Managing the Steady State Chromatin Landscape by Nucleosome Dynamics

Abstract

Gene regulation arises out of dynamic competition between nucleosomes, transcription factors, and other chromatin proteins for the opportunity to bind genomic DNA. The timescales of nucleosome assembly and binding of factors to DNA determine the outcomes of this competition at any given locus. Here, we review how these properties of chromatin proteins and the interplay between the dynamics of different factors are critical for gene regulation. We discuss how molecular structures of large chromatin-associated complexes, kinetic measurements, and high resolution mapping of protein-DNA complexes in vivo set the boundary conditions for chromatin dynamics, leading to models of how the steady state behaviors of regulatory elements arise.

Keywords: RNAPII; chromatin; chromatin remodelers; nucleosome; time; transcription factors.

Figure 1.. Chromatin proteins to scale.

Protein complexes sketched from 3D structures are drawn, and the segment of DNA that each protects is indicated. From left to right: nucleosome (wrapping 150 bp), nucleosome with chromatin remodeler (1) (120 bp footprint), transcription factor (~20 bp footprint), RNAPII and Mediator (2) (80 bp footprint), and a replisome (3) (60 bp footprint). A nucleosome depleted region (NDR) is usually found at promoters of active genes. The wrapping of DNA around a nucleosome causes the DNA to be negatively supercoiled, indicated by black “-” sign below the nucleosomes. The movement of remodelers, RNAPII, and replisome propagates positive supercoiling in front of these complexes and negative supercoiling behind them, indicated by red, green, and gray “+” and “-” signs for supercoiling and arrows for direction of movement of these complexes (4). Lengths of DNA are not drawn to scale as some structures like nucleosome wrap DNA.

Figure 2.. Chromatin duplication after DNA replication.

In this schematic of chromatin replication, the replication fork is shown moving to the right; thus, the parental chromatid is to the right of the fork and newly replicated daughter chromatids are to the left of the fork. Newly replicated chromatids remain nuclease sensitive up to 30 minutes post-replication (15) and the deposited nucleosomes get ordered by remodelers 5–30 minutes post-replication (16) as seen in the map of time post-replication (shown above the daughter chromatids). Similarly, transcription factors (TFs) start rebinding at most sites ~30 minutes post-replication in metazoans, creating nucleosome depleted regions (NDRs) (17).

Figure 3.. DNA wrapping and the subunit structure of the nucleosome.

The top is a sketch of the length of DNA protected by a histone octamer with the arginine-phosphate contacts (sprockets, (24)). Asymmetric unwrapping by processive helicases and polymerases would lead to progressive loss of the arginine contacts (25)(middle). (H3•H4)₂ tetramers are minimal units deposited on newly replicated DNA (26, 27), engaging the central arginine sprockets (bottom).

Figure 4.. The timescales of chromatin dynamics.

(top) Time in seconds plotted on a log scale, annotated with chromatin processes that occur at various timescales. (bottom) Schematic of the dynamics of chromatin proteins on DNA with length of arrows depicting relative rates. Nucleosome assembly is efficient due to chaperones and remodelers. Nucleosome disassembly is fast at regulatory sites to facilitate transcription factor binding compared to non-regulatory sites. Rates of RNA polymerase successfully forming PICs and elongating are much lower relative to the off rates based on observations that only a small fraction of polymerases successfully initiate and elongate (10). TXC - transcription complex; PIC - pre-initiation complex.