Chromatin is the substrate for most processes that occur in the eukaryotic cell nucleus due to its role as the universal genome packaging state. The nucleosome is the fundamental repeating subunit of chromatin so it is unsurprising that the histone proteins organising this structure are highly conserved.
The design principles of the nucleosome are not understood despite its importance and conservation. Our aim is to understand the structure-function relationships of chromatin in molecular detail.
Most textbooks represent nucleosomes as static ‘tuna cans’ that provide a solution to the ‘packaging problem’ of compacting metres of genomic DNA into the micrometre diameter cell nucleus. In fact, this could be achieved by any small and highly positively charged ionic compound.
Determinants of nucleosome dynamics
Nucleosomes appear to have evolved to provide a unique balance of static organisation and dynamic character that can undergo specific transitions such as sliding or histone exchange which are essential for chromatin function.
The dynamic behaviour appears to involve flexing in particular ways defined by the properties of the histone protein core. We are working to understand the determinants of these molecular motions using panels of recombinantly produced histones to create mutated nucleosomes probed by a variety of biochemical and biophysical assays.
We are also looking into other applications for these collections of mutated histone proteins.
Damage-linked histone H2AX
Histone H2AX is a histone variant found in all eukaryotes that makes up a significant but variable proportion of bulk chromatin. It is frequently considered to act as a platform for signalling DNA damage events.
In collaboration with other groups in the Centre for Chromosome Biology, we have been investigating the genomic distribution and mechanism of incorporation of H2AX.
Mechanism of ATP-dependent chromatin remodelling
ATP-dependent chromatin remodelling complexes all contain Snf2 family proteins as molecular engines at their core. The complexes behave as classical enzymes to direct and accelerate the rate of nucleosome structural changes. These enzymes translate the chemical energy of ATP hydrolysis into mechanical motion.
How this action is applied as a force to the nucleosome and how the enzymes are regulated in the high chromatin density of the nucleus are not understood.
The properties of the ‘chromatin remodelling’ mechanism is almost certainly intertwined with the dynamic potential of nucleosomes themselves.