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.
Highlights
Histone modification and chromatin remodelling play an important role in DNA replication, transcription and DNA repair [1,2,3]
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 [9,10,11,12,13,14]
Only Yeast Nucleosome Atlas (YNA) allows users to download a list of genes having a specific combination of histone modifications (e.g. H3K4ac and H3K4me3 in the promoters)
Summary
Histone modification and chromatin remodelling play an important role in DNA replication, transcription and DNA repair [1,2,3]. The procedure of defining a set of genes whose promoters/coding regions contain a specific histone modification (e.g. H3K4ac) is as follows. 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. 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 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. We will keep updating YHMI once new histone modification datasets become available in the literature
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