Nucleosomal Binding Sites Research Articles

DNA-Protein Cross-Linking Sequencing for Genome-Wide Mapping of Thymidine Glycol.

Thymidine glycol (Tg) is the most prevalent form of oxidatively induced pyrimidine lesions in DNA. Tg can arise from direct oxidation of thymidine in DNA. In addition, 5-methyl-2'-deoxycytidine (5-mdC) can be oxidized to 5-mdC glycol, and its subsequent deamination also yields Tg. However, Tg's distribution in the human genome remains unknown. Here, we presented a DNA-protein cross-linking sequencing (DPC-Seq) method for genome-wide mapping of Tg in human cells. Our approach capitalizes on the specificity of a bifunctional DNA glycosylase, i.e., NTHL1, for the covalent labeling, as well as DPC pulldown, SDS-PAGE fractionation, and membrane transfer for highly efficient and selective enrichment of Tg-bearing DNA. By employing DPC-Seq, we detected thousands of Tg sites in the human genome, where dual ablation of NTHL1 and NEIL1, the major DNA glycosylases responsible for Tg repair, led to pronounced increases in the number of Tg peaks. In addition, Tg is depleted in genomic regions associated with active transcription but enriched at nucleosome-binding sites, especially at heterochromatin sites marked with H3K9me2. Collectively, we developed a DPC-Seq method for highly efficient enrichment of Tg-containing DNA and for genome-wide mapping of Tg in human cells. Our work offers a robust tool for future functional studies of Tg in DNA, and we envision that the method can also be adapted for mapping other modified nucleosides in genomic DNA in the future.

Training-free measures based on algorithmic probability identify high nucleosome occupancy in DNA sequences.

We introduce and study a set of training-free methods of an information-theoretic and algorithmic complexity nature that we apply to DNA sequences to identify their potential to identify nucleosomal binding sites. We test the measures on well-studied genomic sequences of different sizes drawn from different sources. The measures reveal the known in vivo versus in vitro predictive discrepancies and uncover their potential to pinpoint high and low nucleosome occupancy. We explore different possible signals within and beyond the nucleosome length and find that the complexity indices are informative of nucleosome occupancy. We found that, while it is clear that the gold standard Kaplan model is driven by GC content (by design) and by k-mer training; for high occupancy, entropy and complexity-based scores are also informative and can complement the Kaplan model.

Analysing structural diversity of seed storage protein gene promoters: Buckwheat a case study

Multiple sequence alignment of 5’UTR of SSP genes from accessions of Fagopyrum esculentumrevealed the invariant nature of sequences with the transcription start site at P761and TATA box located -30bp upstream the TSS. Other cis-elements identified in the sequences included the legumin box (-581, -524, -184, -135, -91), the -131 prolamin box, DOF element (-718, -649, -540,-432, -272,-225, -128) and CAAT box (-692, -530, -475, -411, -282, -168, -54). Other elements identified included those involved in abscisic acid signallingviz., ABI3 at P-470,-95,-68,RAV1 at P-694and -543and AGL15 at P-671. A comparative analysis of regulatory elements of SSP gene promoters of distantly related species the presence of five cis-regulatory elements viz. TATA BOX, E-BOX, RY- element, CAAT box and the Endosperm box, which interplay in seed specific SSP gene expression. Other modulators influencing seed specific gene expression detected in the sequences included the ABA-responsive elements ABI3, RAV1 and AGL15 which play an integral role in seed maturation. Identification of potential nucleosome binding sites in SSP gene promoters of Cicer arietinum, Brassica napus, B. campestris, Vicia faba, and Pisum sativumat positions 78, 635, 195, 112 and 152 respectively surmises the spatial fine tuning of SSP gene transcriptional regulation in these species. On the other hand, absence of nucleosome binding sites in the promoters of Fagopyrum esculentum, Zea mays, Avena sativa, Triticum aestivum and Oryza sativamay indicate relatively easier access of transcription factors to the proximal promoter, thereby providing higher level of gene expression.

Structure‐based design of Nucleosome Binding Peptides for controlling cell function

Proteins that bind the nucleosome, the repetitive unit of chromatin, and the histone H4 tail are critical to establishing chromatin architecture and phenotypic outcomes. A myriad of histone modifications, which strongly induce changes in chromatin structure, have been associated with malignancies and other diseases, highlighting the crucial role of chromatin architectural changes in disease mechanisms. The nucleosome surface was hypothesised as a therapeutic target, however the development, design and function of exogenous nucleosome binding molecules remain unclear.Herein, we performed structure‐based calculations on the nucleosome surface interaction to four peptides (NBMs), which present different nucleosome binding sites, derived from Nucleosome Binding Proteins (NBPs) to analyse the nucleosome sensitivity. Further, we were able to generate a new peptide (GMIP) with two nucleosome binding sites. A series of in vitro studies were performed to verify the impact of all these peptides on the nucleosome, showing differential action on its stability. We also demonstrated that GMIP and a canonical peptide may induce chromatin condensation in vitro. Confocal microscopy using labeled GMIP showed that it penetrates, by a passive mechanism, the cell and binds to chromatin. Cell‐based assays (MTT and FACS) showed that NBMs tested here presented a strong inhibitory activity on tumor cells, but not on non‐tumoral cells, proliferation and viability. It was also shown that these peptides might induce chromatin condensation in vivo. Besides that, the fish embryo toxicity (FET) test showed specificity in actions of NBMs on the ability to induce tissue modifications.Finally, we correlated the structural impact of NBMs to cellular function, providing a unique map on the nucleosome for designing new molecules with important implications. Taking all of this into account, it is clear that the is right to consider the nucleosome surface as a potential therapeutic target to regulate a plethora of cellular disorders.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Cluster analysis of S. Cerevisiae nucleosome binding sites

It is well known that major part of a eukaryotic genome is wrapped around histone proteins forming nucleosomes. It was also demonstrated that the DNA sequence itself is playing an important role in the nucleosome positioning process. In this work, a cluster analysis of 67 517 nucleosome binding sites from the S. Cerevisiae genome was carried out. The classification method is based on the self-adjusting dinucleotides position weight matrix. As a result, 135 significant clusters were discovered that contain 43225 sequences (which constitutes 64% of the initial set). The meaning of the found classes is discussed, as well as the possibility of the further usage.

Biophysical studies of cholesterol effects on chromatin

Changes in chromatin structure regulate gene expression and genome maintenance. Molecules that bind to the nucleosome, the complex of DNA and histone proteins, are key modulators of chromatin structure. Previous work indicated that cholesterol, a ubiquitous cellular lipid, may bind to chromatin in vivo, suggesting a potential function for lipids in modulating chromatin architecture. However, the molecular mechanisms of cholesterol's action on chromatin structure have remained unclear. Here, we explored the biophysical impact of cholesterol on nucleosome and chromatin fibers reconstituted in vitro and characterized in silico the cholesterol binding to the nucleosome. Our findings support that cholesterol assists 10 and 30 nm chromatin formation and induces folding of long chromatin fibers as a result of direct interaction of the cholesterol to six nucleosomal binding sites.

Stepwise Nucleosome Translocation by RSC Remodeling Complexes

The SWI/SNF family of chromatin-remodeling enzymes are important regulators of chromatin structure in transcriptional activation and in the creation and maintenance of nucleosome free regions. These enzymes regulate DNA accessibility by using the free energy from ATP hydrolysis to reposition and restructure nucleosomes, but the mechanism by which these enzymes move DNA around the histone octamer remains unclear. In this work, we study RSC, a prototypical SWI/SNF-family enzyme by using single-molecule FRET to monitor in real time the structural dynamics of individual nucleosomes during remodeling. By employing a variety of labeling schemes, we were able to observe transient intermediates during remodeling and assess the relative contributions of DNA translocation, DNA unwrapping, and octamer conformational change to the nucleosome remodeling process. We found that RSC primarily slides DNA around the nucleosome without large-amplitude lifting of the DNA from the nucleosomal surface or substantial displacement of the H2A-H2B dimer. We also observe that RSC-mediated translocation of DNA across the nucleosome occurs in a stepwise manner and that the translocation step size is 1-2 bp at both sites where the DNA enters and exits the nucleosome. Our results suggest that the motion of DNA around the nucleosome is directly coupled to DNA translocation by the remodeler's ATPase domain at its internal nucleosome binding site, and that other domains of the catalytic subunit or the accessory subunits do not play an active role in translocating DNA around the nucleosome.

A Meier-Gorlin syndrome mutation impairs the ORC1-nucleosome association.

Recent studies have identified several genetic mutations within the BAH domain of human Origin Recognition Complex subunit 1 (hORC1BAH), including the R105Q mutation, implicated in Meier-Gorlin Syndrome (MGS). However, the pathological role of the hORC1 R105Q mutation remains unclear. In this study, we have investigated the interactions of the hORC1BAH domain with histone H4K20me2, DNA, and the nucleosome core particle labeled with H4Kc20me2, a chemical analog of H4K20me2. Our study revealed a nucleosomal DNA binding site for hORC1BAH. The R105Q mutation reduces the hORC1BAH-DNA binding affinity, leading to impaired hORC1BAH-nucleosome interaction, which likely influences DNA replication initiation and MGS pathogenesis. This study provides an etiologic link between the hORC1 R105Q mutation and MGS.

Mutual disposition of nucleosomes and exons differs from common genome pattern at DNA segments containing periodic nucleotide sequences

The correlation was observed between DNA segments characterized by periodic patterns of nucleotides and nucleosome DNA binding sites predicted by the profiles of local DNA flexibility. Exons of human type I and VII collagen genes loci have been chosen as a sample set of periodic DNA segments. It was pointed that short periodic exons coding fibrillar part of these proteins are localized near borders of the DNA sequence that binds the histone core. One of the borders of exon and of this sequence coincide as a rule. In non-fibrillar parts of collagen genes exons (longer on average) dispose, in contrast, in any place of the DNA sequence bound to the nucleosome core.

Bursting with Randomness: A Simple Model for Stochastic Control of Gene Expression

If a gene's promoter were a light switch, you'd probably call an electrician. That's because rather than simply turning on and off in a limited and predictable way, many genes—whose expression is controlled by their promoters—are expressed in bursts, with expression fluctuating randomly over time. Analyzing the nucleosome configuration of single gene molecules by electron microscopy. What is the molecular basis of this transcriptional bursting? Previous work has suggested, but not directly demonstrated, that gene promoters can assume alternative structural configurations, raising the possibility that the promoter might randomly flip among these alternatives. Transcription requires that the polymerase machinery gain access to the promoter, and that access can be inhibited when DNA is tightly wrapped around histone proteins to form nucleosomes, the basic protein–DNA unit of structure within chromosomes. Researchers have speculated that these alternative promoter configurations might be linked to the number and distribution of nucleosomes within the promoter, but there has been no proof. The best way to test that hypothesis is by direct observation, and that is what Christopher Brown, Hinrich Boeger, and colleagues set out to do. Their work confirmed that the promoter of PHO5, a well-studied yeast gene, does indeed adopt alternative configurations based on nucleosome distribution. And they went further, examining the probability distribution of those nucleosomes and constructing a mechanistic model that accounts for that distribution, and hence the phenomenon of transcriptional bursting. The key to their study was to chemically “freeze” the promoter regions of multiple PHO5 genes, and then use the electron microscope to determine the precise configuration of each. The gene's promoter includes three nucleosome binding sites, and they were able to tabulate the relative frequency of each of the eight possible binding states (i.e., occupied-occupied-occupied, occupied-occupied-empty, etc.). Next, they built a mathematical probability model to test various assumptions about the transitions among the binding states. They distinguished three kinds of transitions: assembly of a nucleosome on a binding site, disassembly and removal, or sliding of a nucleosome from one site to another. They found that assembly and disassembly alone accounted for the number of observed nucleosomes, but that sliding was needed to account for their distribution. In particular, it appeared that sliding out of the middle position toward the ends was common. Further, the best fit with the data came when disassembly at the first position occurred only when the second position was unoccupied. Since transcription is maximally repressed in the fully occupied state and maximally permitted in the fully unoccupied state, the stochastic transitions among these and the intermediate states suggest that transcription of the PHO5 gene occurs in random bursts, the authors concluded. Further experimentation and modeling allowed them to predict that binding states in which the middle position was unoccupied were the most conducive to transcription. But the transcription rate was not maximal in all conducive states; other, as-yet unidentified factors presumably play a role in determining the degree of transcription for a given conducive state. The model the authors developed provides a structural basis for transcriptional bursting consistent with a large body of data. While other models might also explain that data, none do so as simply and with as few “working parts” as theirs—generally a sign that a model is pointing in the right direction. Brown CR, Mao C, Falkovskaia E, Jurica MS, Boeger H (2013) Linking Stochastic Fluctuations in Chromatin Structure and Gene Expression. doi:10.1371/journal.pbio.1001621

Rigid-body molecular dynamics of DNA inside a nucleosome

The majority of eukaryotic DNA, about three quarter, is wrapped around histone proteins forming so-called nucleosomes. To study nucleosomal DNA we introduce a coarse-grained molecular dynamics model based on sequence-dependent harmonic rigid base pair step parameters of DNA and nucleosomal binding sites. Mixed parametrization based on all-atom molecular dynamics and crystallographic data of protein-DNA structures is used for the base pair step parameters. The binding site parameters are adjusted by experimental B-factor values of the nucleosome crystal structure. The model is then used to determine the energy cost for placing a twist defect into the nucleosomal DNA which allows us to use Kramers theory to calculate nucleosome sliding caused by such defects. It is shown that the twist defect scenario together with the sequence-dependent elasticity of DNA can explain the slow time scales observed for nucleosome mobility along DNA. With this method we also show how the twist defect mechanism leads to a higher mobility of DNA in the presence of sin mutations near the dyad axis. Finally, by performing simulations on 5s rDNA, 601, and telomeric base pair sequences, it is demonstrated that the current model is a powerful tool to predict nucleosome positioning.

Linker Histone Structural Transitions Upon Binding to DNA, Mononucleosomes, and Oligonucleosomal Arrays

Linker histones are multi-functional proteins that stabilize higher order chromatin structure and play a direct role in regulating gene expression. However the mechanism(s) by which H1s fulfill these disparate functions is unclear. Metazoan linker histones (H1s) exibit a three-domain structure including a short N-terminal domain, a conserved globular domain and an extended C-terminal domain (CTD). While the globular domain is responsible for nucleosome-specific recognition and binding, the chromatin-condensing functionality is primarily contained within the CTD. This domain is unstructured in aqueous solution but peptides derived from various H1 CTDs acquire secondary structures in presence of helix-stabilizing solvents and other conditions thought to mimic the native chromatin environment. We employed FRET to characterize potential structural transitions within the CTD upon binding of H1 to nucleosomes and other native binding targets. Our results indicate a significant condensation of the CTD, consistent with folding of this domain, upon nucleosome binding (Caterino et al., 2011 MCB 31:2341). Importantly, significant differences in both intra- and inter-molecular FRET efficiencies indicate that H1 binds in a fundamentally different manner to linear DNA compared to nucleosomes (Fang, Clark and Hayes, 2012 NAR 40:1475). Likewise, CTD structure appears distinct when H1 is bound to nucleosomes with oliogonucleosomal arrays, where each nucleosome binding site is flanked by authentic linker DNA connecting adjacent nucleosomes. These results support a model in which H1 CTD undergoes a disordered->ordered transition upon binding nucleosomes, DNA, and nucleosome arrays and adopts distinct structures dependent on the particular macromolecular binding partner.

100 Bridging the gap: from 1D to 3D genomics

Combination of the nucleotides A, C, G, and T leads to one-dimensional (1D) DNA sequence that further gives rise to the three-dimensional (3D) structure of DNA. In fact, proteins do not literally read the letters A, C, G, and T. Instead, read out is based on spatial interactions between 3D objects, in which the structures of both DNA and proteins are important for the interactions to occur (Rohs et al. 2009; Rohs et al. 2010). On the other hand, while the 3D structure of DNA is dependent on the primary sequence, there is degeneracy in mapping DNA sequence to shape. Moreover, while high-throughput sequencing technologies continue to produce large amounts of DNA sequence information, experimental data on 3D structures of DNA is limited. These facts all urge to develop new approaches that provide new insights into DNA structure. Given such motivation, we have developed a high-throughput tool for predicting shape of “naked” DNA on a genomic scale (Slattery et al. 2011) and a web server for predicting DNA shape information. In parallel, we constructed a database of shape that features of transcription factor binding sites using sequence-based databases as the source for binding motifs. These tools provide a novel approach for studying transcription factor binding sites, especially those of paralogous transcription factors which share highly similar core-binding motifs but bind different genome sites in vivo. Our approach can also be used to study less-specific protein–DNA interactions, for example, histone–DNA interactions in nucleosomes. Here, we present structural profiles of transcription factor and nucleosome binding sites of various organisms and provide evidence that DNA shape generally plays an important role in protein–DNA recognition. Specifically, we present insights in how paralogous transcription factors recognize DNA shape to achieve differential binding specificity and suggest that mechanisms for nucleosome formation are somewhat different in Plasmodium falciparum whose genome has an extremely high A/T content compared with Saccharomyces cerevisiae and Drosophila melanogaster.

Wrapped Up Right

Genetics All eukaryotic chromosomes have a centromere, which ensures that the genomic DNA is shared equally between daughter cells during cell division. Centromeres are defined by the presence of nucleosomes that contain a special histone H3 variant, CenH3. Accumulating evidence suggests that CenH3-containing nucleosomes have an unusual structure: Rather than consisting of the highly conserved octamer of histone proteins, which wraps up ∼147 bp of DNA, they may instead form tetramers, which wrap only half as much DNA. To understand how widespread this unusual centromeric nucleosome conformation might be, Krassovsky et al. fine-map the positions of budding yeast centromeres, which consist of a single CenH3 (known as Cse4) nucleosome binding site on each chromosome. Cse4 binds a region of DNA that is 80 bp in length, consistent with a tetramer nucleosome conformation. The highly AT-rich DNA sequence at the centromere and two protein-binding sites that flank the centromere site probably exclude binding of the canonical octamer nucleosome and recruit and stabilize the binding of the Cse4 nucleosome. Cse4 nucleosomes that become misincorporated at noncentromere sites, on the other hand, form octamers and are found in regions of high nucleosome turnover, the latter observation hinting how such excess Cse4, which could impede the function of the centromere, might be purged from the genome. Proc. Natl. Acad. Sci. U.S.A. 109 , 243 (2012).

Occlusion of Regulatory Sequences by Promoter Nucleosomes In Vivo

Nucleosomes are believed to inhibit DNA binding by transcription factors. Theoretical attempts to understand the significance of nucleosomes in gene expression and regulation are based upon this assumption. However, nucleosomal inhibition of transcription factor binding to DNA is not complete. Rather, access to nucleosomal DNA depends on a number of factors, including the stereochemistry of transcription factor-DNA interaction, the in vivo kinetics of thermal fluctuations in nucleosome structure, and the intracellular concentration of the transcription factor. In vitro binding studies must therefore be complemented with in vivo measurements. The inducible PHO5 promoter of yeast has played a prominent role in this discussion. It bears two binding sites for the transcriptional activator Pho4, which at the repressed promoter are positioned within a nucleosome and in the linker region between two nucleosomes, respectively. Earlier studies suggested that the nucleosomal binding site is inaccessible to Pho4 binding in the absence of chromatin remodeling. However, this notion has been challenged by several recent reports. We therefore have reanalyzed transcription factor binding to the PHO5 promoter in vivo, using ‘chromatin endogenous cleavage’ (ChEC). Our results unambiguously demonstrate that nucleosomes effectively interfere with the binding of Pho4 and other critical transcription factors to regulatory sequences of the PHO5 promoter. Our data furthermore suggest that Pho4 recruits the TATA box binding protein to the PHO5 promoter.

Binding of the Rett syndrome protein, MeCP2, to methylated and unmethylated DNA and chromatin

Methylated CpG Binding Protein 2 (MeCP2) is a nuclear protein named for its ability to selectively recognize methylated DNA. Much attention has been focused on understanding MeCP2 structure and function in the context of its role in Rett syndrome, a severe neurodevelopmental disorder that afflicts one in 10,000-15,000 girls. Early studies suggested a connection between DNA methylation, MeCP2, and establishment of a repressive chromatin structure at specific gene promoters. However, it is now recognized that MeCP2 can both activate and repress specific genes depending on the context. Likewise, in the cell, MeCP2 is bound to unmethylated DNA and chromatin in addition to methylated DNA. Thus, to understand the molecular basis of MeCP2 functionality, it is necessary to unravel the complex interrelationships between MeCP2 binding to unmethylated and methylated regions of the genome. MeCP2 is unusual and interesting in that it is an intrinsically disordered protein, that is, much of its primary sequence fails to fold into secondary structure and yet is functional. The unique structure of MeCP2 is the subject of the first section of this article. We then discuss recent investigations of the in vitro binding of MeCP2 to unmethylated and methylated DNA, and the potential ramifications of this work for in vivo function. We close by focusing on mechanistic studies indicating that the binding of MeCP2 to chromatin results in compaction into local (secondary) and global (tertiary) higher order structures. MeCP2 also competes with histone H1 for nucleosomal binding sites. The recent finding that MeCP2 is found at near stoichiometric levels with nucleosomes in neuronal cells underscores the multiple modes of engagement of MeCP2 with the genome, which include the cooperative tracking of methylation density.

Apples and oranges: avoiding different priors in Bayesian DNA sequence analysis

BackgroundOne of the challenges of bioinformatics remains the recognition of short signal sequences in genomic DNA such as donor or acceptor splice sites, splicing enhancers or silencers, translation initiation sites, transcription start sites, transcription factor binding sites, nucleosome binding sites, miRNA binding sites, or insulator binding sites. During the last decade, a wealth of algorithms for the recognition of such DNA sequences has been developed and compared with the goal of improving their performance and to deepen our understanding of the underlying cellular processes. Most of these algorithms are based on statistical models belonging to the family of Markov random fields such as position weight matrix models, weight array matrix models, Markov models of higher order, or moral Bayesian networks. While in many comparative studies different learning principles or different statistical models have been compared, the influence of choosing different prior distributions for the model parameters when using different learning principles has been overlooked, and possibly lead to questionable conclusions.ResultsWith the goal of allowing direct comparisons of different learning principles for models from the family of Markov random fields based on the same a-priori information, we derive a generalization of the commonly-used product-Dirichlet prior. We find that the derived prior behaves like a Gaussian prior close to the maximum and like a Laplace prior in the far tails. In two case studies, we illustrate the utility of the derived prior for a direct comparison of different learning principles with different models for the recognition of binding sites of the transcription factor Sp1 and human donor splice sites.ConclusionsWe find that comparisons of different learning principles using the same a-priori information can lead to conclusions different from those of previous studies in which the effect resulting from different priors has been neglected. We implement the derived prior is implemented in the open-source library Jstacs to enable an easy application to comparative studies of different learning principles in the field of sequence analysis.

Identification of distinct SET/TAF-Iβ domains required for core histone binding and quantitative characterisation of the interaction

BackgroundThe assembly of nucleosomes to higher-order chromatin structures is finely tuned by the relative affinities of histones for chaperones and nucleosomal binding sites. The myeloid leukaemia protein SET/TAF-Iβ belongs to the NAP1 family of histone chaperones and participates in several chromatin-based mechanisms, such as chromatin assembly, nucleosome reorganisation and transcriptional activation. To better understand the histone chaperone function of SET/TAF-Iβ, we designed several SET/TAF-Iβ truncations, examined their structural integrity by circular Dichroism and assessed qualitatively and quantitatively the histone binding properties of wild-type protein and mutant forms using GST-pull down experiments and fluorescence spectroscopy-based binding assays.ResultsWild type SET/TAF-Iβ binds to histones H2B and H3 with Kd values of 2.87 and 0.15 μM, respectively. The preferential binding of SET/TAF-Iβ to histone H3 is mediated by its central region and the globular part of H3. On the contrary, the acidic C-terminal tail and the amino-terminal dimerisation domain of SET/TAF-Iβ, as well as the H3 amino-terminal tail, are dispensable for this interaction.ConclusionThis type of analysis allowed us to assess the relative affinities of SET/TAF-Iβ for different histones and identify the domains of the protein required for effective histone recognition. Our findings are consistent with recent structural studies of SET/TAF-Iβ and can be valuable to understand the role of SET/TAF-Iβ in chromatin function.

The dynamics of HMG protein–chromatin interactions in living cellsThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process.

The dynamic interaction between nuclear proteins and chromatin leads to the functional plasticity necessary to mount adequate responses to regulatory signals. Here, we review the factors regulating the chromatin interactions of the high mobility group proteins (HMGs), an abundant and ubiquitous superfamily of chromatin-binding proteins in living cells. HMGs are highly mobile and interact with the chromatin fiber in a highly dynamic fashion, as part of a protein network. The major factors that affect the binding of HMGs to chromatin are operative at the level of the single nucleosome. These factors include structural features of the HMGs, competition with other chromatin-binding proteins for nucleosome binding sites, complex formation with protein partners, and post-translational modifications in the protein or in the chromatin-binding sites. The versatile modulation of the interaction between HMG proteins and chromatin plays a role in processes that establish the cellular phenotype.

Acetylated Histone Tail Peptides Induce Structural Rearrangements in the RSC Chromatin Remodeling Complex

Post-translational acetylation of histone tails is often required for the recruitment of ATP-dependent chromatin remodelers, which in turn mobilize nucleosomes on the chromatin fiber. Here we show that the lower lobe of the ATP-dependent chromatin remodeler RSC exists in a dynamic equilibrium and can be found extended away or retracted against the tripartite upper lobe of the complex. Extension of the lower lobe increases the size of a central cavity that has been proposed to be the nucleosome binding site. We show that the presence of acetylated histone 3 N-terminal tail peptides stabilizes the lower lobe of RSC in the retracted state, suggesting that domains recognizing the acetylated histone tails reside at the interface between the two lobes. Based on three-dimensional reconstructions, we propose a model for the interaction of RSC with acetylated nucleosomes.