Project Summary
Though the three-dimensional (3D) organization of chromatin regulates all DNA-dependent processes,
determining chromatin mechanisms and functions in cells is challenging. One well-described 3D chromatin
structure is the topologically associated domain (TAD). TADs are chromatin loop domains created by cohesin
through a process called loop extrusion. TADs are strongly implicated in transcriptional regulation and have
recently been linked to DNA replication and repair. However, significant questions about the underlying
mechanisms of TADs remain, and even less is known about the mechanisms and functions of loop domains
created by other extruding complexes such as condensin. At the local scale, the pattern of interactions
between nucleosomes on the DNA strand determines the 3D arrangement of the chromatin fiber. Chromatin
fiber compaction is hypothesized to be a major form of gene regulation, however, obtaining sufficient resolution
to determine fiber structure in cells has been a major barrier. As a result, little is known about chromatin fiber
function in cells. To address these gaps, the Swygert lab uses high-resolution genomics, microscopy, and
biochemistry in a quiescent budding yeast model. Quiescence is a reversible state in which the cell exits the
cell cycle, and is essential for stem cell maintenance and implicated in cancer recurrence. As the hallmarks of
quiescent cells are global transcriptional repression and chromatin condensation, they are an excellent model
for uncovering the functions of chromatin structural dynamics. In quiescent yeast, condensin binds coding gene
promoters throughout the genome, forming chromatin loop domains that resemble TADs. At the same time,
histone deacetylation drives the compaction of chromatin fibers. Disruption of either structure leads to the mis-
activation of up to 40% of all genes. Over the next five years, the Swygert lab will expand current projects
examining 3D chromatin structural mechanisms in quiescent cells. A strength of the lab is the ability to resolve
and perturb functional chromatin fiber structure genome-wide. They will use genomics and single-molecule
biophysics to uncover how condensin relocates during quiescence entry and how chromatin obstacles such as
fiber compaction affect loop extrusion. They will also determine the essential roles of HMG proteins that bend
DNA at sharp angles during quiescence entry. Finally, they will examine how quiescent chromatin structure,
which takes a week to assemble during quiescence entry, is disassembled within minutes during quiescence
exit. These studies will form the foundation of a unique and independent research program in which
complementary genomics and biochemical methods are used in the context of yeast quiescence to uncover 3D
chromatin structure and function and all scales. As the mechanisms underlying chromatin condensation in
quiescent yeast are conserved in quiescent human cells, their results will inform both basic chromatin
mechanisms and quiescence-specific mechanisms relevant to human health.