All cells of an organism contain the same genetic information (DNA), but each cell expresses only a subset of the genes it contains. There is increasing evidence that the transcription of DNA into RNA is often controlled by the way the DNA is packaged into chromatin. In Heterochromatin, DNA is tightly packaged by proteins, and most genes cannot normally be expressed. In Euchromatin, the DNA is less tightly packaged and its packaging state can be modified by proteins. They either loosen it to allow, or tighten it to prevent, expression of a gene.
The Nucleosome Remodelling Deacetylase complex (NuRD) contains two subunits RbAp46 and RbAp48 (pRB–associated proteins p46 and p48, also known as RBBP7 and RBBP4, respectively), which are highly homologous histone chaperones. RbAp46/p48 belong to the WD40–repeat protein family and they are found in a large number of different complexes that either covalently modify histones or aid their assembly into nucleosomes.
We recently reported the crystal structure of human RbAp46 bound to histone H4. RbAp46 folds into a seven-bladed β-propeller structure and binds histone H4 in a groove formed between an N–terminal α–helix and an extended loop inserted into blade six. Surprisingly, histone H4 adopts a different conformation when interacting with RbAp46 than it does in either the nucleosome or in a complex with ASF1, another histone chaperone. Our structure suggested that when a histone H3/H4 dimer (or tetramer) binds to RbAp46 or RbAp48, helix-1 of histone H4 unfolds to interact with the histone chaperone (see Figure).
In EPR and FRET experiments we have confirmed that there are major structural rearrangements in the core fold of the histone H3–H4 complex when it binds RbAp48. Importantly, these results also suggest that RbAp48 binding leads to conformational changes within the H3–H3 interface such that RbAp48 only binds to H3–H4 dimers, rather than (H3–H4)2 tetramers. Comparison of the affinity of ASF1 for the H3–H4 and RbAp48/H3–H4 complexes, using fluorescence polarisation experiments, suggests that an allosteric mechanism facilitates the exchange of H3–H4 between the RbAp48 and ASF1 histone chaperones. The finding that RbAp48 binds histone H3–H4 heterodimers, but not histone (H3–H4)2 heterotetramers, has important implications for understanding the role(s) of these proteins and of histones H3–H4 in epigenetic inheritance.
For further details see: Zhang et al., Nat Struct Mol Biol, 2013, 20 (1): 29-35.
Members of our group currently involved in this project are: Dr. Wei Zhang, Dr Jennifer Balmer, Dr Aleksandra Watson, Tom Drury