The Histone Database: an integrated resource for histones and histone fold-containing proteins

L Marino-Ramirez,M Morales,K M Levine,D Landsman,R T Moreland,S Zhang,A D Baxevanis

doi:10.1093/database/bar048

Abstract

Eukaryotic chromatin is composed of DNA and protein components—core histones—that act to compactly pack the DNA into nucleosomes, the fundamental building blocks of chromatin. These nucleosomes are connected to adjacent nucleosomes by linker histones. Nucleosomes are highly dynamic and, through various core histone post-translational modifications and incorporation of diverse histone variants, can serve as epigenetic marks to control processes such as gene expression and recombination. The Histone Sequence Database is a curated collection of sequences and structures of histones and non-histone proteins containing histone folds, assembled from major public databases. Here, we report a substantial increase in the number of sequences and taxonomic coverage for histone and histone fold-containing proteins available in the database. Additionally, the database now contains an expanded dataset that includes archaeal histone sequences. The database also provides comprehensive multiple sequence alignments for each of the four core histones (H2A, H2B, H3 and H4), the linker histones (H1/H5) and the archaeal histones. The database also includes current information on solved histone fold-containing structures. The Histone Sequence Database is an inclusive resource for the analysis of chromatin structure and function focused on histones and histone fold-containing proteins.Database URL: The Histone Sequence Database is freely available and can be accessed at http://research.nhgri.nih.gov/histones/.

Highlights

Histones play central roles in both chromatin organization and gene regulation, as they constitute the fundamental protein units of the nucleosome [1]
The PSI-BLAST searches were run to convergence with an E-value inclusion threshold of 0.01; the core histone seeds were excluded from the final list of histone fold-containing proteins
The Histone Database contains entries that represent a total of 7356 unique NCBI taxonomic identifiers, which correspond to approximately the same number of organisms

Summary

Introduction

Histones play central roles in both chromatin organization and gene regulation, as they constitute the fundamental protein units of the nucleosome [1]. Even though each individual histone protein family is highly conserved, the histone fold is not conserved at the sequence level but, rather, at the structural level [12]. The linker histones, which do not contain the histone fold motif and have a different evolutionary origin from the core histones [15], are critical to chromatin higher-order compaction and facilitate internucleosomal interactions [16].

Results

Conclusion