Chromatin is composed of nucleosomes, the universally repeating protein±DNA complex in eukaryotic cells. The crystal structure of the nucleosome core particle from Saccharomyces cerevisiae reveals that the structure and function of this fundamental complex is conserved between single-cell organisms and metazoans. Our results show that yeast nucleosomes are likely to be subtly destabilized as compared with nucleosomes from higher eukaryotes, consistent with the idea that much of the yeast genome remains constitutively open during much of its life cycle. Importantly, minor sequence variations lead to dramatic changes in the way in which nucleosomes pack against each other within the crystal lattice. This has important implications for our understanding of the formation of higher order chromatin structure and its modulation by post-translational modi®cations. Finally, the yeast nucleosome core particle provides a structural context by which to interpret genetic data obtained from yeast. Coordinates have been deposited with the Protein Data Bank under accession number 1ID3.

Increased synthesis of Apolipoprotein A-I (ApoA-I) and HDL is believed to provide a new approach to treating atherosclerosis through the stimulation of reverse cholesterol transport. RVX-208 increases the production of ApoA-I in hepatocytes in vitro, and in vivo in monkeys and humans, which results in increased HDL-C, but the molecular target was not previously reported. Using binding assays and X-ray crystallography, we now show that RVX-208 selectively binds to bromodomains of the BET (Bromodomain and Extra Terminal) family, competing for a site bound by the endogenous ligand, acetylated lysine, and that this accounts for its pharmacological activity. siRNA experiments further suggest that induction of ApoA-I mRNA is mediated by BET family member BRD4. These data indicate that RVX-208 increases ApoA-I production through an epigenetic mechanism and suggests that BET inhibition may be a promising new approach to the treatment of atherosclerosis.

No abstract

Activation of transcription within chromatin has been correlated with the incorporation of the essential histone variant H2A.Z into nucleosomes. H2A.Z and other histone variants may establish structurally distinct chromosomal domains; however, the molecular mechanism by which they function is largely unknown. Here we report the 2.6 A crystal structure of a nucleosome core particle containing the histone variant H2A.Z. The overall structure is similar to that of the previously reported 2.8 A nucleosome structure containing major histone proteins. However, distinct localized changes result in the subtle destabilization of the interaction between the (H2A.Z-H2B) dimer and the (H3-H4)(2) tetramer. Moreover, H2A.Z nucleosomes have an altered surface that includes a metal ion. This altered surface may lead to changes in higher order structure, and/or could result in the association of specific nuclear proteins with H2A.Z. Finally, incorporation of H2A.Z and H2A within the same nucleosome is unlikely, due to significant changes in the interface between the two H2A.Z-H2B dimers.

Bone morphogenetic proteins (BMPs) are used clinically to induce new bone formation in spinal fusions and long bone nonunion fractures. However, large amounts of BMPs are needed to achieve these effects. BMPs were found to increase the expression of antagonists, which potentially limit their therapeutic efficacy. However, the relative susceptibility of osteoinductive BMPs to different antagonists is not well characterized. Here we show that BMP-6 is more resistant to noggin inhibition and more potent in promoting osteoblast differentiation in vitro and inducing bone regeneration in vivo when compared with its closely related BMP-7 paralog. Noggin was found to play a critical role as a negative feedback regulator of BMP-7 but not BMP-6-induced biological responses. Using BMP-6/7 chimeras, we identified lysine 60 as a key residue conferring noggin resistance within the BMP-6 protein. A remarkable correlation was found between the presence of a lysine at this position and noggin resistance among a panel of osteoinductive BMPs. Introduction of a lysine residue at the corresponding positions of BMP-2 and BMP-7 allowed for molecular engineering of recombinant BMPs with increased resistance to noggin antagonism. Bone morphogenetic proteins (BMPs)3 are dimeric secreted cytokines that were discovered based on their ability to induce ectopic bone and cartilage formation in vivo (1-4). BMPs belong to the transforming growth factor-␤ superfamily, which also includes transforming growth factors-␤ and activins. Over 15 distinct BMP family members have been identified that signal via specific BMP type I and type II serine/threonine kinase receptors (5). Three BMP type II receptors (BMPR-II (BMP type II receptor), ActR-II (activin type II receptor), and ActR-IIB) and four distinct BMP type I receptors (ALK1 (activin receptor-like kinase 1), ALK2, ALK3, and ALK6) have been described (5-8). Cell surface binding of BMPs to their receptors results in heteromeric complex formation, upon which the constitutively active type II receptor phosphorylates the type I receptor on specific serine and threonine residues in the juxtamembrane region. Different BMPs bind with different affinities and specificities to different BMPR complexes (6 -10). The activated BMP type I receptor initiates intracellular signaling by phosphorylating specific receptor-regulated Smad (R-Smad) proteins (Smad1, Smad5, and Smad8). Activated R-Smads form heteromeric complexes with Smad4, which translocate to the nucleus and regulate, in cooperation with transcriptional coactivators and co-repressors, the transcription of target genes (5). BMP signaling is controlled at different levels by both positive and negative regulators. At the extracellular level, BMP antagonists bind BMPs and interfere with their binding to BMP receptors. An important extracellular BMP antagonist of the osteogenic activity of BMPs is noggin. The crystal structure of the noggin-BMP-7 complex demonstrated that binding of noggin to BMPs resembles that of BMP receptors and thereby prevents the ...