Chromatin fibers: oh what a tangled web we weave

From the Tsukiyama Lab, Basic Sciences Division

Scientists tend to describe DNA as a long string. But this metaphor fails to accurately describe the complex three-dimensional structure that DNA adopts within our cells. In truth, our DNA could more aptly be thought of as the world’s gnarliest rollercoaster, with long soaring loops, tight corkscrews, and criss-crossing banked turns. And on this rollercoaster, you never get the same ride twice, as the track is constantly deforming itself into new configurations. But these complex structures are more than just fun and games – the shape of DNA can have serious implications for gene expression, and it tends to be tightly regulated in different cells and circumstances to help control which genes are turned on and which are turned off. A new research article in eLife from the lab of Dr. Toshi Tsukiyama, a Professor in Fred Hutch’s Basic Sciences Division and member of the Fred Hutch/UW Cancer Consortium, led by former postdoctoral fellow (now Assistant Professor at Colorado State University) Dr. Sarah Swygert, examined how changes in chromatin structure affect gene expression during the process of quiescence.

Chromatin structure is present at many levels. First, the authors explained, “nucleosomes are arranged on DNA into a “beads on a string” conformation approximately 10 nanometers (nm) in diameter called the 10 nm fiber.” Those fibers can then be compacted into larger-diameter fibers, as well as formed into large looping structures called chromatin loop domains, which are mediated by the condensin protein complex. While the structure of chromatin is proposed to influence gene expression, the authors noted that “the causality relationship between local chromatin fiber conformation and transcription has yet to be firmly established.” To better understand this relationship, the authors turned to the budding yeast Saccharomyces cerevisiae. Yeast cells can enter a state of quiescence that is marked by large-scale repression of gene transcription, making it a good system in which to probe the genomic changes that promote transcriptional repression. First, they used a technique called micro-C to map interactions between nucleosomes. They found that, in active yeast, nucleosomes mostly interacted with their nearest neighbors, indicative of thinner, less compacted fibers, while in quiescent cells nucleosomes interacted with more distant neighbors, indicative of thicker, more compacted fibers. This conclusion was confirmed by using electron microscopy to directly measure the diameter of active and quiescent fibers.

The group next asked what caused this change in chromatin fiber folding. One major change that occurs between the active and quiescent states is that histone H4, one of the proteins that forms the core of nucleosomes, is deacetylated. Suspecting that this may contribute to chromatin folding, the authors treated quiescent cells with drugs to increase H4 acetylation and found that this led to chromatin fiber decompaction. Using mutational analysis, they further identified a small region of the H4 protein – the basic patch – as critical for compaction. This finding was particularly valuable, the authors explained, because “the ability to disrupt quiescence-specific chromatin fiber folding through H4 mutation gave us the opportunity to determine the role of this compaction in transcriptional regulation during quiescence.” They used ChIP-seq to measure the localization of RNA polymerase II – an indicator of active transcription – in quiescent H4 mutants and observed dramatic increases in RNA polymerase II binding throughout the genome. These findings, explained Dr. Swygert, “show that during quiescence, yeast cells are able to alter [chromatin fiber] structure in order to regulate transcription genome-wide.” She added: “Interestingly, we also show that changes in this local level of chromatin structure affect larger levels of chromatin structure,” in reference to the fact that they observed the H4 mutation also affected condensin localization and appeared to alter the formation of repressive chromatin loop domains.

 “These results reveal a mechanism by which the cell is able to regulate processes globally during a change in cell state,” Dr. Swygert concluded. She was also excited to point out that this may be just the beginning of a revolution in our understanding of the importance of chromatin structure. “As technologies to determine in vivo chromatin structure at single-nucleosome resolution become more readily available, chromatin fiber structure may emerge as a major regulator of biological processes across organisms and cell types.”

gene expression model
Left: An open chromatin conformation promotes an on state for gene expression; Right: A closed chromatin conformation, mediated by condensin-dependent looping and chromatin fiber compaction (zoom-in in circle), promotes an off state for gene expression. Image provided by Dr. Sarah Swygert.

This work was supported by the National Institutes of Health, Academia Sinica, the National Science Foundation, Philip Morris International Inc., and Philip Morris USA Inc.

Fred Hutch/UW Cancer Consortium member Toshio Tsukiyama contributed to this work

Swygert SG, Lin D, Portillo-Ledesma S, Lin PY, Hunt DR, Kao CF, Schlick T, Noble WS, Tsukiyama T. Local chromatin fiber folding represses transcription and loop extrusion in quiescent cells. Elife. 2021 Nov 4;10:e72062. doi: 10.7554/eLife.72062. PMID: 34734806; PMCID: PMC8598167.