Systematic Study of Nucleosome-Displacing Factors in Budding Yeast

Molecular Cell
Chao YanLu Bai

Abstract

Nucleosomes present a barrier for the binding of most transcription factors (TFs). However, special TFs known as nucleosome-displacing factors (NDFs) can access embedded sites and cause the depletion of the local nucleosomes as well as repositioning of the neighboring nucleosomes. Here, we developed a novel high-throughput method in yeast to identify NDFs among 104 TFs and systematically characterized the impact of orientation, affinity, location, and copy number of their binding motifs on the nucleosome occupancy. Using this assay, we identified 29 NDF motifs and divided the nuclear TFs into three groups with strong, weak, and no nucleosome-displacing activities. Further studies revealed that tight DNA binding is the key property that underlies NDF activity, and the NDFs may partially rely on the DNA replication to compete with nucleosome. Overall, our study presents a framework to functionally characterize NDFs and elucidate the mechanism of nucleosome invasion.

Citations

Nov 2, 2019·Science·Youpi YeZhucheng Chen
Aug 10, 2019·Nucleic Acids Research·Manyu DuLu Bai
Apr 17, 2020·Molecular Genetics and Genomics : MGG·Xinyang Yu, Michael J Buck
Mar 20, 2019·Nature Reviews. Genetics·Paul B TalbertSteven Henikoff
Jul 26, 2019·Proceedings of the National Academy of Sciences of the United States of America·Christian A ShivelyRobi D Mitra
Sep 12, 2018·Proceedings of the National Academy of Sciences of the United States of America·Robert M YarringtonDana Carroll
Dec 18, 2019·Interdisciplinary Sciences, Computational Life Sciences·Yuan WangZhifeng Shao
Oct 21, 2020·Proceedings of the National Academy of Sciences of the United States of America·Daniel S Saxton, Jasper Rine
Sep 5, 2020·Annual Review of Genetics·Kenneth S Zaret
Jan 12, 2021·PLoS Computational Biology·Hungyo Kharerin, Lu Bai
Aug 23, 2019·Trends in Biotechnology·Ronald P H de JonghDick de Ridder
Oct 22, 2019·Trends in Biochemical Sciences·Sandipan Brahma, Steven Henikoff
Mar 6, 2021·ELife·Michael Roland WolffUlrich Gerland
May 10, 2021·Cancer Cell International·Joby IssacAni V Das
May 30, 2021·Nature Communications·Elisa OberbeckmannPhilipp Korber
May 30, 2021·Nature Communications·Elisa OberbeckmannSebastian Eustermann
Aug 14, 2021·IScience·Benjamin D SunkelBenjamin Z Stanton
Jul 5, 2021·Current Opinion in Structural Biology·Wataru Kagawa, Hitoshi Kurumizaka

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