Nucleosome mobility and the regulation of gene expression: Insights from single‐molecule studies

Abstract

Nucleosomes at the promoters of genes regulate the accessibility of the transcription machinery to DNA, and function as a basic layer in the complex regulation of gene expression. Our understanding of the role of the nucleosome's spontaneous, thermally driven position changes in modulating expression is lacking. This is the result of the paucity of experimental data on these dynamics, at high-resolution, and for DNA sequences that belong to real, transcribed genes. We have developed an assay that uses partial, reversible unzipping of nucleosomes with optical tweezers to repeatedly probe a nucleosome's position over time. Using the nucleosomes at the promoters of two model genes, Cga and Lhb, we show that the mobility of nucleosomes is modulated by the sequence of DNA and by the use of alternative histone variants, and describe how the mobility can affect transcription, at the initiation and elongation phases.

Mobile nucleosomes and the accessibility of transcription factors to DNA: a modified dynamic equilibrium model

“…[25]) and D=1.5 bp 2 /s (Ref. [24]). Interestingly, the fact that the accessibility of certain sites is increased, while the accessibility of others is decreased, means that the modulation by the mobility can have both a repressing as well as a facilitating effect on transcription.…”

“…In addition, they lacked the resolution to detect movements in the bp scale, and suffered from the limitations of bulk biochemical methods, with their intrinsic averaging over an unsynchronized population. Recently, we were able to probe the mobility of nucleosomes at the single molecule level, with bp---scale resolution, and on natural, biologically relevant sequences, using single molecule DNA unzipping with optical tweezers to probe the position of a single nucleosome several times as a function of time [23,24]. The single molecule experiments used as a model the promoters of Cga and Lhb, the genes that encode for the two subunits of the Luteinizing Hormone (LH), which are expressed under the same hormonal control but at levels that differ by as much as 7000---fold [23].…”

Multifaceted Targeting of the Chromatin Mediates Gonadotropin-Releasing Hormone Effects on Gene Expression in the Gonadotrope

“…This organization of the Cga gene differs fundamentally from that of Lhb whose proximal promoter is packaged into a nucleosome (Figure 2 ) that encompasses binding sites of Sf-1, Pitx-1, and Egr-1, which activate this gene ( 91 , 92 ). The initiation of transcription must thus require reorganization to allow access of these factors to the DNA, likely facilitated by the incorporation of H2A.Z at the Lhb promoter ( 48 , 93 ). The binding of TFs to sites that are buried inside the nucleosome is thought to be modulated by the thermally driven spontaneous “breathing” ( 94 ).…”

“…This involves partial wrapping and unwrapping of the DNA at the entry and exit to nucleosome which can expose the binding site, such that its ability to bind is also a function of the distance of the binding site from the nucleosome dyad ( 95 , 96 ). These fluctuations, which are typically much faster than rates of nucleosome repositioning, likely work together with increased nucleosome mobility to facilitate the initial access of Sf-1 and/or Pitx-1 to their binding sites ( 93 ). Binding of either of these “pioneer” factors would destabilize the nucleosome both through the binding itself and the recruitment of the histone-modifying enzymes described above, as well as quite possibly ATP-dependent chromatin-remodeling enzymes.…”

Exploring the Link between Nucleosome Occupancy and DNA Methylation

“…Two particular mechanisms, nucleosome occupancy and DNA methylation, have been reported to form specific patterns around promoters and these patterns were shown to correlate with gene expression (Portela and Esteller, 2010 ). With the existence of such correlations, it is investigated whether DNA methylation and nucleosome occupancy play a direct and decisive role in regulating gene activity (Vojta et al, 2016 ; Lai and Pugh, 2017 ; Rudnizky et al, 2017 ).…”