Precise genome-wide mapping of single nucleosomes and linkers in vivo

Răzvan V Chereji,Srinivas Ramachandran,Steven Henikoff,Terri D Bryson

doi:10.1186/s13059-018-1398-0

Abstract

We developed a chemical cleavage method that releases single nucleosome dyad-containing fragments, allowing us to precisely map both single nucleosomes and linkers with high accuracy genome-wide in yeast. Our single nucleosome positioning data reveal that nucleosomes occupy preferred positions that differ by integral multiples of the DNA helical repeat. By comparing nucleosome dyad positioning maps to existing genomic and transcriptomic data, we evaluated the contributions of sequence, transcription, and histones H1 and H2A.Z in defining the chromatin landscape. We present a biophysical model that neglects DNA sequence and shows that steric occlusion suffices to explain the salient features of nucleosome positioning.

Highlights

Nucleosomes are the basic units of DNA packaging in eukaryotes
We found that H3Q85C cleaves nucleosomal DNA and releases 51-bp fragments, as expected from the position of this residue close to the DNA minor groove based on the crystal structure of the nucleosome (Additional file 1: Figure S1)
By using 51-bp fragments generated by H3Q85C cleavages for mapping rather than the linker-spanning fragments generated by H4S47C cleavages, we avoid the background due to cleavages within linkers, which is especially important for distinguishing regions that are merely nucleosome-depleted from those that are virtually nucleosome-free (Fig. 1a; compare tracks 6–8 with tracks 1–5)

Summary

Introduction

Nucleosomes are the basic units of DNA packaging in eukaryotes. They contain ~ 147 bp of DNA, wrapped around a histone octamer, in about 1.7 superhelical turns [1,2,3]. In addition to DNA packaging, nucleosome organization plays a crucial role in controlling DNA accessibility of many DNA-binding proteins to regulatory elements on the chromosomes. Nucleosome positions influence gene expression regulation [4,5,6,7], DNA replication [8, 9], DNA repair [8, 10], and DNA recombination [11]. The most generally accepted view is that nucleosome positioning is determined by a combination of DNA sequence, ATP-dependent remodeling enzymes, transcription factors, and elongating RNA polymerases [15]. The validity of this paradigm depends on the accuracy and precision with which the in vivo positions of nucleosomes are mapped

Methods

Results

Discussion

Conclusion