Professor Jon Widom

Contact Dr. Widom: e-mail: j-widom@northwestern.edu telephone: (847) 467-1887 fax: (847) 467-1380 Jon's CV

Our mission...

The long term goal of our research is to develop a concrete mechanistic understanding of gene regulation. We seek to understand how specific proteins or protein assemblies, acting in accord with the laws of physical chemistry, recognize and gain access to their DNA target sites in chromatin; and, conversely, we seek to understand how the nucleosomal organization of chromatin and higher order chromatin folding modulate the action these proteins and assemblies. We are attacking these questions from several different directions.

Nucleosome dynamics and function:

In earlier work we discovered that nucleosomes have an inherent dynamic property termed "site exposure", such that DNA sequences which in the time average are buried inside nucleosomes are nevertheless transiently accessible to exogenous DNA binding proteins. This property also confers a novel nucleosome-dependent cooperativity on the binding of pairs of regulatory proteins to target sites contained within the same nucleosome. In subsequent work we discovered that site exposure does not arise via translocation of the histone octamer (nucleosome), but rather involves a conformational change in which a stretch of the nucleosomal DNA is transiently released off the surface of the histone octamer.
Our current work in this area seeks to characterize the nature and rates of these conformational changes. Additional studies are planned for analyzing site exposure for test nucleosomes embedded in the middle of longer chains of nucleosomes.
A second current project seeks to understand the molecular mechanisms by which ATP-dependent nucleosome "remodeling" factors act on nucleosomes to alter the wrapping of the nucleosomal DNA or to catalyze and drive the motion of nucleosomes to new positions along the DNA. Our initial studies are focusing on the Drosophila protein ISWI.

Chromatin folding:

Our earlier work on chromatin folding showed that interactions between consecutive nucleosomes in a chain sufficed to overcome the bending resistance of linker DNA, allowing consecutive nucleosomes to pack together. In a new project, we are characterizing how such interactions between adjacent nucleosomes depend on the exact length (i.e., the integrated helical twist) of the linker DNA.

Nucleosome Positioning:

In earlier studies we carried out a selection experiment for DNA sequences having exceptionally high affinity for histone octamer, and concomitantly, exceptionally high nucleosome positioning power. Analysis of those sequences led to the discovery of a set of DNA sequences rules and motifs that govern the high affinity interactions. In separate earlier studies we discovered that some of these sequence motifs are present as strongly statistically significant signals in eukaryotic genomes. In subsequent work we discovered that these same signals are present in the genomes of histone-containing archaebacteria but not in histone-lacking bacteria.
Our current work in this area is focused on elucidating the biological role of these nucleosome positioning signals. We are carrying out selection experiments to isolate the strongest nucleosome positioning sequences in the yeast and human genomes, with the goal of correlating their locations with the physical and genetic organization of the genome; and, in yeast, experimentally manipulating them to determine their role in vivo.
A second project utilizes in vitro selection methods to isolate the strongest possible nucleosome positioning sequence. These will be used for studies of nucleosome positioning in vitro and in vivo.

DNA Structure and Mechanics:

A third research area in the group concerns the sequence-dependence of the structure and mechanics of DNA. Whenever a protein binds DNA, inevitably the detailed structure that the DNA adopts in the complex differs from the conformation it prefers as naked DNA. Consequently, free energy of protein-DNA bond formation (including all solvent effects, etc.) is used up doing work to distort the structure of the DNA. Differing DNA sequences can adopt the needed conformations with greater or less ease. This leads to sequence-dependent differences in free energies of distortion that contribute significantly to the overall affinity and sequence-specificity of complex formation -- even for DNA basepairs that are not touched by the protein or by protein-bound waters. This phenomenon is known as "indirect readout" in gene regulation.
We have initiated a new project that has as its goals: (i) discovering which DNA sequence motif(s) have the very greatest bending flexibility; and the lengthscale of those motifs; (ii) corresponding studies for DNA twisting flexibility; (iii) discovering the basis in molecular mechanics for the particularly high bending and twisting flexibilities; and (iv) developing new methods to measure DNA flexibility, especially in the highly-distorted regime.