HIstome--a Relational Knowledgebase of Human Histone Proteins and Histone Modifying Enzymes

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2011 Dec 6

PMID 22140112

Citations 64

Authors

Satyajeet P Khare

Farhat Habib

Rahul Sharma

Nikhil Gadewal

Sanjay Gupta

Sanjeev Galande

Affiliations

Soon will be listed here.

Abstract

Histones are abundant nuclear proteins that are essential for the packaging of eukaryotic DNA into chromosomes. Different histone variants, in combination with their modification 'code', control regulation of gene expression in diverse cellular processes. Several enzymes that catalyze the addition and removal of multiple histone modifications have been discovered in the past decade, enabling investigations of their role(s) in normal cellular processes and diverse pathological conditions. This sudden influx of data, however, has resulted in need of an updated knowledgebase that compiles, organizes and presents curated scientific information to the user in an easily accessible format. Here, we present HIstome, a browsable, manually curated, relational database that provides information about human histone proteins, their sites of modifications, variants and modifying enzymes. HIstome is a knowledgebase of 55 human histone proteins, 106 distinct sites of their post-translational modifications (PTMs) and 152 histone-modifying enzymes. Entries have been grouped into 5 types of histones, 8 types of post-translational modifications and 14 types of enzymes that catalyze addition and removal of these modifications. The resource will be useful for epigeneticists, pharmacologists and clinicians. HIstome: The Histone Infobase is available online at http://www.iiserpune.ac.in/∼coee/histome/ and http://www.actrec.gov.in/histome/.

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References

Bonasio R, Tu S, Reinberg D . Molecular signals of epigenetic states. Science. 2010; 330(6004):612-6. PMC: 3772643. DOI: 10.1126/science.1191078. View

Marino-Ramirez L, Hsu B, Baxevanis A, Landsman D . The Histone Database: a comprehensive resource for histones and histone fold-containing proteins. Proteins. 2005; 62(4):838-42. PMC: 1800941. DOI: 10.1002/prot.20814. View

Pruitt K, Tatusova T, Maglott D . NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2006; 35(Database issue):D61-5. PMC: 1716718. DOI: 10.1093/nar/gkl842. View

Chow J, Heard E . X inactivation and the complexities of silencing a sex chromosome. Curr Opin Cell Biol. 2009; 21(3):359-66. DOI: 10.1016/j.ceb.2009.04.012. View

Koina E, Chaumeil J, Greaves I, Tremethick D, Marshall Graves J . Specific patterns of histone marks accompany X chromosome inactivation in a marsupial. Chromosome Res. 2009; 17(1):115-26. DOI: 10.1007/s10577-009-9020-7. View

Li H, Xing X, Ding G, Li Q, Wang C, Xie L . SysPTM: a systematic resource for proteomic research on post-translational modifications. Mol Cell Proteomics. 2009; 8(8):1839-49. PMC: 2722767. DOI: 10.1074/mcp.M900030-MCP200. View

. The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res. 2009; 38(Database issue):D142-8. PMC: 2808944. DOI: 10.1093/nar/gkp846. View

Marino-Ramirez L, Levine K, Morales M, Zhang S, Moreland R, Baxevanis A . The Histone Database: an integrated resource for histones and histone fold-containing proteins. Database (Oxford). 2011; 2011:bar048. PMC: 3199919. DOI: 10.1093/database/bar048. View

Tarakhovsky A . Tools and landscapes of epigenetics. Nat Immunol. 2010; 11(7):565-8. DOI: 10.1038/ni0710-565. View

10.

Chi P, Allis C, Wang G . Covalent histone modifications--miswritten, misinterpreted and mis-erased in human cancers. Nat Rev Cancer. 2010; 10(7):457-69. PMC: 3262678. DOI: 10.1038/nrc2876. View

11.

van Attikum H, Gasser S . Crosstalk between histone modifications during the DNA damage response. Trends Cell Biol. 2009; 19(5):207-17. DOI: 10.1016/j.tcb.2009.03.001. View

12.

Amberger J, Bocchini C, Scott A, Hamosh A . McKusick's Online Mendelian Inheritance in Man (OMIM). Nucleic Acids Res. 2008; 37(Database issue):D793-6. PMC: 2686440. DOI: 10.1093/nar/gkn665. View

13.

Bannister A, Kouzarides T . Regulation of chromatin by histone modifications. Cell Res. 2011; 21(3):381-95. PMC: 3193420. DOI: 10.1038/cr.2011.22. View

14.

Seal R, Gordon S, Lush M, Wright M, Bruford E . genenames.org: the HGNC resources in 2011. Nucleic Acids Res. 2010; 39(Database issue):D514-9. PMC: 3013772. DOI: 10.1093/nar/gkq892. View

15.

Zhu Q, Wani A . Histone modifications: crucial elements for damage response and chromatin restoration. J Cell Physiol. 2010; 223(2):283-8. PMC: 2930755. DOI: 10.1002/jcp.22060. View

16.

Oliver S, Denu J . Dynamic interplay between histone H3 modifications and protein interpreters: emerging evidence for a "histone language". Chembiochem. 2011; 12(2):299-307. PMC: 3073147. DOI: 10.1002/cbic.201000474. View

17.

Huang H, Maertens A, Hyland E, Dai J, Norris A, Boeke J . HistoneHits: a database for histone mutations and their phenotypes. Genome Res. 2009; 19(4):674-81. PMC: 2666297. DOI: 10.1101/gr.083402.108. View

18.

Zhang Y, Lv J, Liu H, Zhu J, Su J, Wu Q . HHMD: the human histone modification database. Nucleic Acids Res. 2009; 38(Database issue):D149-54. PMC: 2808954. DOI: 10.1093/nar/gkp968. View

19.

Martin-Subero J, Esteller M . Profiling epigenetic alterations in disease. Adv Exp Med Biol. 2011; 711:162-77. DOI: 10.1007/978-1-4419-8216-2_12. View

20.

OConnor T, Wyrick J . ChromatinDB: a database of genome-wide histone modification patterns for Saccharomyces cerevisiae. Bioinformatics. 2007; 23(14):1828-30. DOI: 10.1093/bioinformatics/btm236. View