TY - JOUR
T1 - Systematic Study of Nucleosome-Displacing Factors in Budding Yeast
AU - Yan, Chao
AU - Chen, Hengye
AU - Bai, Lu
N1 - Funding Information:
The authors are grateful to Dr. B. Franklin Pugh, Dr. Shaun Mahony, Dr. William K.M. Lai, Nina P. Farrell, Dr. Bongsoo Park, and Kylie Bocklund for help with the amplicon sequencing. We also thank Dr. David Stillman, Dr. Hiten Madhani, Dr. David Clark, and Dr. David MacAlpine for sharing plasmids, strains, and protocols. We acknowledge all members in the Bai lab for insightful comments on the manuscript. We thank the members of the Center of Eukaryotic Gene Regulation at PSU for discussions and technical support. This work is supported by the National Institutes of Health ( R01 GM121858 ).
Funding Information:
The authors are grateful to Dr. B. Franklin Pugh, Dr. Shaun Mahony, Dr. William K.M. Lai, Nina P. Farrell, Dr. Bongsoo Park, and Kylie Bocklund for help with the amplicon sequencing. We also thank Dr. David Stillman, Dr. Hiten Madhani, Dr. David Clark, and Dr. David MacAlpine for sharing plasmids, strains, and protocols. We acknowledge all members in the Bai lab for insightful comments on the manuscript. We thank the members of the Center of Eukaryotic Gene Regulation at PSU for discussions and technical support. This work is supported by the National Institutes of Health (R01 GM121858).
Publisher Copyright:
© 2018 Elsevier Inc.
PY - 2018/7/19
Y1 - 2018/7/19
N2 - 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. Nucleosome-displacing factors (NDFs) open chromosomes and allow transcription factors to bind and initiate gene expression. Yan et al. developed a high-throughput method to identify NDFs and study their activities. Comparison between NDFs and other factors with no NDF activities generates insights into the mechanism of nucleosome invasion.
AB - 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. Nucleosome-displacing factors (NDFs) open chromosomes and allow transcription factors to bind and initiate gene expression. Yan et al. developed a high-throughput method to identify NDFs and study their activities. Comparison between NDFs and other factors with no NDF activities generates insights into the mechanism of nucleosome invasion.
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U2 - 10.1016/j.molcel.2018.06.017
DO - 10.1016/j.molcel.2018.06.017
M3 - Article
C2 - 30017582
AN - SCOPUS:85048856287
SN - 1097-2765
VL - 71
SP - 294-305.e4
JO - Molecular cell
JF - Molecular cell
IS - 2
ER -