Ubiquitous nucleosome crowding in the yeast genome

Abstract

Nucleosomes may undergo a conformational change in which a stretch of DNA peels off the histone octamer surface as a result of thermal fluctuations or interactions with chromatin remodelers. Thus, neighboring nucleosomes may invade each other's territories by DNA unwrapping and translocation, or through initial assembly in partially wrapped states. A recent high-resolution map of distances between dyads of neighboring nucleosomes in Saccharomyces cerevisiae reveals that nucleosomes frequently overlap DNA territories of their neighbors. This conclusion is supported by lower-resolution maps of S. cerevisiae nucleosome lengths based on micrococcal nuclease digestion and paired-end sequencing. The average length of wrapped DNA follows a stereotypical pattern in genes and promoters, correlated with the well-known distribution of nucleosome occupancy: nucleosomal DNA tends to be shorter in promoters and longer in coding regions. To explain these observations, we have developed a biophysical model that uses a 10-11-bp periodic histone-DNA binding energy profile. The profile is based on the pattern of histone-DNA contacts in nucleosome crystal structures, as well as the idea of linker length discretization caused by higher-order chromatin structure. Our model is in agreement with the observed genome-wide distributions of interdyad distances, wrapped DNA lengths, and nucleosome occupancies. Furthermore, our approach explains in vitro measurements of the accessibility of nucleosome-covered target sites and nucleosome-induced cooperativity between DNA-binding factors. We rule out several alternative scenarios of histone-DNA interactions as inconsistent with the genomic data.partially unwrapped nucleosomes | DNA accessibility | gene regulation E ukaryotic genomes are organized into arrays of nucleosomes (1). Each nucleosome consists of a stretch of genomic DNA wrapped around a histone octamer core (2). The resulting complex of DNA with histones and other regulatory and structural proteins is called chromatin (1). Arrays of nucleosomes form 10-nm fibers that resemble beads on a string and, in turn, fold into higher-order structures (3). Depending on the organism and cell type, 75-90% of genomic DNA is packaged into nucleosomes (1). Because nucleosomal DNA is wrapped tightly around the histone octamer, its accessibility to various DNA-binding proteins, such as repair enzymes, transcription factors (TFs), polymerases, and recombinases, is suppressed. The question of how cellular functions are carried out on the chromatin template is one of the outstanding puzzles in eukaryotic biology.Recently, nucleosome dyad positions and distances between dyads of neighboring nucleosomes were mapped genome-wide with high precision in Saccharomyces cerevisiae (4). The in vivo map was obtained by chemical modification of engineered histones, DNA backbone cleavage by hydroxyl radicals, and highthroughput sequencing (Fig. 1A). Although more precise than methods based on micrococcal nuclease (MNase) digestion, whose accuracy is affected by MNase...

Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions

“…For both yeast species, we observe "negative" linker lengths representing two nucleosomes with dyads being closer than 147 bp (Fig. 4C), supporting findings from paired-end chemical mapping and the hypothesis that chromatin can exist in a state with partially unwrapped nucleosomes (Chereji and Morozov 2014). We also determine nucleosome-free region lengths by identifying regions of low nucleosome occupancy between nucleosome calls (Fig.…”

“…The apex of the V shape is at 117 bp, while the most abundant position in the V-plot represents fragments of 143 bp centered at the dyad. These smaller-than-expected fragment sizes may arise from stochastic "breathing" of DNA associated with nucleosomes, allowing for transposase insertions within the 147 bp that are canonically considered to be nucleosome-associated ( Anderson et al 2002) or from nucleosomes packed closer than 147 bp apart (Chereji and Morozov 2014).…”

A unified computational framework for modeling genome-wide nucleosome landscape

“…The work of Locke et al . has provided refreshing perspectives in the field, and their approach has been extended in several subsequent studies [23, 24, 26]. However, we here show that the calculation performed by Locke et al .…”

“…In order to further account for sequence effects, a 1D sequence-dependent binding energy can be introduced into the model. This resulting model of 1D hard rods subjected to an external potential has been widely applied to study the genome-wide distribution of nucleosomes [15,16,20–26]. In particular, Locke et al .…”

The role of DNA sequence in nucleosome breathing

“…The second exception is ref. [58] which, however, is not based on a microscopic model but is trained on high-throughput maps of nucleosome positions.…”