubiquitination and 1 histone variant). See Supplementary Table 1 for details

Type of histone modificationData valueType of histone modificationData value
Acetylation (H2AK5ac)alog2(H2AK5ac/Inputb)Methylation (H3R2me2a)clog2(H3R2me2a/H3)
Acetylation (H3K4ac)log2(H3K4ac/H3)Methylation (H3K4me)log2(H3K4me/H3)
Acetylation (H3K9ac)log2(H3K9ac/H3)Methylation (H3K4me2)log2(H3K4me2/H3)
Acetylation (H3K14ac)log2(H3K14ac/H3)Methylation (H3K4me3)log2(H3K4me3/H3)
Acetylation (H3K14ac [H2O2]d)log2(H3K14ac/H3)Methylation (H3K36me)alog2(H3K36me/Input)
Acetylation (H3K18ac)alog2(H3K18ac/Input)Methylation (H3K36me2)alog2(H3K36me2/Input)
Acetylation (H3K23ac)alog2(H3K23ac/Input)Methylation (H3K36me3)log2(H3K36me3/H3)
Acetylation (H3K27ac)alog2(H3K27ac/Input)Methylation (H3K79me)alog2(H3K79me/Input)
Acetylation (H3K56ac)alog2(H3K56ac/Input)Methylation (H3K79me2)MATe score (H3K79me2/Input)
Acetylation (H4ac)log2(H4ac/H3)Methylation (H3K79me3)MAT score (H3K79me3/Input)
Acetylation (H4ac [H2O2]d)log2(H4ac/H3)Methylation (H4R3me)alog2(H4R3me/Input)
Acetylation (H4K5ac)alog2(H4K5ac/Input)Methylation (H4R3me2s)alog2(H4R3me2s/Input)
Acetylation (H4K8ac)alog2(H4K8ac/Input)Methylation (H4K20me)alog2(H4K20me/Input)
Acetylation (H4K12ac)alog2(H4K12ac/Input)Phosphorylation (H2AS129ph)alog2(H2AS129ph/Input)
Acetylation (H4K16ac)alog2(H4K16ac/Input)Phosphorylation (H3S10ph)alog2(H3S10ph/Input)
Histone Variant (H2AZ)log2(H2AZ/H2B)Ubiquitination (H2BK123ub)MAT score (H2BK123ub/Input)
Type of histone modificationData valueType of histone modificationData value
Acetylation (H2AK5ac)alog2(H2AK5ac/Inputb)Methylation (H3R2me2a)clog2(H3R2me2a/H3)
Acetylation (H3K4ac)log2(H3K4ac/H3)Methylation (H3K4me)log2(H3K4me/H3)
Acetylation (H3K9ac)log2(H3K9ac/H3)Methylation (H3K4me2)log2(H3K4me2/H3)
Acetylation (H3K14ac)log2(H3K14ac/H3)Methylation (H3K4me3)log2(H3K4me3/H3)
Acetylation (H3K14ac [H2O2]d)log2(H3K14ac/H3)Methylation (H3K36me)alog2(H3K36me/Input)
Acetylation (H3K18ac)alog2(H3K18ac/Input)Methylation (H3K36me2)alog2(H3K36me2/Input)
Acetylation (H3K23ac)alog2(H3K23ac/Input)Methylation (H3K36me3)log2(H3K36me3/H3)
Acetylation (H3K27ac)alog2(H3K27ac/Input)Methylation (H3K79me)alog2(H3K79me/Input)
Acetylation (H3K56ac)alog2(H3K56ac/Input)Methylation (H3K79me2)MATe score (H3K79me2/Input)
Acetylation (H4ac)log2(H4ac/H3)Methylation (H3K79me3)MAT score (H3K79me3/Input)
Acetylation (H4ac [H2O2]d)log2(H4ac/H3)Methylation (H4R3me)alog2(H4R3me/Input)
Acetylation (H4K5ac)alog2(H4K5ac/Input)Methylation (H4R3me2s)alog2(H4R3me2s/Input)
Acetylation (H4K8ac)alog2(H4K8ac/Input)Methylation (H4K20me)alog2(H4K20me/Input)
Acetylation (H4K12ac)alog2(H4K12ac/Input)Phosphorylation (H2AS129ph)alog2(H2AS129ph/Input)
Acetylation (H4K16ac)alog2(H4K16ac/Input)Phosphorylation (H3S10ph)alog2(H3S10ph/Input)
Histone Variant (H2AZ)log2(H2AZ/H2B)Ubiquitination (H2BK123ub)MAT score (H2BK123ub/Input)
a

aThis is a ChIP-seq dataset.

b

b`Input’ means the control experiment, which is the ChIP-chip/ChIP-seq experiment without using any anti-histone modification (e.g. anti-H3K79me2) antibody.

c

cWe used the ChIP-chip dataset mapped to the plus strand.

d

dThe yeast cells are grown in the rich medium adding H2O2.

e

eMAT stands for Model-based Analysis of Tiling-arrays (48), which is an algorithm for reliably detecting enriched regions. The higher the MAT score, the higher the enrichment.

Previous studies have produced several valuable genome-wide ChIP-chip/ChIP-seq datasets of histone modifications and binding occupancy of histone/chromatin regulators in yeast Saccharomyces cerevisiae to facilitate epigenetics research (18–24). Since these datasets are scattered across the literature, several resources have been developed to provide histone modification information in yeast. For example, the Saccharomyces Genome Database (SGD) comprehensively collects the yeast histone modification datasets from the literature and allows users to visualize various histone modifications using JBrowse (a genome browser) (25). The Yeast Nucleosome Atlas (YNA) implements a tool for users to retrieve a list of yeast genes whose promoters and/or coding regions contain a specific combination of histone modifications (26). The ChromatinDB implements a tool for users to analyze specific histone modifications from the input gene list (27). These three resources altogether greatly help yeast biologists to do epigenetics research. Unfortunately, ChromatinDB is no longer available since 2014. Yeast biologists now are lacking a convenient tool to identify the enriched/depleted histone modifications in their gene lists routinely generated from high-throughput experimental technologies (e.g. microarray or next-generation sequencing).

To fill this gap, we developed a web tool called Yeast Histone Modification Identifier (YHMI). YHMI uses ChIP-chip/ChIP-seq datasets of 32 histone modifications (15 histone acetylation, 13 histone methylation, 2 histone phosphorylation, 1 histone ubiquitination and 1 histone variant) and 83 histone/chromatin regulators (18–24). When a user inputs a gene list, YHMI will identify the enriched/depleted histone modifications in the promoters/coding regions and the enriched histone/chromatin regulators in the promoters of the genes in the input list. The identification results are shown both in tables and figures. Therefore, YHMI can be used to shed light on what is unknown in a gene list of interest. Several possible biological questions could be answered by YHMI. For example, what are the enriched/depleted histone codes in a gene list of a specific property (e.g. highly transcribed genes, stress-responsive genes or genes in a specific pathway)? What are the enriched/depleted histone codes in a gene list associated with a specific factor (e.g. target genes of a transcription factor, lipid-binding proteins or hexose transporter genes)?

The input page. To use YHMI, users have to go through a three-step process.
Figure 2

The input page. To use YHMI, users have to go through a three-step process.

The result page (first part). The first part of the result page contains the information of the user’s settings. Uniquely, users can download all the sets of genes containing specific histone modifications defined by the users for further investigation.
Figure 3

The result page (first part). The first part of the result page contains the information of the user’s settings. Uniquely, users can download all the sets of genes containing specific histone modifications defined by the users for further investigation.

Construction and contents

Collection of ChIP-chip/ChIP-seq datasets of histone modifications, histone regulators and chromatin regulators

All the ChIP-chip/ChIP-seq data (18–24) used in YHMI were downloaded from SGD (Figure 1). SGD (25) collected the raw data of ChIP-chip/ChIP-seq from GEO (28) and ArrayExpress (29), mapped the raw data to the latest yeast reference genome sacCer3 (R64) and allowed everyone to download the processed data. Therefore, we directly downloaded the ChIP-chip/ChIP-seq datasets of 32 histone modifications (Table 2 and Supplementary Table 1 for more details about the strain, reference genome, original data source, etc.) and 83 histone/chromatin regulators (Supplementary Table 2) from SGD.

The result page (second part). The second part of the result page provides tables and figures to show the identified enriched/depleted histone modifications (acetylation, methylation, phosphorylation, ubiquitination and histone variant) in the promoters/coding regions of the input gene list. The table contains the name of the histone modification, trend (enriched/depleted), P-value, fold enrichment, observed ratio and expected ratio. Moreover, two kinds of figures (a volcano plot and two-bar charts) are also provided for visualization.
Figure 4

The result page (second part). The second part of the result page provides tables and figures to show the identified enriched/depleted histone modifications (acetylation, methylation, phosphorylation, ubiquitination and histone variant) in the promoters/coding regions of the input gene list. The table contains the name of the histone modification, trend (enriched/depleted), P-value, fold enrichment, observed ratio and expected ratio. Moreover, two kinds of figures (a volcano plot and two-bar charts) are also provided for visualization.

Defining genes whose promoters/coding regions contain a specific histone modification

Following previous studies (19, 23), a gene’s promoter is defined as the region between 500 bp upstream and 100 bp downstream of the start codon. A gene’s coding region is defined as the region between the start codon and the stop codon. The procedure of defining a set of genes whose promoters/coding regions contain a specific histone modification (e.g. H3K4ac) is as follows. First, for each of the 6572 genes in the yeast genome, we extracted the maximal data value (⁠|${\mathit{log}}_2\left(\mathrm{H}3\mathrm{K}4\mathrm{ac}/\mathrm{H}3\right)$| in this case) in its promoter/coding region from the corresponding ChIP-chip/ChIP-seq dataset (Table 2). Second, the promoter/coding region of a gene is said to contain H3K4ac if it satisfies |${\mathit{log}}_2\left(\mathrm{H}3\mathrm{K}4\mathrm{ac}/\mathrm{H}3\right)\ge threshold,$| where the threshold is set by the user. For example, when the threshold is set to one, 1656 genes’ promoters and 977 genes’ coding regions are said to contain H3K4ac.

The result page (third part). The third part of the result page provides tables and figures to show the identified enriched histone/chromatin regulators in the promoters of the input gene list. The table contains the name of the histone/chromatin regulator, temperature, P-value, fold enrichment, observed ratio and expected ratio. Moreover, two kinds of figures (a volcano plot and two-bar charts) are also provided for visualization.
Figure 5

The result page (third part). The third part of the result page provides tables and figures to show the identified enriched histone/chromatin regulators in the promoters of the input gene list. The table contains the name of the histone/chromatin regulator, temperature, P-value, fold enrichment, observed ratio and expected ratio. Moreover, two kinds of figures (a volcano plot and two-bar charts) are also provided for visualization.

Defining genes whose promoters are bound by a specific histone/chromatin regulator

Venters et al. (18) identified high-confident [less than 5% false discovery rate (FDR)] interactions between a specific histone/chromatin regulator and genomic DNA (in the yeast genome) under normal (25°C) and acute heat-shock conditions (37°C) by ChIP-chip experiments. Using Venters et al.’s results (18) and based on the definition of a gene’s promoter region (see the previous subsection), we can determine the genes whose promoters are bound by a specific histone/chromatin regulator. Supplementary Table 2 provides the names of these 83 histone/chromatin regulators and their target genes.

Identifying the enriched/depleted histone modifications and the enriched histone/chromatin regulators for the user’s input genes

The main functionality of YHMI is to identify the enriched/depleted histone modifications and the enriched histone/chromatin regulators for the user’s input genes. The procedure for checking whether a specific histone modification (e.g. H3K4ac) is enriched/depleted in the promoters of the user’s input genes is as follows. Let S be the set of genes whose promoters contain the histone modification H3K4ac (see the subsection before the previous one for details), R be the set of the user’s input genes, |$T=S\cap R$| be the set of genes whose promoters contain H3K4ac and are also in the set of the user’s input genes and F be the set of all genes in the yeast genome. Then H3K4ac is said to be enriched/depleted in the promoters of the user’s input genes if the observed ratio (|T|/|R|) in the input genes is significantly higher/lower than the expected ratio (|S|/|F|) in the yeast genome. |S| stands for the number of genes in the set S and |F| = 6572. The statistical significance is calculated using the hypergeometric testing (30) as follows. The |${P}_{value}(enrichment)$| and |${P}_{value}(depletion)$| for rejecting the null hypothesis (H0: H3K4ac is not enriched/depleted in the promoters of the user’s input genes) are calculated as
where |$\left|S\right|$| means the number of genes in set S and
$$\left(\begin{array}{@{}c@{}}\left|F\right|\\ {}\left|R\right|\end{array}\right)$$
is a binomial coefficient. The |${P}_{value}(enrichment)$| and |${P}_{value}(depletion)$| are then corrected by the Bonferroni correction or the FDR to represent the true alpha level in the multiple hypotheses testing. Finally, H3K4ac is said to be enriched/depleted in the promoters of the user’s input genes if the corrected |${P}_{value}(enrichment)$| or corrected |${P}_{value}(depletion)$| is less than the user-defined threshold. Note that Bonferroni correction and FDR are two statistical methods for multiple hypotheses correction. Bonferroni correction is more conservative than FDR. That is, Bonferroni correction has a smaller type I error rate, resulting in a smaller power, than FDR does.

The procedure for checking whether a specific histone modification is enriched/depleted in the coding regions of the user’s input genes is the same as mentioned above except for the definitions of two terms. Now S becomes the set of genes whose coding regions contain the histone modification H3K4ac and |$T=S\cap R$| becomes the set of genes whose coding regions contain H3K4ac and are also in the set of the user’s input genes.

The procedure for checking whether a specific histone/chromatin regulator (e.g. Esa1) is enriched in the promoters of the user’s input genes is the same as mentioned above except for the definitions of two terms. Now S becomes the set of genes whose promoters are bound by Esa1 and |$T=S\cap R$| becomes the set of genes whose promoters are bound by Esa1 and are also in the set of the user’s input genes.

Implementation and maintenance of the web interface of YHMI

Figure 1 illustrates the overall configuration of YHMI. The web interface of YHMI was developed in Python using the Django MTV framework. The processed histone modification data were deposited in MySQL. All tables, volcano plots and bar charts were produced by the JavaSscript and feature-rich JavaScript libraries (jQuery, DataTables and Plotly.js) to visualize data on the webpage. We also provide the command line version of YHMI (written in Python) for users who want to run YHMI on their local computers (see the Help page of YHMI website). YHMI will be maintained by our lab’s research assistants and we have a backup site (http://cosbi5.ee.ncku.edu.tw/YHMI/). Therefore, the long-term stability of YHMI is guaranteed. In the future, we will keep updating YHMI once new histone modification datasets become available in the literature.

Table 3

YHMI successfully identifies most known histone modifications of highly transcribed genes

Type of histone modificationIdentified histone modificationIdentified enzyme known to achieve this histone modificationLiterature evidence
AcetylationH3K4ac enriched in promoterGcn5Guillemette et al. (19)
AcetylationH3K4ac enriched in coding regionGcn5Guillemette et al. (19)
AcetylationH3K9ac enriched in promoterGcn5Pokholok et al. (20)
AcetylationH3K14ac enriched in promoterGcn5Pokholok et al. (20)
AcetylationH4ac enriched in promoterEsa1Pokholok et al. (20)
MethylationH3R2me2a depleted in coding regionKirmizis et al. (21)
MethylationH3K4me3 enriched in promoterSet1Guillemette et al. (19) Pokholok et al. (20) Kirmizis et al. (21) Schulze et al. (22)
MethylationH3K36me3 enriched in coding regionPokholok et al. (20) Schulze et al. (22)
MethylationH3K79me2 depleted in coding regionSchulze et al. (22)
MethylationH3K79me3 depleted in coding regionSchulze et al. (22)
UbiquitinationH2BK123ub enriched in coding regionSchulze et al. (22)
Histone variantH2AZ depleted in promoterGuillemette et al. (23)
Type of histone modificationIdentified histone modificationIdentified enzyme known to achieve this histone modificationLiterature evidence
AcetylationH3K4ac enriched in promoterGcn5Guillemette et al. (19)
AcetylationH3K4ac enriched in coding regionGcn5Guillemette et al. (19)
AcetylationH3K9ac enriched in promoterGcn5Pokholok et al. (20)
AcetylationH3K14ac enriched in promoterGcn5Pokholok et al. (20)
AcetylationH4ac enriched in promoterEsa1Pokholok et al. (20)
MethylationH3R2me2a depleted in coding regionKirmizis et al. (21)
MethylationH3K4me3 enriched in promoterSet1Guillemette et al. (19) Pokholok et al. (20) Kirmizis et al. (21) Schulze et al. (22)
MethylationH3K36me3 enriched in coding regionPokholok et al. (20) Schulze et al. (22)
MethylationH3K79me2 depleted in coding regionSchulze et al. (22)
MethylationH3K79me3 depleted in coding regionSchulze et al. (22)
UbiquitinationH2BK123ub enriched in coding regionSchulze et al. (22)
Histone variantH2AZ depleted in promoterGuillemette et al. (23)
Table 3

YHMI successfully identifies most known histone modifications of highly transcribed genes

Type of histone modificationIdentified histone modificationIdentified enzyme known to achieve this histone modificationLiterature evidence
AcetylationH3K4ac enriched in promoterGcn5Guillemette et al. (19)
AcetylationH3K4ac enriched in coding regionGcn5Guillemette et al. (19)
AcetylationH3K9ac enriched in promoterGcn5Pokholok et al. (20)
AcetylationH3K14ac enriched in promoterGcn5Pokholok et al. (20)
AcetylationH4ac enriched in promoterEsa1Pokholok et al. (20)
MethylationH3R2me2a depleted in coding regionKirmizis et al. (21)
MethylationH3K4me3 enriched in promoterSet1Guillemette et al. (19) Pokholok et al. (20) Kirmizis et al. (21) Schulze et al. (22)
MethylationH3K36me3 enriched in coding regionPokholok et al. (20) Schulze et al. (22)
MethylationH3K79me2 depleted in coding regionSchulze et al. (22)
MethylationH3K79me3 depleted in coding regionSchulze et al. (22)
UbiquitinationH2BK123ub enriched in coding regionSchulze et al. (22)
Histone variantH2AZ depleted in promoterGuillemette et al. (23)
Type of histone modificationIdentified histone modificationIdentified enzyme known to achieve this histone modificationLiterature evidence
AcetylationH3K4ac enriched in promoterGcn5Guillemette et al. (19)
AcetylationH3K4ac enriched in coding regionGcn5Guillemette et al. (19)
AcetylationH3K9ac enriched in promoterGcn5Pokholok et al. (20)
AcetylationH3K14ac enriched in promoterGcn5Pokholok et al. (20)
AcetylationH4ac enriched in promoterEsa1Pokholok et al. (20)
MethylationH3R2me2a depleted in coding regionKirmizis et al. (21)
MethylationH3K4me3 enriched in promoterSet1Guillemette et al. (19) Pokholok et al. (20) Kirmizis et al. (21) Schulze et al. (22)
MethylationH3K36me3 enriched in coding regionPokholok et al. (20) Schulze et al. (22)
MethylationH3K79me2 depleted in coding regionSchulze et al. (22)
MethylationH3K79me3 depleted in coding regionSchulze et al. (22)
UbiquitinationH2BK123ub enriched in coding regionSchulze et al. (22)
Histone variantH2AZ depleted in promoterGuillemette et al. (23)

Utility and discussion

The usage of YHMI

YHMI is a web tool for identifying the enriched/depleted histone modifications and the enriched histone/chromatin regulators in the input gene list. To use YHMI, users have to go through a three-step process (Figure 2). [Step 1] Users need to input a list of N genes, which will be analyzed by YHMI. Standard names, systematic names or aliases are all acceptable. [Step 2] Users need to define the sets of genes (in the yeast genome) whose promoters/coding regions contain specific histone modifications by setting the thresholds. For example, by setting |${\mathit{log}}_2\left(\mathrm{H}3\mathrm{K}9\mathrm{ac}/\mathrm{H}3\right)\ge 1$| (meaning 2-fold enrichment over the background) in the promoters, a set of 2129 yeast genes whose promoters contain H3K9ac could be defined. Then the expected ratio of promoters having H3K9ac in the yeast genome is equal to 0.32 (2129/6572). Further, by intersecting the input list of N genes and the set of 2129 genes, the number (denoted as M) of input genes whose promoters having H3K9ac can be calculated. Then the observed ratio of promoters having H3K9ac in the input list of genes is equal to M/N. Finally, the input list of N genes is said to be enriched with H3K9ac in the promoters if the observed ratio (M/N) is much larger than the expected ratio (2129/6572). The statistical significance is calculated using hypergeometric testing (30). [Step 3] Since YHMI tests the enrichment/depletion of many histone modifications (i.e. multiple hypotheses testing), users have to select a statistical method (Bonferroni correction or FDR) for multiple hypotheses correction and set the P-value threshold (0.01 is used as the default). The P-value threshold determines the statistical significance of the identified enriched/depleted histone modifications. The more stringent the P-value threshold, the higher the statistical significance of the identified enriched/depleted histone modifications. Therefore, if a user cannot find any enriched/depleted histone modifications for their gene list, they may want to loosen the P-value threshold to find some less statistically significant enriched/depleted histone modifications. Note that if a user wants to see all the results without defining the statistical significance level, he/she can choose ‘No P-value cutoff’.

The identification results for the Esa1-targeting promoters. (a) YHMI identified four enriched acetylations (H3K4ac, H3K14ac, H3K9ac and H4ac). (b) YHMI identified two enriched methylations (H3K4me3 and H3K36me3) and one depleted methylation (H3K79me2). (c) YHMI identified one enriched ubiquitination (H2BK123ub).
Figure 6

The identification results for the Esa1-targeting promoters. (a) YHMI identified four enriched acetylations (H3K4ac, H3K14ac, H3K9ac and H4ac). (b) YHMI identified two enriched methylations (H3K4me3 and H3K36me3) and one depleted methylation (H3K79me2). (c) YHMI identified one enriched ubiquitination (H2BK123ub).

After submission, YHMI will return the identification results that can be divided into two parts. First, the information of the user’s settings is shown. We allow users to download all the sets of genes containing specific histone modifications defined by the users for further investigation (Figure 3). Second, the identified enriched/depleted histone modifications (acetylation, methylation, phosphorylation, ubiquitination and histone variant) in the promoters/coding regions of the input gene list are shown as tables and figures. The table contains the following information: the name of the histone modification, trend (enriched/depleted), P-value, fold enrichment, observed ratio and expected ratio (Figure 4). Two kinds of figures (bar charts and volcano plots) are also provided for visualization (Figure 4). Two different bar charts (a fold enrichment bar chart and a P-value bar chart) are available. In the fold enrichment bar chart, the identified histone modifications are sorted by the fold enrichment values. In the P-value bar chart, the identified histone modifications are sorted by the P-values. The other kind of figure (the volcano plot) is a nice combination of the fold enrichment (x-axis) and P-value (y-axis). Moreover, the enriched histone/chromatin regulators in the promoters of the input gene list are provided as tables and figures (Figure 5).

Two case studies

We use two case studies to show the high-quality and biological insight of YHMI’s identification results for the user’s input genes. Since several histone modifications are already known to be correlated with highly transcribed genes (19–23), we would like to check (in the first case study) whether YHMI can successfully identify these known histone modifications and their related enzymes. To do that, we retrieved a list of 174 highly transcribed (>50 mRNA/hr) genes under YPD condition from Holstege et al. (31). Strikingly, YHMI did successfully identify most histone modifications known to be enriched/depleted in highly transcribed genes (Table 3). For example, H3K4ac, H3K9ac and H3K14ac are identified to be enriched both in the promoters and the coding regions of the highly transcribed genes, consistent with existing knowledge (19). Moreover, YHMI successfully identifies the enrichment of Gcn5 [the known acetyltransferase which targets H3K4, H3K9 and H3K14 (19)] in the promoters of the highly transcribed genes, further supporting the biological significance of identifying the enrichment of H3K4ac, H3K9ac and H3K14ac. More examples could be found in Table 3. All these examples validate the high quality of YHMI’s identification results.

In the second case study, we used a list of 538 genes whose promoters are bound by Esa1 at 25°C (retrieved from Venters et al.’s study (18)) as the input to investigate the signature of histone modifications and histone/chromatin regulators of these Esa1-targeting promoters. Esa1 is a histone acetyltransferase specifically targeting histone H2A, H2AZ and H4 (17). Esa1 together with the other 12 subunits forms the NuA4 complex (17). YHMI identified several histone modifications and histone/chromatin regulators that are enriched in these Esa1-targeting promoters; in other words, the signature of histone modifications and regulators of these Esa1-targeting promoters.

Table 4

YHMI identified several histone/chromatin regulators that are related to NuA4 complex, SAGA complex or COMPASS complex

Related to the complexIdentified regulatorEnrichment P-valueFold enrichmentaObserved ratiobExpected ratioc
NuA4Esa1012.22100%8.19%
NuA4Rsc81.51E-211.5951.3%32.29%
NuA4Eaf31.36E-162.1621%9.72%
NuA4Hif11.09E-091.9415.43%7.97%
NuA4Yaf92.31E-071.6717.1%10.24%
SAGASnf19.64E-512.5642.57%16.63%
SAGARph12.22E-171.4852.42%35.36%
SAGAAhc14.15E-171.6639.03%23.57%
SAGASpt213.59E-122.2813.75%6.03%
SAGASnf27.03E-091.8815.06%8%
SAGAAda21.01E-081.6322.3%13.72%
SAGASnf52.13E-081.3344.42%33.44%
SAGARxt13.57E-081.5424.72%16.02%
SAGARvb22.02E-061.3830.11%21.88%
SAGARpt61.96E-051.997.25%3.64%
COMPASSSet11.41E-386.711.52%1.72%
COMPASSBre21.36E-061.3435.13%26.28%
Related to the complexIdentified regulatorEnrichment P-valueFold enrichmentaObserved ratiobExpected ratioc
NuA4Esa1012.22100%8.19%
NuA4Rsc81.51E-211.5951.3%32.29%
NuA4Eaf31.36E-162.1621%9.72%
NuA4Hif11.09E-091.9415.43%7.97%
NuA4Yaf92.31E-071.6717.1%10.24%
SAGASnf19.64E-512.5642.57%16.63%
SAGARph12.22E-171.4852.42%35.36%
SAGAAhc14.15E-171.6639.03%23.57%
SAGASpt213.59E-122.2813.75%6.03%
SAGASnf27.03E-091.8815.06%8%
SAGAAda21.01E-081.6322.3%13.72%
SAGASnf52.13E-081.3344.42%33.44%
SAGARxt13.57E-081.5424.72%16.02%
SAGARvb22.02E-061.3830.11%21.88%
SAGARpt61.96E-051.997.25%3.64%
COMPASSSet11.41E-386.711.52%1.72%
COMPASSBre21.36E-061.3435.13%26.28%
a

aFold enrichment = (Observed ratio) / (Expected ratio).

b

bObserved ratio = (number of input genes bound by the identified regulator) / (number of input genes).

c

cExpected ratio = (number of genes in the genome bound by the identified regulator) / (number of genes in the genome).

Table 4

YHMI identified several histone/chromatin regulators that are related to NuA4 complex, SAGA complex or COMPASS complex

Related to the complexIdentified regulatorEnrichment P-valueFold enrichmentaObserved ratiobExpected ratioc
NuA4Esa1012.22100%8.19%
NuA4Rsc81.51E-211.5951.3%32.29%
NuA4Eaf31.36E-162.1621%9.72%
NuA4Hif11.09E-091.9415.43%7.97%
NuA4Yaf92.31E-071.6717.1%10.24%
SAGASnf19.64E-512.5642.57%16.63%
SAGARph12.22E-171.4852.42%35.36%
SAGAAhc14.15E-171.6639.03%23.57%
SAGASpt213.59E-122.2813.75%6.03%
SAGASnf27.03E-091.8815.06%8%
SAGAAda21.01E-081.6322.3%13.72%
SAGASnf52.13E-081.3344.42%33.44%
SAGARxt13.57E-081.5424.72%16.02%
SAGARvb22.02E-061.3830.11%21.88%
SAGARpt61.96E-051.997.25%3.64%
COMPASSSet11.41E-386.711.52%1.72%
COMPASSBre21.36E-061.3435.13%26.28%
Related to the complexIdentified regulatorEnrichment P-valueFold enrichmentaObserved ratiobExpected ratioc
NuA4Esa1012.22100%8.19%
NuA4Rsc81.51E-211.5951.3%32.29%
NuA4Eaf31.36E-162.1621%9.72%
NuA4Hif11.09E-091.9415.43%7.97%
NuA4Yaf92.31E-071.6717.1%10.24%
SAGASnf19.64E-512.5642.57%16.63%
SAGARph12.22E-171.4852.42%35.36%
SAGAAhc14.15E-171.6639.03%23.57%
SAGASpt213.59E-122.2813.75%6.03%
SAGASnf27.03E-091.8815.06%8%
SAGAAda21.01E-081.6322.3%13.72%
SAGASnf52.13E-081.3344.42%33.44%
SAGARxt13.57E-081.5424.72%16.02%
SAGARvb22.02E-061.3830.11%21.88%
SAGARpt61.96E-051.997.25%3.64%
COMPASSSet11.41E-386.711.52%1.72%
COMPASSBre21.36E-061.3435.13%26.28%
a

aFold enrichment = (Observed ratio) / (Expected ratio).

b

bObserved ratio = (number of input genes bound by the identified regulator) / (number of input genes).

c

cExpected ratio = (number of genes in the genome bound by the identified regulator) / (number of genes in the genome).

Table 5

YHMI’s identification results are robust against different data sources

Histone ModificationData SourceTrendP-valueFold EnrichmentObserved RatioExpected Ratio
H3K4me3Guillemette 2011 (19)Enriched1.25E-411.9395.40% (166/174)49.33% (3242/6572)
H3K4me3Kirmizis 2007 (21)Enriched4.18E-091.1697.70% (170/174)84.25% (5537/6572)
H3K4me3Schulze 2011 (22)Enriched1.95E-081.1697.13% (169/174)84.04% (5523/6572)
H3K4meKirmizis 2007 (21)Depleted7.41E-390.1910.92% (19/174)57.59% (3785/6572)
H3K4mePokholok 2005 (20)Depleted7.19E-180.312.64% (22/174)42.29% (2779/6572)
H3K36me3Pokholok 2005 (20)Enriched6.23E-352.2381.61% (142/174)36.59% (2405/6572)
H3K36me3Schulze 2011 (22)Enriched5.18E-141.3690.80% (158/174)66.81% (4391/6572)
Histone ModificationData SourceTrendP-valueFold EnrichmentObserved RatioExpected Ratio
H3K4me3Guillemette 2011 (19)Enriched1.25E-411.9395.40% (166/174)49.33% (3242/6572)
H3K4me3Kirmizis 2007 (21)Enriched4.18E-091.1697.70% (170/174)84.25% (5537/6572)
H3K4me3Schulze 2011 (22)Enriched1.95E-081.1697.13% (169/174)84.04% (5523/6572)
H3K4meKirmizis 2007 (21)Depleted7.41E-390.1910.92% (19/174)57.59% (3785/6572)
H3K4mePokholok 2005 (20)Depleted7.19E-180.312.64% (22/174)42.29% (2779/6572)
H3K36me3Pokholok 2005 (20)Enriched6.23E-352.2381.61% (142/174)36.59% (2405/6572)
H3K36me3Schulze 2011 (22)Enriched5.18E-141.3690.80% (158/174)66.81% (4391/6572)
Table 5

YHMI’s identification results are robust against different data sources

Histone ModificationData SourceTrendP-valueFold EnrichmentObserved RatioExpected Ratio
H3K4me3Guillemette 2011 (19)Enriched1.25E-411.9395.40% (166/174)49.33% (3242/6572)
H3K4me3Kirmizis 2007 (21)Enriched4.18E-091.1697.70% (170/174)84.25% (5537/6572)
H3K4me3Schulze 2011 (22)Enriched1.95E-081.1697.13% (169/174)84.04% (5523/6572)
H3K4meKirmizis 2007 (21)Depleted7.41E-390.1910.92% (19/174)57.59% (3785/6572)
H3K4mePokholok 2005 (20)Depleted7.19E-180.312.64% (22/174)42.29% (2779/6572)
H3K36me3Pokholok 2005 (20)Enriched6.23E-352.2381.61% (142/174)36.59% (2405/6572)
H3K36me3Schulze 2011 (22)Enriched5.18E-141.3690.80% (158/174)66.81% (4391/6572)
Histone ModificationData SourceTrendP-valueFold EnrichmentObserved RatioExpected Ratio
H3K4me3Guillemette 2011 (19)Enriched1.25E-411.9395.40% (166/174)49.33% (3242/6572)
H3K4me3Kirmizis 2007 (21)Enriched4.18E-091.1697.70% (170/174)84.25% (5537/6572)
H3K4me3Schulze 2011 (22)Enriched1.95E-081.1697.13% (169/174)84.04% (5523/6572)
H3K4meKirmizis 2007 (21)Depleted7.41E-390.1910.92% (19/174)57.59% (3785/6572)
H3K4mePokholok 2005 (20)Depleted7.19E-180.312.64% (22/174)42.29% (2779/6572)
H3K36me3Pokholok 2005 (20)Enriched6.23E-352.2381.61% (142/174)36.59% (2405/6572)
H3K36me3Schulze 2011 (22)Enriched5.18E-141.3690.80% (158/174)66.81% (4391/6572)

For example, YHMI found significant enrichment of H3K4ac, H3K9ac, H3K14ac and H4ac in these Esa1-targeting promoters (Figure 6a). The enrichment of H4ac at these promoters is consistent with the function of Esa1 (17). Additionally, H3K4ac, H3K9ac and H3K14ac are also enriched in these promoters, indicating that the SAGA complex (which targets and acetylates H3K4, H3K9 and H3K14) might also act in these promoters along with Esa1 (32). Therefore, YHMI provides a testable hypothesis that SAGA might bind to promoters along with Esa1. This hypothesis awaits further experimental validation. Interestingly, YHMI found that H3K4me3 and H3K36me3 are also enriched in these Esa1-targeted promoters (Figure 6b). Therefore, YHMI provides another testable hypothesis that H3K4me3 and H3K36me3 might be important for regulating the acetyltransferase activity of NuA4. Indeed, several studies have shown that the methylated H3K4 and H3K36 interact with PHD and chromodomain within the NuA4 complex by using the GST pull-down, immunoprecipitation and protein array assays (9, 11, 12). Furthermore, the set1Δ set2Δ mutants or mutants with combined mutations of the PHD and chromodomains show defective acetyltransferases activity of NuA4 (33, 34). Additionally, an experiment has shown that the interaction of H3K4me3 with Tudor domain in Sgf29 within the SAGA complex is also essential for the acetyltransferase activity of SAGA (35). These experiments suggest the usefulness of YHMI.

YHMI also found that H2BK123ub is enriched in these Esa1-targeting promoters (Figure 6c). H2BK123ub is a transient histone mark, which is established by the Rad6/Bre1 ubiquitin ligase complex during transcription initiation and elongation (36). Previous studies have shown that H2BK123ub is essential for establishing H3K4me3 and H3K79me3 (37). In that sense, H3K4me3 and H3K79me3 are expected to be enriched in these Esa1-targeting promoters. YHMI successfully identified H3K4me3 enriched but did not see H3K79me3 enriched in these Esa1-targeting promoters (Figure 6b). Surprisingly, YHMI identified H3K79me2 depleted in these Esa1-targeting promoters (Figure 6b). The reason underlying H3K79me2 depletion is unclear. This awaits further experimental investigation. These examples illustrate how YHMI’s identification results can provide testable hypotheses for experimental investigation.

Consistent with H4ac, H3K4ac, H3K9ac and H3K14ac enrichment, YHMI found that several proteins within or interacting with the NuA4 complex (the H4 histone acetyltransferase complex) and the SAGA complex (the H3 histone acetyltransferase complex) are also enriched in these Esa1-targeting promoters (Table 4). These include Esa1, Eaf3, Rsc8, Yaf9 and Hif1 related to the NuA4 complex (38–40) and Ada2, Snf1, Ahc1, Rph1, Spt21, Snf2, Rxt1, SNF5, Rvb2 and Rpt6 related to the SAGA complex (41–46). Moreover, consistent with H3K4me3 enrichment, YHMI found Set1 and Bre2 in the COMPASS complex (the H3K4 methyltransferase complex) in these Esa1-targeting promoters (47). All these results show that YHMI is likely to return biologically meaningful results for the user’s input genes and provide user’s testable hypotheses for further investigation.

Robustness of the identification results

Several histone modifications (e.g. H3K4me, H3K4me3 and H3K36me3) have ChIP-chip data in different sources and can be used to test whether YHMI’s identification results are robust against different data sources. For example, we tested whether the coding regions of the 174 highly transcribed genes (same input as in the case study 1) are enriched/depleted in H3K4me3. Strikingly, no matter which one of three ChIP-chip data sources of H3K4me3 is used, YHMI always returns the same trend (enrichment of H3K4me3). This observation is also true for H3K4me (depletion) and H3K36me3 (enrichment) shown in Table 5. These examples illustrate that the YHMI’s identification results are robust against different data sources.

Comparison with our previously published YNA website

In 2014, we published YNA (26) which allows users to retrieve a list of yeast genes whose promoters and/or coding regions contain a user-specified combination of histone modifications (e.g. H3K4ac and H3K4me3). Since we published YNA, we received many requests for a reverse use (i.e. identifying the enriched histone modifications for a user’s gene list). This motivated us to develop YHMI. Compared to YNA, YHMI includes additional 17 histone modifications (9 histone acetylation, 6 histone methylation and 2 histone phosphorylation) from Weiner et al.’s ChIP-seq data (24). Moreover, users can download the lists of genes with a specific histone modification in YHMI. However, only YNA (but not YHMI) allows users to download a list of genes having a specific combination of histone modifications (e.g. H3K4ac and H3K4me3 in the promoters). To inform YHMI users about the related database YNA, we have provided a link and an introduction of YNA on the homepage of YHMI.

Conclusion

In this study, we developed a web tool called YHMI. YHMI uses the ChIP-chip/ChIP-seq datasets of 32 histone modifications (15 histone acetylation, 13 histone methylation, 2 phosphorylation, 1 histone ubiquitination and 1 histone variant) and 83 histone/chromatin regulators. When a user inputs a gene list, YHMI will identify the enriched/depleted histone modifications in the promoters/coding regions and enriched histone/chromatin regulators in the promoters of the genes in the input list. The identification results are shown both in figures and tables. The high quality of YHMI’s results is validated by identifying most known histone modifications enriched/depleted in highly transcribed genes. The biological insight of YHMI’s results is demonstrated by generating experimentally testable hypotheses of novel histone modifications and their enzymes enriched in the target genes of the histone acetyltransferase Esa1. We believe that YHMI is a valuable tool for yeast biologists to do epigenetics research.

Acknowledgement

We thank the National Cheng Kung University (NCKU), MOST AI Biomedical Research Center at NCKU and Ministry of Science and Technology of Taiwan for their support.

Funding

National Cheng Kung University and Ministry of Science and Technology of Taiwan [MOST-105-2221-E-006-203-MY2, MOST-106-2628-E-006-006-MY2, MOST-107-2221-E-006-225-MY3, MOST-107-2634-F-006-009]. Funding for open access charge: National Cheng Kung University and Ministry of Science and Technology of Taiwan.

Conflict of interest. None declared.

Database URL:http://cosbi4.ee.ncku.edu.tw/YHMI/

References

1.

Jenuwein
,
T.
and
Allis
,
C.D.
(
2001
)
Translating the histone code
.
Science
,
293
,
1074
1080
.

2.

Li
,
B.
,
Carey
,
M.
and
Workman
,
J.L.
(
2007
)
The role of chromatin during transcription
.
Cell
,
128
,
707
719
.

3.

Rando
,
O.J.
and
Winston
,
F.
(
2012
)
Chromatin and transcription in yeast
.
Genetics
,
190
,
351
387
.

4.

Zhao
,
Y.
and
Garcia
,
B.A.
(
2015
)
Comprehensive catalog of currently documented histone modifications
.
Cold Spring Harb. Perspect. Biol.
,
7
,
a025064
.

5.

Kouzarides
,
T.
(
2007
)
Chromatin modifications and their function
.
Cell
,
128
,
693
705
.

6.

Rando
,
O.J.
(
2012
)
Combinatorial complexity in chromatin structure and function: revisiting the histone code
.
Curr. Opin. Genet. Dev.
,
22
,
148
155
.

7.

Dhalluin
,
C.
,
Carlson
,
J.E.
,
Zeng
,
L.
et al.  (
1999
)
Structure and ligand of a histone acetyltransferase bromodomain
.
Nature
,
399
,
491
496
.

8.

Yu
,
X.
,
Chini
,
C.C.
,
He
,
M.
et al.  (
2003
)
The BRCT domain is a phospho-protein binding domain
.
Science
,
302
,
639
642
.

9.

Joshi
,
A.A.
and
Struhl
,
K.
(
2005
,
978
)
Eaf3 chromodomain interaction with methylated H3-K36 links histone deacetylation to Pol II elongation
.
Mol. Cell
,
20
,
971
--
978
.

10.

Xu
,
C.
,
Cui
,
G.
,
Botuyan
,
M.V.
et al.  (
2008
)
Structural basis for the recognition of methylated histone H3K36 by the Eaf3 subunit of histone deacetylase complex Rpd3S
.
Structure
,
16
,
1740
1750
.

11.

Gozani
,
O.
,
Karuman
,
P.
,
Jones
,
D.R.
et al.  (
2003
)
The PHD finger of the chromatin-associated protein ING2 functions as a nuclear phosphoinositide receptor
.
Cell
,
114
,
99
111
.

12.

Shi
,
X.
,
Kachirskaia
,
I.
,
Walter
,
K.L.
et al.  (
2007
)
Proteome-wide analysis in Saccharomyces cerevisiae identifies several PHD fingers as novel direct and selective binding modules of histone H3 methylated at either lysine 4 or lysine 36
.
J. Biol. Chem.
,
282
,
2450
2455
.

13.

Lu
,
R.
and
Wang
,
G.G.
(
2013
)
Tudor: a versatile family of histone methylation ‘readers’
.
Trends Biochem. Sci.
,
38
,
546
555
.

14.

Eissenberg
,
J.C.
(
2012
)
Structural biology of the chromodomain: form and function
.
Gene
,
496
,
69
78
.

15.

Ali
,
M.
,
Yan
,
K.
,
Lalonde
,
M.E.
et al.  (
2012
)
Tandem PHD fingers of MORF/MOZ acetyltransferases display selectivity for acetylated histone H3 and are required for the association with chromatin
.
J. Mol. Biol.
,
424
,
328
338
.

16.

Lee
,
T.I.
,
Causton
,
H.C.
,
Holstege
,
F.C.
et al.  (
2000
)
Redundant roles for the TFIID and SAGA complexes in global transcription
.
Nature
,
405
,
701
704
.

17.

Doyon
,
Y.
and
Cote
,
J.
(
2004
)
The highly conserved and multifunctional NuA4 HAT complex
.
Curr. Opin. Genet. Dev.
,
14
,
147
154
.

18.

Venters
,
B.J.
,
Wachi
,
S.
,
Mavrich
,
T.N.
et al.  (
2011
)
A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces
.
Mol. Cell
,
41
,
480
492
.

19.

Guillemette
,
B.
,
Drogaris
,
P.
,
Lin
,
H.H.
et al.  (
2011
)
H3 lysine 4 is acetylated at active gene promoters and is regulated by H3 lysine 4 methylation
.
PLoS Genet.
,
7
,
e1001354
.

20.

Pokholok
,
D.K.
,
Harbison
,
C.T.
,
Levine
,
S.
et al.  (
2005
)
Genome-wide map of nucleosome acetylation and methylation in yeast
.
Cell
,
122
,
517
527
.

21.

Kirmizis
,
A.
,
Santos-Rosa
,
H.
,
Penkett
,
C.J.
et al.  (
2007
)
Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylation
.
Nature
,
449
,
928
932
.

22.

Schulze
,
J.M.
,
Hentrich
,
T.
,
Nakanishi
,
S.
et al.  (
2011
)
Splitting the task: Ubp8 and Ubp10 deubiquitinate different cellular pools of H2BK123
.
Genes Dev.
,
25
,
2242
2247
.

23.

Guillemette
,
B.
,
Bataille
,
A.R.
,
Gevry
,
N.
et al.  (
2005
)
Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning
.
PLoS Biol.
,
3
,
e384
.

24.

Weiner
,
A.
,
Hsieh
,
T.H.
,
Appleboim
,
A.
et al.  (
2015
)
High-resolution chromatin dynamics during a yeast stress response
.
Mol. Cell
,
58
,
371
386
.

25.

Lang
,
O.W.
,
Nash
,
R.S.
,
Hellerstedt
,
S.T.
et al.  (
2018
)
An introduction to the Saccharomyces Genome Database (SGD)
.
Methods Mol. Biol.
,
1757
,
21
30
.

26.

Hung
,
P.C.
,
Yang
,
T.H.
,
Liaw
,
H.J.
et al.  (
2014
)
The Yeast Nucleosome Atlas (YNA) database: an integrative gene mining platform for studying chromatin structure and its regulation in yeast
.
BMC Genomics
,
15
,
S5
.

27.

O’Connor
,
T.R.
and
Wyrick
,
J.J.
(
2007
)
ChromatinDB: a database of genome-wide histone modification patterns for Saccharomyces cerevisiae
.
Bioinformatics
,
23
,
1828
1830
.

28.

Barrett
,
T.
,
Wilhite
,
S.E.
,
Ledoux
,
P.
et al.  (
2013
)
NCBI GEO: archive for functional genomics data sets—update
.
Nucleic Acids Res.
,
41
,
D991
D995
.

29.

Kolesnikov
,
N.
,
Hastings
,
E.
,
Keays
,
M.
et al.  (
2015
)
ArrayExpress update—simplifying data submissions
.
Nucleic Acids Res.
,
43
,
D1113
D1116
.

30.

Yang
,
T.H.
and
Wu
,
W.S.
(
2012
)
Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data
.
BMC Syst. Biol.
,
6
,
102
.

31.

Holstege
,
F.C.
,
Jennings
,
E.G.
,
Wyrick
,
J.J.
et al.  (
1998
)
Dissecting the regulatory circuitry of a eukaryotic genome
.
Cell
,
95
,
717
728
.

32.

Rodriguez-Navarro
,
S.
(
2009
)
Insights into SAGA function during gene expression
.
EMBO Rep.
,
10
,
843
850
.

33.

Ginsburg
,
D.S.
,
Anlembom
,
T.E.
,
Wang
,
J.
et al.  (
2014
)
NuA4 links methylation of histone H3 lysines 4 and 36 to acetylation of histones H4 and H3
.
J. Biol. Chem.
,
289
,
32656
32670
.

34.

Su
,
W.P.
,
Hsu
,
S.H.
,
Chia
,
L.C.
et al.  (
2016
)
Combined interactions of plant homeodomain and chromodomain regulate NuA4 activity at DNA double-strand breaks
.
Genetics
,
202
,
77
92
.

35.

Bian
,
C.
,
Xu
,
C.
,
Ruan
,
J.
et al.  (
2011
)
Sgf29 binds histone H3K4me2/3 and is required for SAGA complex recruitment and histone H3 acetylation
.
EMBO J.
,
30
,
2829
2842
.

36.

Wood
,
A.
,
Schneider
,
J.
,
Dover
,
J.
et al.  (
2005
)
The Bur1/Bur2 complex is required for histone H2B monoubiquitination by Rad6/Bre1 and histone methylation by COMPASS
.
Mol. Cell
,
20
,
589
599
.

37.

Nakanishi
,
S.
,
Lee
,
J.S.
,
Gardner
,
K.E.
et al.  (
2009
)
Histone H2BK123 monoubiquitination is the critical determinant for H3K4 and H3K79 trimethylation by COMPASS and Dot1
.
J. Cell. Biol.
,
186
,
371
377
.

38.

Gavin
,
A.C.
,
Aloy
,
P.
,
Grandi
,
P.
et al.  (
2006
)
Proteome survey reveals modularity of the yeast cell machinery
.
Nature
,
440
,
631
636
.

39.

Mitchell
,
L.
,
Huard
,
S.
,
Cotrut
,
M.
et al.  (
2013
)
mChIP-KAT-MS, a method to map protein interactions and acetylation sites for lysine acetyltransferases
.
Proc. Natl. Acad. Sci. USA
,
110
,
E1641
E1650
.

40.

Lin
,
Y.Y.
,
Lu
,
J.Y.
,
Zhang
,
J.
et al.  (
2009
)
Protein acetylation microarray reveals that NuA4 controls key metabolic target regulating gluconeogenesis
.
Cell
,
136
,
1073
1084
.

41.

Liu
,
Y.
,
Xu
,
X.
,
Singh-Rodriguez
,
S.
et al.  (
2005
)
Histone H3 Ser10 phosphorylation-independent function of Snf1 and Reg1 proteins rescues a gcn5- mutant in HIS3 expression
.
Mol. Cell Biol.
,
25
,
10566
10579
.

42.

Lee
,
K.K.
,
Sardiu
,
M.E.
,
Swanson
,
S.K.
et al.  (
2011
)
Combinatorial depletion analysis to assemble the network architecture of the SAGA and ADA chromatin remodeling complexes
.
Mol. Syst. Biol.
,
7
,
503
.

43.

Li
,
F.
,
Zheng
,
L.D.
,
Chen
,
X.
et al.  (
2017
)
Gcn5-mediated Rph1 acetylation regulates its autophagic degradation under DNA damage stress
.
Nucleic Acids Res.
,
45
,
5183
5197
.

44.

Kurat
,
C.F.
,
Lambert
,
J.P.
,
Petschnigg
,
J.
et al.  (
2014
)
Cell cycle-regulated oscillator coordinates core histone gene transcription through histone acetylation
.
Proc. Natl. Acad. Sci. USA
,
111
,
14124
14129
.

45.

Kim
,
J.H.
,
Saraf
,
A.
,
Florens
,
L.
et al.  (
2010
)
Gcn5 regulates the dissociation of SWI/SNF from chromatin by acetylation of Swi2/Snf2
.
Genes Dev.
,
24
,
2766
2771
.

46.

Papamichos-Chronakis
,
M.
,
Petrakis
,
T.
,
Ktistaki
,
E.
et al.  (
2002
)
Cti6, a PHD domain protein, bridges the Cyc8-Tup1 corepressor and the SAGA coactivator to overcome repression at GAL1
.
Mol. Cell
,
9
,
1297
1305
.

47.

Shilatifard
,
A.
(
2012
)
The COMPASS family of histone H3K4 methylases: mechanisms of regulation in development and disease pathogenesis
.
Annu. Rev. Biochem.
,
81
,
65
95
.

48.

Johnson
,
W.E.
,
Li
,
W.
,
Meyer
,
C.A.
et al.  (
2006
)
Model-based analysis of tiling-arrays for ChIP-chip
.
Proc. Natl. Acad. Sci. USA.
,
103
,
12457
12462
.

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