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theses

The packaging of DNA into nucleosomes impedes the binding and access of molecules involved in its processing. The yeast SWI/SNF complex is a regulatory factor in yeast, which stimulates the mobilization of chromatin DNA required for transcription. Amino acid point mutations in the genes coding for histones H3 and H4 can partially bypass the requirement of the SWI/SNF complex. The atomic mechanisms, which underlie the observed remodeling, however, are difficult to discern from the crystal structures of nucleosomes bearing these so-called Sin (SWI-INdependent) mutations. The modified nucleosomes are only minimally distorted from the wild-type structure, with the loss of a few direct protein-DNA contacts near the sites of amino acid mutation and no large-scale change in overall structure (Muthurajan et al. (2004) EMBO J. 23, 260).
Detailed analysis of the conformation and interactions of the histone proteins and DNA in the SIN-mutant structures reveals additional loss of intermolecular contacts and accompanying variation in the orientation and displacement of individual base-pair steps in the vicinity of histones H2A and H2B. The modified amino acids seemingly transmit information relevant to DNA binding across the nucleosome structure.
Nucleosomal DNA in the wild-type and SIN-mutant structures is represented in a
cylindrical frame as the shape of a nucleosome resembles a cylinder with the nucleosomal DNA wrapping along a superhelical pathway around the histone core. This analysis shows an increase in radius at the successive or neighboring dimer steps in the SIN-mutants, compared to the wild-type, either toward the end of nucleosomal DNA or near the histone dimerization interface.
The structural templates of the wild-type and SIN-mutant nucleosomes are threaded on nucleosomal DNA sequences, which measure the relative ease of deforming a DNA sequence on the surface of a histone protein core. Surprisingly, the threading scores can discriminate among different SIN-mutant structures. Highly deformed steps in terms of large deformation scores in the SIN-mutant structures are located near one end and near the central dyad of the nucleosomal DNA. Models, which incorporate the highly deformed steps, are suggestive of ways in which the DNA might loop away from or peel off the nucleosome core particle.
Two nucleosome structures have identical histone cores but different DNA sequences are compared to each other. The difference in the superhelical shapes and the shifted locations of highly deformed steps show how nucleosomal DNA adjusts its conformation according to its sequence specificity.

Ph.D.

Includes bibliographical references.

http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.16798

ETD_390

doi:10.7282/T3H132DF

ETD doctoral

The author owns the copyright to this work.

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