Structural role of linker histone H5 tails in the formation of the 30nm fiber of chromatin

Abstract

Eukaryotic DNA associates with histones to form nucleosomes, the fundamental component of chromatin. There are two functionally distinct classes of histones, core histones and linker histones. The core histones form an octamer around which DNA winds and a molecule of linker histone associates with this complex completing the nucleosome. The binding of linker histones to chromatin appears to be directed by the interaction of two sites in the folded globular domain with a site or sites close to the dyad axis of the core particle at the point where the DNA enters and exits after making two turns around the core histone octamer. This interaction must determine the location and orientation of the ‘tails’ of the linker histones allowing them to neutralize the linker DNA and permit the nucleosomal chain to adopt higher-order folding. However, there is little evidence of how the tails are organized or how they affect this folding process. It is toward this problem that this project is directed. The tails of the linker histones are rich in basic amino acids with the majority of the lysines and arginines found in the C-terminal and N-terminal tails. The tails also remain unstructured in contrast to the globular domain, which is folded even in low ionic strength buffers. Taking advantage of the structured and unstructured nature of the linker histone the proteolytic enzyme trypsin will be used as a probe to assess the structure of the tails. The aim is to mildly cleave the molecule and identify the sites of the cutting under a variety of relevant conditions using mass spectrometry to measure the mass of the digest products. The organization of the tails was probed under the following conditions; by first digesting the H5 alone, then digesting the H5 in the presence of DNA and finally by digesting the H5 in the presence of chromatin, previously stripped of linker histones, in varying ionic strength buffers. The digest products were run on SDS/PAGE gel and by direct mass spectrometric analysis. The aim of investigating the linker histone tails is to build upon the body of evidence regarding the higher-order organization of chromatin.