Cryo-EM structure of the nucleosome containing the ALB1 enhancer DNA sequence.

Yoshimasa Takizawa,Matthias Wolf,Yasuyuki Ohkawa,Hitoshi Kurumizaka,Paul A Wade,Hiroki Tanaka,Shinichi Machida,Kazumitsu Maehara,Masako Koyama

doi:10.1098/rsob.170255

Abstract

Pioneer transcription factors specifically target their recognition DNA sequences within nucleosomes. FoxA is the pioneer transcription factor that binds to the ALB1 gene enhancer in liver precursor cells, and is required for liver differentiation in embryos. The ALB1 enhancer DNA sequence is reportedly incorporated into nucleosomes in cells, although the nucleosome structure containing the targeting sites for FoxA has not been clarified yet. In this study, we determined the nucleosome structure containing the ALB1 enhancer (N1) sequence, by cryogenic electron microscopy at 4.0 Å resolution. The nucleosome structure with the ALB1 enhancer DNA is not significantly different from the previously reported nucleosome structure with the Widom 601 DNA. Interestingly, in the nucleosomes, the ALB1 enhancer DNA contains local flexible regions, as compared to the Widom 601 DNA. Consistently, DNaseI treatments revealed that, in the nucleosome, the ALB1 enhancer (N1) DNA is more accessible than the Widom 601 sequence. The histones also associated less strongly with the ALB1 enhancer (N1) DNA than the Widom 601 DNA in the nucleosome. Therefore, the local histone–DNA contacts may be responsible for the enhanced DNA accessibility in the nucleosome with the ALB1 enhancer DNA.

Highlights

In eukaryotes, genomic DNA is organized into chromatin, in which the nucleosome is the fundamental unit [1]
Nucleosome formation generally restricts the binding of transcription factors (TFs) to the DNA wrapped around the histone octamer
The histone octamer was formed with human recombinant histones H2A, H2B, H3.1 and H4, and the nucleosome was reconstituted by the saltdialysis method

Summary

Introduction

Genomic DNA is organized into chromatin, in which the nucleosome is the fundamental unit [1]. A DNA segment of about 145 base pairs is wrapped around the histone octamer in the nucleosome [2]. Nucleosome formation generally restricts the binding of transcription factors (TFs) to the DNA wrapped around the histone octamer. In active promoters, TFs predominantly bind nucleosome-free DNA regions [5]. Pioneer transcription factors bind their target sequences within nucleosomes, and create open chromatin conformations around their target sequences [6,7,8]. This nucleosome reconfiguration by pioneer TFs may be an

Methods

Results

Conclusion