The 3-D structure of chromosomes is the richest unexplored territory in cell science.
Chromosomes are the largest, most dynamic, and most complex of all cellular
organelles. They are most fundamental, underlying cell differentiation, cell physiology,
and disease. They are also most enigmatic, exhibiting at the same time structural
heterogeneity and order, physical flexibility and rigidity, and functional activity and
silencing. We will dispel the mysteries by the determination of chromosome structure.
Virtually nothing is known about chromosome structure at the present time. And yet
chromosome structure is the key to chromosome function; it is inextricably linked to all
DNA transactions, to epigenetics, and to aberrations in disease.
We propose a comprehensive solution of the chromosome structure problem. We will
trace the path of the chromatin fiber, from nucleosome to nucleosome, through TADs
and intervening regions. We will "walk" the 3-D genome at single nucleosome resolution.
We will employ super resolution light microscopy with DNA sequence-specific dye
molecules (fluorescence emitters) for the purpose. A resolution of 10-20 nm,
comparable to the size of a nucleosome (10 nm) is routinely achieved with current
microscopes. The localization of an emitter to an individual nucleosome can be
accomplished with the use of specially designed pyrrole-imidazole polyamides and zinc
finger proteins. These molecules, once designed, will be applicable to chromosome
structure determination in all types of cell, at all stages of the cell cycle, in both normal
and disease states. They will transform the field, by providing structural paradigms, and
by enabling others to address innumerable problems in genetic chemistry and biology in
a facile, penetrating manner.