Structural and dynamic mechanisms of CBF3-guided centromeric nucleosome formation

Tengfei Lian,Martin Singleton,Bing-Rui Zhou,Emily He,Ruifang Guan,Yawen Bai,Carl Wu

doi:10.1038/s41467-021-21985-9

Abstract

Accurate chromosome segregation relies on the specific centromeric nucleosome–kinetochore interface. In budding yeast, the centromere CBF3 complex guides the deposition of CENP-A, an H3 variant, to form the centromeric nucleosome in a DNA sequence-dependent manner. Here, we determine the structures of the centromeric nucleosome containing the native CEN3 DNA and the CBF3core bound to the canonical nucleosome containing an engineered CEN3 DNA. The centromeric nucleosome core structure contains 115 base pair DNA including a CCG motif. The CBF3core specifically recognizes the nucleosomal CCG motif through the Gal4 domain while allosterically altering the DNA conformation. Cryo-EM, modeling, and mutational studies reveal that the CBF3core forms dynamic interactions with core histones H2B and CENP-A in the CEN3 nucleosome. Our results provide insights into the structure of the budding yeast centromeric nucleosome and the mechanism of its assembly, which have implications for analogous processes of human centromeric nucleosome formation.

Highlights

Accurate chromosome segregation relies on the specific centromeric nucleosome–kinetochore interface
Human centromeres are regional, including megabase DNA with repeats of two alternating ~171 base pairs α-satellite DNA sequences[6,7,8]; one of them consists of the 17 bp CENP-B box DNA motif that is recognized by the centromere CENP-B protein[9,10]
To understand the mechanism of the centromeric nucleosome formation guided by CBF3core–nucleosomeCEN3-601 and (CBF3), we first tried to use the single-particle cryo-EM method to determine the structure of the CEN3 CENPACse[4] nucleosome

Summary

Introduction

Accurate chromosome segregation relies on the specific centromeric nucleosome–kinetochore interface. The centromere CBF3 complex guides the deposition of CENP-A, an H3 variant, to form the centromeric nucleosome in a DNA sequence-dependent manner. The centromeric nucleosome core structure contains 115 base pair DNA including a CCG motif. Human centromeres are regional, including megabase DNA with repeats of two alternating ~171 base pairs (bp) α-satellite DNA sequences[6,7,8]; one of them consists of the 17 bp CENP-B box DNA motif that is recognized by the centromere CENP-B protein[9,10]. The cryo-EM structure of budding yeast CENP-A (Cse[4] or CENP-ACse4) nucleosome containing the Widom 601 nucleosome positioning DNA was determined at 2.7 Å resolution[23].

Methods

Results

Conclusion