Effect of Histone Modification on Nucleosome Remodeling by SWI/SNF and RSC Nucleosome Remodelers

Tharathorn(Joy) Rimchala

Massachusetts Institute of Technology

ปริญญาโท

Genomic DNA must be compacted in the small volume of the nuclues, while retaining the accessibility to DNA-involving cellular processes such as DNA replication and RNA transcription. The wrapping of DNA around histones to form a structural unit called nucleosome and its further packaging into higher order structure represents physical barriers to protein binding to DNA, which are essential for DNA-related transactions [9]. This packing serves as a higher regulation of gene expression and the understanding of its dynamics are necessary in making prediction on gene expression levels in eukaryotes [2, 4]. Biochemical experiments over the past decades reveal two groups of protein complexes that modulate the accessibility of chromosomal DNA to protein binding. The first group, known as ATP-dependent nucleosome remodeling proteins, are believed to physically expose the histone-bound DNA to protein binding utilizing the energy from ATP hydrolysis. The other, known as nucleosome modifying proteins, add or remove covalent function groups at particular sites on histone protein and marks the sites for binding of other regulatory proteins [9].
One of the central questions in nucleosome research is how the modulations of nucleosome - physically by ATP dependent nucleosome remodeling proteins and chemically by nucleosome modifying proteins - affects the accessibility of DNA to protein binding and consequently the regulation of gene expression. In 2005, Jonathan Widom and colleagues reports that the have fond a way to determine nucleosome accessibility in unmethylated, unacetylated DNA. On the other hand, Carlos Bustamante and colleagues recently report that SWI/SNF and RSC proteins, which are one of the most prevalent nucleosome remodeling proteins, enhance accessibility of nucleosomal DNA to protein bininding by loop formation[13, 14]. In this study, the group shows that at least in vitro SWI/SNF remodels nucleosome by translocating along the DNA at a rates of 13 bp/s and generating DNA loops on nucleosomal DNA but not on unbound DNA template. As a result, the part of the DNA in the loop is transiently accessibility to protein binding.
The focus of this study is to compare the effect of histone modifications especially histone acetylation and methylation on a few aspects of nucleosome remodeling dynamics including nucleosome accessibility, the velocity and processivity of nucleosome remodeling proteins, the average loop size resulting from nucleosome remodeling, as well as the force generated by nucleosome remodeling. These results can be obtained by performing a set of experiments on minimally modified and heavily methylated and acetylated nucleosome template.

finalprop.pdf(December 17, 2007 5:34)