Abstract
Over the past two decades, epigenetics has evolved into a key concept for understanding regulation of gene expression. Among many epigenetic mechanisms, covalent modifications such as acetylation and methylation of lysine residues on core histones emerged as a major mechanism in epigenetic regulation. Here, we present the database for histone-modifying enzymes (dbHiMo; http://hme.riceblast.snu.ac.kr/) aimed at facilitating functional and comparative analysis of histone-modifying enzymes (HMEs). HMEs were identified by applying a search pipeline built upon profile hidden Markov model (HMM) to proteomes. The database incorporates 11 576 HMEs identified from 603 proteomes including 483 fungal, 32 plants and 51 metazoan species. The dbHiMo provides users with web-based personalized data browsing and analysis tools, supporting comparative and evolutionary genomics. With comprehensive data entries and associated web-based tools, our database will be a valuable resource for future epigenetics/epigenomics studies.Database URL: http://hme.riceblast.snu.ac.kr/
Highlights
IntroductionNuclear proteins that provide physical means for eukaryotic DNA to be organized and packaged into chromatin
Histones are highly basic, nuclear proteins that provide physical means for eukaryotic DNA to be organized and packaged into chromatin
It has been shown that both the histone tails and globular domains are subjected to a diverse array of the posttranslational covalent modifications, and that such modifications are pivotal for regulating chromatin dynamics and transcriptional output of the gene/genome [1,2,3,4]
Summary
Nuclear proteins that provide physical means for eukaryotic DNA to be organized and packaged into chromatin. Recent surge in the number of sequenced genomes increased the demand for a repository that organizes and compiles information on histone-modifying enzymes (HMEs) in an accessible format. To date, databases such as HistoneHits [6], ChromDB [7] and HIstome [8] were presented to provide researchers with information on different histone modifications and enzymes responsible for each modification. Databases such as HistoneHits [6], ChromDB [7] and HIstome [8] were presented to provide researchers with information on different histone modifications and enzymes responsible for each modification Those databases are centered primarily on yeast, plants and human, lacking curated information on HMEs in the fungal kingdom (other than yeast). To take great advantage of such datasets, it is imperative to have a centralized and organized data repository that ensures accessibility to researchers
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