dbHiMo: a web-based epigenomics platform for histone-modifying enzymes

Jaeyoung Choi; Ki-Tae Kim; Aram Huh; Seomun Kwon; Changyoung Hong; Fred O Asiegbu; Junhyun Jeon; Yong-Hwan Lee

doi:10.1093/database/bav052

dbHiMo: a web-based epigenomics platform for histone-modifying enzymes

Database (Oxford). 2015 Jun 8:2015:bav052. doi: 10.1093/database/bav052. Print 2015.

Authors

Jaeyoung Choi¹, Ki-Tae Kim², Aram Huh¹, Seomun Kwon¹, Changyoung Hong¹, Fred O Asiegbu¹, Junhyun Jeon³, Yong-Hwan Lee⁴

Affiliations

¹ Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland, Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea, Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, Seoul 151-921, Korea, School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea, and Research Institute of Agriculture and Life Sciences, Center for Fungal Pathogenesis, Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea.
² Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland, Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea, Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, Seoul 151-921, Korea, School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea, and Research Institute of Agriculture and Life Sciences, Center for Fungal Pathogenesis, Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland, Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea, Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, Seoul 151-921, Korea, School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea, and Research Institute of Agriculture and Life Sciences, Center for Fungal Pathogenesis, Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea.
³ Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland, Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea, Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, Seoul 151-921, Korea, School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea, and Research Institute of Agriculture and Life Sciences, Center for Fungal Pathogenesis, Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea yonglee@snu.ac.kr.
⁴ Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland, Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea, Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, Seoul 151-921, Korea, School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea, and Research Institute of Agriculture and Life Sciences, Center for Fungal Pathogenesis, Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland, Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea, Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, Seoul 151-921, Korea, School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea, and Research Institute of Agriculture and Life Sciences, Center for Fungal Pathogenesis, Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland, Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea, Department of Agricultural Biotechnology, College of Agriculture and Life Science, Seoul National University, Seoul 151-921, Korea, School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 712-749, Korea, and Research Institute of Agriculture and Life Sciences, Center for Fungal Pathogenesis, Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland, Fungal Bioinformatics Laboratory, Seoul National University, Seoul 151-921, Korea, Department of Agricultural Biotechnology, College of Agriculture

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.

Publication types

Dataset
Research Support, Non-U.S. Gov't

MeSH terms

Acetylation
Databases, Protein*
Epigenesis, Genetic*
Epigenomics / methods*
Histones* / genetics
Histones* / metabolism
Methylation
Protein Processing, Post-Translational
Proteome* / genetics
Proteome* / metabolism
Web Browser*

Substances

Histones
Proteome