proteins STRUCTURE O FUNCTION O BIOINFORMATICS SHORT COMMUNICATION Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A-H2B histone dimer Cedric R. Clapier,1 Srinivas Chakravarthy,2 Carlo Petosa,1 Carlos Fern a´ndez-Tornero,1,3 Karolin Luger,2 and Christoph W. Mu¨ ller1,3* 1 European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble Cedex 9, France 2 Howard Hughes Medical Institute and Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870 3 European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, Heidelberg D-69117, Germany ABSTRACT We determined the 2.45 A˚ crystal structure of the nucleosome core particle from Drosophila mela- nogaster and compared it to that of Xenopus laevis bound to the identical 147 base-pair DNA fragment derived from human a-satellite DNA. Differences between the two structures primarily reflect 16 amino acid substitutions between species, 15 of which are in histones H2A and H2B. Four of these involve histone tail residues, resulting in subtly altered protein–DNA interactions that exemplify the structural plasticity of these tails. Of the 12 substitutions occurring within the histone core regions, five involve small, solvent- exposed residues not involved in intraparticle inter- actions. The remaining seven involve buried hydro- phobic residues, and appear to have coevolved so as to preserve the volume of side chains within the H2A hydrophobic core and H2A-H2B dimer interface. Thus, apart from variations in the histone tails, amino acid substitutions that differentiate Drosoph- ila from Xenopus histones occur in mutually com- pensatory combinations. This highlights the tight ev- olutionary constraints exerted on histones since the vertebrate and invertebrate lineages diverged. Proteins 2008; 71:1–7. VC 2007 Wiley-Liss, Inc. Key words: chromatin; nucleosome core particles; protein–DNA interaction; Drosophila; crystal structure. VC 2007 WILEY-LISS, INC. INTRODUCTION Genomic DNA in the eukaryotic nucleus is compacted and organ- ized in protein–DNA complexes called chromatin. The notion of a repeating unit of chromatin structure, composed of eight histone proteins and 200 base pairs of DNA, was proposed over 30 years ago.1,2 Within this unit, the first level of chromatin organization, revealed by micrococcal nuclease digestion, is the nucleosome core particle (NCP). The NCP is composed of an octamer containing two copies of each of the four histone proteins (H3, H4, H2A, and H2B), around which 146 base pairs of DNA are tightly wrapped in 1.65 turns of a left-handed superhelix (reviewed in Ref. 3). In addition to its structural role in genome organization, the nucleosome is the point of convergence for many DNA regulatory processes: recombination, repair, replication, and transcription. In particular, nucleosomes are highly dynamic and are directly involved in the regulation of transcription.4 ATP-dependent remodeling com- plexes physically modulate chromatin structure at the nucleosome level, actively altering the accessibility of specific sequences to tran- scription factors.5,6 Nucleosomes also carry information via changes in composition (histone variants) and posttranslational modifications (PTMs).7,8 The role of both types of modification on the regulation of genomic activity is currently the subject of intense research. Grant sponsors: March of Dimes; Howard Hughes Medical Institute. *Correspondence to: Christoph W. Mu¨ller, European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, Heidelberg D-69117, Germany. E-mail: christoph.mueller@embl.de Received 17 May 2007; Accepted 10 July 2007 Published online 23 October 2007 in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/prot.21720 PROTEINS 1