ATP-dependent Nucleosome Remodelers

The model by Machné and Murray (2012) remains indirectly supported and extended by more recent nucleosome remodeler binding studies (Kubik et al. 2019), where pushers (RSC, SWI) push nucleosomes out of promoters to allow for transcription and pullers pull nucleosomes into promoters (ISW2, INO80). Both types are active genome-wide, but additional domains can confer some specificity.

Existing measurements of DNA occupancy during the YRO do not have the required spatial and temporal resolution to study this on gene level, but both reveal two chromatin reset points, where occupancy peaks genome-wide in gene bodies in early LOC and promoters in mid LOC phase (Amariei et al. 2014; Nocetti and Whitehouse 2016).

References

Amariei, C., R. Machné, V. Stolc, T. Soga, M. Tomita, and D. B. Murray. 2014. "Time Resolved DNA Occupancy Dynamics During the Respiratory Oscillation Uncover a Global Reset Point in the Yeast Growth Program." Microb Cell 1 (9): 279-88. https://doi.org/10.15698/mic2014.09.166.

Kubik, S., M. J. Bruzzone, D. Challal, R. Dreos, S. Mattarocci, P. Bucher, D. Libri, and D. Shore. 2019. "Opposing Chromatin Remodelers Control Transcription Initiation Frequency and Start Site Selection." Nat Struct Mol Biol 26 (8): 744-54. https://doi.org/10.1038/s41594-019-0273-3.

Machné, R., and D. B. Murray. 2012. "The Yin and Yang of Yeast Transcription: Elements of a Global Feedback System Between Metabolism and Chromatin." PLoS One 7 (6): e37906. https://doi.org/10.1371/journal.pone.0037906.

Nocetti, N., and I. Whitehouse. 2016. "Nucleosome Repositioning Underlies Dynamic Gene Expression." Genes Dev 30 (6): 660-72. https://doi.org/10.1101/gad.274910.115.