Eukaryotic genomes are packaged into nucleosome particles that occlude the DNA from interacting with most DNA binding proteins. Nucleosomes have higher affinity for particular DNA sequences, reflecting the ability of the sequence to bend sharply, as required by the nucleosome structure. However, it is not known whether these sequence preferences have a significant influence on nucleosome position in vivo, and thus regulate the access of other proteins to DNA. Here we isolated nucleosome-bound sequences at high resolution from yeast and used these sequences in a new computational approach to construct and validate experimentally a nucleosome–DNA interaction model, and to predict the genome-wide organization of nucleosomes. Our results demonstrate that genomes encode an intrinsic nucleosome organization and that this intrinsic organization can explain ∼50% of the in vivo nucleosome positions. This nucleosome positioning code may facilitate specific chromosome functions including transcription factor binding, transcription initiation, and even remodelling of the nucleosomes themselves.

http://absimage.aps.org/image/MAR08/MWS_MAR08-2008-020581.pdf

The Genomic Code for Nucleosome Positioning

The ability of proteins to locate specific target sequences or structures among a vast excess of nonspecific DNA is a fundamental property that affects virtually all aspects of biology. Despite this importance, experimental methods have lagged behind the establishment of theoretical principles describing potential target location mechanisms. However, recent advances in single-molecule detection now allow direct visual observation of proteins diffusing along DNA. Here we present an overview of these new observations and discuss the advantages, limitations and future prospects for imaging the motion of proteins along DNA.

Visualizing one-dimensional diffusion of proteins along DNA.

Stochastic mechano-chemical kinetics of molecular motors: A multidisciplinary enterprise from a physicist’s perspective

Nucleosomes are stable DNA–histone protein complexes that must be unwrapped and disassembled for genome expression, replication, and repair. Histone posttranslational modifications (PTMs) are major regulatory factors of these nucleosome structural changes, but the molecular mechanisms associated with PTM function remains poorly understood. Here we demonstrate that histone PTMs within distinct structured regions of the nucleosome directly regulate the inherent dynamic properties of the nucleosome. Precise PTMs were introduced into nucleosomes by chemical ligation. Single molecule magnetic tweezers measurements determined that only PTMs near the nucleosome dyad increase the rate of histone release in unwrapped nucleosomes. In contrast, FRET and restriction enzyme analysis reveal that only PTMs throughout the DNA entry–exit region increase unwrapping and enhance transcription factor binding to nucleosomal DNA. These results demonstrate that PTMs in separate structural regions of the nucleosome control distinct dynamic events, where the dyad regulates disassembly while the DNA entry–exit region regulates unwrapping. These studies are consistent with the conclusion that histone PTMs may independently influence nucleosome dynamics and associated chromatin functions.

https://www.pnas.org/content/pnas/108/31/12711.full.pdf

Histone fold modifications control nucleosome unwrapping and disassembly

SSB Functions as a Sliding Platform that Migrates on DNA via Reptation

Chromatin function in vivo is intimately connected with changes in its structure: a prime example is occlusion or exposure of regulatory sequences via repositioning of nucleosomes. Cell extracts used in concert with single-DNA micromanipulation can control and monitor these dynamics under in vivo-like conditions. We analyze a theory of the assembly–disassembly dynamics of chromatin fiber in such experiments, including effects of lateral nucleosome diffusion (“sliding”) and sequence positioning. Experimental data determine the force-dependent on- and off-rates as well as the nucleosome sliding diffusion rate. The resulting theory simply explains the very different nucleosome displacement kinetics observed in constant-force and constant-pulling velocity experiments. We also show that few-piconewton tensions comparable to those generated by polymerases and helicases drastically affect nucleosome positions in a sequence-dependent manner and that there is a long-lived structural “memory” of force-driven nucleosome rearrangement events.

Nucleosome hopping and sliding kinetics determined from dynamics of single chromatin fibers in Xenopus egg extracts

During the filling of a one-dimensional lattice by k-site-long hard particles, we find that after initial "jamming" a power-law-like decay of the density of interparticle gaps occurs, described by a much larger exponent than that expected from mean-field theory. We show that this effect dominates post-jamming filling for large k and should be observable, e.g., during the binding of proteins along a long, stretched DNA molecule.

Padinhateeri Ranjith

Papers

Nucleosome hopping and sliding kinetics determined from dynamics of single chromatin fibers in Xenopus egg extracts

Filling of the one-dimensional lattice by k-mers proceeds via fast power-law-like kinetics.