Polycomb proteins are required for maintenance of silent chromatin states via histone H3 Lys27 trimethylation (H3K27me3) in animals, but homologs are not found in plant genomes. Using a DamID-chip method, we found that the Arabidopsis thaliana chromodomain-containing protein LHP1 colocalizes with H3K27me3 genome-wide. The LHP1 chromodomain also binds H3K27me3 with high affinity, suggesting that LHP1 has functions similar to those of Polycomb.

MSL3 resides in the MSL (male-specific-lethal) complex that upregulates transcription by spreading the H4K16 acetyl-mark. We discovered a DNA-dependent interaction of MSL3 chromodomain with the histone H4K20 monomethyl-mark. Structure of a ternary complex shows DNA minor groove accommodates the histone H4 tail, and monomethyllysine inserts in a four-residue aromatic cage in MSL3. Histone H4K16 acetyl-mark antagonizes MSL3 binding, suggesting MSL function is regulated by a combination of post-translational modifications.

Double chromodomains occur in CHD proteins which are ATP-dependent chromatin remodeling factors implicated in RNA polymerase II transcription regulation. Biochemical studies suggest important differences in the histone H3 tail binding of different CHD chromodomains. In human and Drosophila, CHD1 double chromodomains bind lysine 4-methylated histone H3 tail which is a hallmark of transcriptionally active chromatin in all eukaryotes. Here, we present the crystal structure of the yeast CHD1 double chromodomains, and pinpoint its differences with that of the human CHD1 double chromodomains. The most conserved residues in these double chromodomains are the two chromoboxes that orient adjacently. Only a subset of CHD chromoboxes can form an aromatic cage for methyllysine binding, and methyllysine binding requires correctly oriented inserts. These factors preclude yeast CHD1 double chromodomains to interact with the histone H3 tail. Despite great sequence similarity between the human CHD1 and CHD2 chromodomains, variation within an insert likely prevents CHD2 double chromodomains to bind lysine 4-methylated histone H3 tail as efficiently as in CHD1. By using the available structural and biochemical data we highlight the evolutionary specialization of CHD double chromodomains, and provide insights about their targeting capacities.

The chromatin organization modifier domain (chromodomain) was first identified as a motif associated with chromatin silencing in Drosophila. There is growing evidence that chromodomains are evolutionary conserved across different eukaryotic species to control diverse aspects of epigenetic regulation. Although originally reported as histone H3 methyllysine readers, the chromodomain functions have now expanded to recognition of other histone and non-histone partners as well as interaction with nucleic acids. Chromodomain binding to a diverse group of targets is mediated by a conserved substructure called the chromobox homology region. This motif can be used to predict methyllysine binding and distinguish chromodomains from related Tudor “Royal” family members. In this review, we discuss and classify various chromodomains according to their context, structure and the mechanism of target recognition.

At the center of the nuclear pore complex (NPC) is a uniquely versatile central transport channel. Structural analyses of distinct segments ("protomers") of the three "channel" nucleoporins yielded a model for how this channel is constructed. Its principal feature is a midplane ring that can undergo regulated diameter changes of as much as an estimated 30 nm. To better understand how a family of "adaptor" nucleoporins-concentrically surrounding this channel-might cushion these huge structural changes, we determined the crystal structure of one adaptor nucleoporin, Nup157. Here, we show that a recombinant Saccharomyces cerevisiae Nup157 protomer, representing two-thirds of Nup157 (residues 70-893), folds into a seven-bladed β-propeller followed by an α-helical domain, which together form a C-shaped architecture. Notably, the structure contains a large patch of positively charged residues, most of which are evolutionarily conserved. Consistent with this surface feature, we found that Nup157 70-893 binds to nucleic acids, although in a sequence-independent manner. Nevertheless, this interaction supports a previously reported role of Nup157, and its paralogue Nup170, in chromatin organization. Based on its nucleic acid binding capacity, we propose a dual location and function of Nup157. Finally, modeling the remaining C-terminal portion of Nup157 shows that it projects as a superhelical stack from the compact C-shaped portion of the molecule. The predicted four hinge regions indicate an intrinsic flexibility of Nup157, which could contribute to structural plasticity within the NPC.gene gating | X-ray crystallography | DNA-binding protein | RNA-binding protein M ultiple copies of only ∼30 distinct proteins, collectively termed nucleoporins (nups), form a large nuclear pore complex (NPC) that, in vertebrates, amounts to an estimated mass of more than 100 MDa. Purification of sufficient quantities of intact and monodisperse NPCs that would be suitable for crystallographic analyses is presently not feasible. In an alternative approach, a recombinant full-length nup, or a nup fragment ("protomer"), or complexes thereof, are crystallized and their atomic structures are modeled into higher-order assemblies that represent distinct regions of the NPC (reviewed in ref. 1).Arguably, the most notable insights stemming from the aforementioned strategy were obtained from the crystal structures of protomers representing several structured regions of the three "channel" nups, Nup58, Nup54, and Nup62 (2-4). The outcome of these crystallographic analyses was a model of the atomic structure of the central transport channel, the heart of the NPC. The crucial features of this model are midplane rings that undergo dramatic structural rearrangements from the dilated to constricted state of the nuclear pore. In the dilated state, helical segments of four Nup58 and eight Nup54 protomers form a dodecameric module. The arrangement of eight such dodecamers results in a single, heterooligomeric midplane ring with a flexible diameter of 40 to 50...