Accessibility Of Nucleosomal DNA Research Articles

Dependence of nucleosome mechanical stability on DNA mismatches

The organization of nucleosomes into chromatin and their accessibility are shaped by local DNA mechanics. Conversely, nucleosome positions shape genetic variations, which may originate from mismatches during replication and chemical modification of DNA. To investigate how DNA mismatches affect the mechanical stability and the exposure of nucleosomal DNA, we used an optical trap combined with single-molecule FRET and a single-molecule FRET cyclization assay. We found that a single base-pair C-C mismatch enhances DNA bendability and nucleosome mechanical stability for the 601-nucleosome positioning sequence. An increase in force required for DNA unwrapping from the histone core is observed for single base-pair C-C mismatches placed at three tested positions: at the inner turn, at the outer turn, or at the junction of the inner and outer turn of the nucleosome. The results support a model where nucleosomal DNA accessibility is reduced by mismatches, potentially explaining the preferred accumulation of single-nucleotide substitutions in the nucleosome core and serving as the source of genetic variation during evolution and cancer progression. Mechanical stability of an intact nucleosome, that is mismatch-free, is also dependent on the species as we find that yeast nucleosomes are mechanically less stable and more symmetrical in the outer turn unwrapping compared to Xenopus nucleosomes.

Dependence of nucleosome mechanical stability on DNA mismatches.

The organization of nucleosomes into chromatin and their accessibility are shaped by local DNA mechanics. Conversely, nucleosome positions shape genetic variations, which may originate from mismatches during replication and chemical modification of DNA. To investigate how DNA mismatches affect the mechanical stability and the exposure of nucleosomal DNA, we used an optical trap combined with single-molecule FRET and a single-molecule FRET cyclization assay. We found that a single base-pair C-C mismatch enhances DNA bendability and nucleosome mechanical stability for the 601-nucleosome positioning sequence. An increase in force required for DNA unwrapping from the histone core is observed for single base-pair C-C mismatches placed at three tested positions: at the inner turn, at the outer turn, or at the junction of the inner and outer turn of the nucleosome. The results support a model where nucleosomal DNA accessibility is reduced by mismatches, potentially explaining the preferred accumulation of single-nucleotide substitutions in the nucleosome core and serving as the source of genetic variation during evolution and cancer progression. Mechanical stability of an intact nucleosome, that is mismatch-free, is also dependent on the species as we find that yeast nucleosomes are mechanically less stable and more symmetrical in the outer turn unwrapping compared to Xenopus nucleosomes.

Down-regulated m6A reader FTO destabilizes PHF1 that triggers enhanced stemness capacity and tumor progression in lung adenocarcinoma

Aberrant epigenetic drivers or suppressors contribute to LUAD progression and drug resistance, including KRAS, PTEN, Keap1. Human Plant Homeodomain (PHD) finger protein 1 (PHF1) coordinates with H3K36me3 to increase nucleosomal DNA accessibility. Previous studies revealed that PHF1 is markedly upregulated in various tumors and enhances cell proliferation, migration and tumorigenesis. However, its roles in LUAD are still unknown. We aimed to depict the biological roles of PHF1 and identify useful targets for clinical treatment of LUAD. Based on the bioinformatic analysis, we found that PHF1 was down-regulated in LUAD samples and low PHF1 expressions correlated with unfavorable clinical characteristics. Patients with low PHF1 had poorer survival outcomes relative to those with high PHF1. Targeting PHF1 potentiated cell growth, migration and in vivo proliferation. Mechanistically, FTO mediated the stabilization of PHF1 mRNA by demethylating m6A, which particularly prevented YTHDF2 from degrading PHF1 transcripts. Of note, FTO also expressed lowly in LUAD that predicts poor prognosis of patients. FTO inhibition promoted LUAD progression, and PHF1 overexpression could reverse the effect. Lastly, down-regulated FTO/PHF1 axis could mainly elevate FOXM1 expression to potentiate the self-renewal capacity. Targeting FOXM1 was effective to suppress PHF1low/− LUAD growth. Collectively, our findings revealed that FTO positively regulates PHF1 expression and determined the tumor-suppressive role of FTO/PHF1 axis, thereby highlighting insights into its epigenetic remodeling mechanisms in LUAD progression and treatment.

The Effects of Site Specific Histone Modifications on Nucleosomal DNA Accessibility

Chromatin accessibility is the ability of nucleosomal DNA to be physically accessed by cellular biomachinery. Accessibility of chromatin is controlled by a slew of post translational modifications to histone proteins, DNA, and chromatin‐binding factors. This growing field of research has become increasingly important as chromatin accessibility has a large effect on transcription and gene regulation. Gene and cell cycle regulation must be understood to properly study their misregulation which commonly occurs in most, if not all, cancers. Thus, understanding the organization and regulation of the chromatin state by post translational modifications plays an important role in understanding the dysfunction of cancerous cells. The most basic unit of chromatin is the nucleosome core particle. The nucleosome core particle is made up of an octamer that has two copies each of the 4 histone proteins H2A, H2B, H3, and H4 with DNA wrapping around the octamer itself. It is on the N‐terminal tails of these histone proteins that many post‐translational modifications take place the regulate the chromatin state. In this study, the effect of histone lysine acetylation on the DNA‐histone core interaction will be assessed by its thermal stability and accessibility of nucleosomal DNA to Pst1 Digestion. We propose to assay singly acetylated mononucleosomes at the following sites: H2A: K5; H2B: K5, K12, K15, and K20; H3: K9, K14, K18, K23, K27, K36, K37, K64, K56, K79, K115, and K122; H4: K5, K8, K12, and K16. We predict that, as previously shown with nu′‐H3K18ac and nu′‐H3K36ac acetylation at lysine sites will facilitate unwrapping of nucleosomal DNA.

Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails

Little is known about the roles of histone tails in modulating nucleosomal DNA accessibility and its recognition by other macromolecules. Here we generate extensive atomic level conformational ensembles of histone tails in the context of the full nucleosome, totaling 65 microseconds of molecular dynamics simulations. We observe rapid conformational transitions between tail bound and unbound states, and characterize kinetic and thermodynamic properties of histone tail-DNA interactions. Different histone types exhibit distinct binding modes to specific DNA regions. Using a comprehensive set of experimental nucleosome complexes, we find that the majority of them target mutually exclusive regions with histone tails on nucleosomal/linker DNA around the super-helical locations ± 1, ± 2, and ± 7, and histone tails H3 and H4 contribute most to this process. These findings are explained within competitive binding and tail displacement models. Finally, we demonstrate the crosstalk between different histone tail post-translational modifications and mutations; those which change charge, suppress tail-DNA interactions and enhance histone tail dynamics and DNA accessibility.

Abstract P-9: Excess of Nhp6 over Spt16/Pob3 is Necessary for Efficient Nucleosome Unfolding by yFACT

Background: DNA accessibility in chromatin is important for proper gene expression and is regulated by multiple factors. One of them is histone chaperone FACT, which conducts large-scale ATP-independent nucleosome unfolding that increases the accessibility of nucleosomal DNA. FACT binding results in dramatic DNA uncoiling from nucleosome, occurs without apparent loss of histones, and proceeds via an ‘all-or-none’ mechanism, but the detailed mechanism of this process is still unknown. FACT-dependent nucleosome unfolding modulates the accessibility of nucleosomal DNA, and it is an important function of FACT in the processes of transcription, DNA replication, and repair in vivo. Methods: Nucleosome-positioning DNA sequences containing fluorescent labels (Cy3 and Cy5) at positions 13/91 or 35/112 from the nucleosome boundary were used. Nucleosomes were assembled by transfer of histone octamers from chicken chromatin to nucleosomal DNA during dialysis from 2M NaCl. After dialysis nucleosomes were gel purified and used at a final concentration of 0.5nM for spFRET measurements or at 10nM for EMSA analysis. For complex formation nucleosomes were incubated in the presence of Spt16/Pob3(0.13μM) and Nhp6(1.3μM) for 10 min at 30°C in buffer containing 17mM HEPES, 2mM Tris-HCl, 0.8mM Na3EDTA, 0.11mM 2-merсaptoethanol, 150mM KCl, 11mM NaCl, 1.1%glycerin, 12% sucrose. In spFRET microscopy analysis, the proximity ratio EPR from each nucleosome was calculated based on the intensity of the signals, corrected to the background and plotted as relative frequency distribution. Each plot was fitted as a sum of two Gaussians to describe two conformational states of nucleosomes. The fractions of nucleosomes in different states were estimated by calculating the surface of areas under the corresponding Gaussian peaks as a fraction of the total area of the plot. Results: Here we report the results of our analysis of nucleosome unfolding by yeast FACT (yFACT) at different ratios of Spt16/Pob3 and Nhp6 using single-particle Förster resonance energy transfer (spFRET) microscopy. Our analysis suggests that the optimal ratio of Spt16/Pob3 to Nhp6 for the most efficient FACT-dependent nucleosome unfolding is 1:10. Importantly, a mere increase in the concentration of FACT results in a decrease of the functional activity, suggesting that the formation of a functional complex having a certain stoichiometry of Spt16/Pob3 to Nhp6 is essential for efficient FACT-dependent nucleosome unfolding. Conclusion: We determined that a certain ratio of Spt16/Pob3 to Nhp6 is essential for efficient FACT-dependent nucleosome unfolding, suggesting the formation of a functional FACT: Nhp6 complex.

The Effects of Site Specific Histone Modifications on Nucleosomal DNA Accessibility

Chromatin accessibility is the ability of nucleosomal DNA to be physically accessed by cellular biomachinery. Accessibility of chromatin is controlled by a slew of post translational modifications to histone proteins, DNA, and chromatin-binding factors. This growing field of research has become increasingly important as chromatin accessibility has a large effect on transcription and gene regulation. Gene and cell cycle regulation must be understood to properly study their misregulation which commonly occurs in most, if not all, cancers. Thus, understanding the organization and regulation of the chromatin state by post translational modifications plays an important role in understanding the dysfunction of cancerous cells. The most basic unit of chromatin is the nucleosome core particle. The nucleosome core particle is made up of an octamer that has two copies each of the 4 histone proteins H2A, H2B, H3, and H4 with DNA wrapping around the octamer itself. It is on the N-terminal tails of these histone proteins that many post-translational modifications take place the regulate the chromatin state. In this study, the effect of histone lysine acetylation on the DNA-histone core interaction will be assessed by its thermal stability and accessibility of nucleosomal DNA to Pst1 Digestion. We propose to assay singly acetylated mononucleosomes at the following sites: H2A: K5; H2B: K5, K12, K15, and K20; H3: K9, K14, K18, K23, K27, K36, K37, K64, K56, K79, K115, and K122; H4: K5, K8, K12, and K16. We predict that, as previously shown with nu′-H3K18ac and nu′-H3K36ac acetylation at lysine sites will facilitate unwrapping of nucleosomal DNA.

The RSC complex remodels nucleosomes in transcribed coding sequences and promotes transcription in Saccharomyces cerevisiae.

RSC (Remodels the Structure of Chromatin) is a conserved ATP-dependent chromatin remodeling complex that regulates many biological processes, including transcription by RNA polymerase II (Pol II). We report that RSC contributes in generating accessible nucleosomes in transcribed coding sequences (CDSs). RSC MNase ChIP-seq data revealed that RSC-bound nucleosome fragments were very heterogenous (∼80 bp to 180 bp) compared to a sharper profile displayed by the MNase inputs (140 bp to 160 bp), supporting the idea that RSC promotes accessibility of nucleosomal DNA. Notably, RSC binding to +1 nucleosomes and CDSs, but not with -1 nucleosomes, strongly correlated with Pol II occupancies, suggesting that RSC enrichment in CDSs is linked to transcription. We also observed that Pol II associates with nucleosomes throughout transcribed CDSs, and similar to RSC, Pol II-protected fragments were highly heterogenous, consistent with the idea that Pol II interacts with remodeled nucleosomes in CDSs. This idea is supported by the observation that the genes harboring high-levels of Pol II in their CDSs were the most strongly affected by ablating RSC function. Additionally, rapid nuclear depletion of Sth1 decreases nucleosome accessibility and results in accumulation of Pol II in highly transcribed CDSs. This is consistent with a slower clearance of elongating Pol II in cells with reduced RSC function, and is distinct from the effect of RSC depletion on PIC assembly. Altogether, our data provide evidence in support of the role of RSC in promoting Pol II elongation, in addition to its role in regulating transcription initiation.

Lysine succinylation on non-histone chromosomal protein HMG-17 (HMGN2) regulates nucleosomal DNA accessibility by disrupting the HMGN2-nucleosome association.

Lysine succinylation (Ksucc) is a novel posttranslational modification that frequently occurs on chromatin proteins including histones and non-histone proteins. Histone Ksucc affects nucleosome dynamics by increasing the DNA unwrapping rate and accessibility. However, very little is known about the regulation and functions of Ksucc located on non-histone chromosomal proteins. Here, we site-specifically installed a succinyl lysine analogue (Kcsucc) onto the non-histone chromosomal protein HMG-17 (HMGN2) to mimic the natural succinylated protein. We found that the incorporation of Kcsucc into HMGN2 at the K30 site (HMGN2Kc30succ), which is located within the nucleosome-binding domain (NBD), leads to significantly decreased HMGN2 binding to the mononucleosome. HMGN2Kc30succ also increased the nucleosomal DNA accessibility by promoting nucleosomal DNA unwrapping in the entry/exit region. This study reveals a novel mechanism of non-histone protein succinylation on altering chromatin recruitment, which can further affect nucleosome and chromatin dynamics.

Generation of Remosomes by the SWI/SNF Chromatin Remodeler Family

Chromatin remodelers are complexes able to both alter histone-DNA interactions and to mobilize nucleosomes. The mechanism of their action and the conformation of remodeled nucleosomes remain a matter of debates. In this work we compared the type and structure of the products of nucleosome remodeling by SWI/SNF and ACF complexes using high-resolution microscopy combined with novel biochemical approaches. We find that SWI/SNF generates a multitude of nucleosome-like metastable particles termed “remosomes”. Restriction enzyme accessibility assay, DNase I footprinting and AFM experiments reveal perturbed histone-DNA interactions within these particles. Electron cryo-microscopy shows that remosomes adopt a variety of different structures with variable irregular DNA path, similar to those described upon RSC remodeling. Remosome DNA accessibility to restriction enzymes is also markedly increased. We suggest that the generation of remosomes is a common feature of the SWI/SNF family remodelers. In contrast, the ACF remodeler, belonging to ISWI family, only produces repositioned nucleosomes and no evidence for particles associated with extra DNA, or perturbed DNA paths was found. The remosome generation by the SWI/SNF type of remodelers may represent a novel mechanism involved in processes where nucleosomal DNA accessibility is required, such as DNA repair or transcription regulation.

Ledgf/P75 Decreases Nucleosome Accessibility

LEDGF/p75 is a chromatin-binding protein that has been tied to integration of HIV-1 cDNA into human chromosomes and reduction of cellular stress-induced apoptosis. While the structural basis for the binding of the N-terminal PWWP domain of LEDGF to chromatin has been detailed, the binding mechanism and effects of LEDGF binding to chromatin is still not well understood. Here we detail the effects of LEDGF binding to nucleosomes through ensemble and single-molecule FRET assays and report that LEDGF binding to nucleosomes decreases accessibility of nucleosomal DNA to transcription factors.

Modulation of nucleosomal DNA accessibility via charge-altering post-translational modifications in histone core

BackgroundControlled modulation of nucleosomal DNA accessibility via post-translational modifications (PTM) is a critical component to many cellular functions. Charge-altering PTMs in the globular histone core—including acetylation, phosphorylation, crotonylation, propionylation, butyrylation, formylation, and citrullination—can alter the strong electrostatic interactions between the oppositely charged nucleosomal DNA and the histone proteins and thus modulate accessibility of the nucleosomal DNA, affecting processes that depend on access to the genetic information, such as transcription. However, direct experimental investigation of the effects of these PTMs is very difficult. Theoretical models can rationalize existing observations, suggest working hypotheses for future experiments, and provide a unifying framework for connecting PTMs with the observed effects.ResultsA physics-based framework is proposed that predicts the effect of charge-altering PTMs in the histone core, quantitatively for several types of lysine charge-neutralizing PTMs including acetylation, and qualitatively for all phosphorylations, on the nucleosome stability and subsequent changes in DNA accessibility, making a connection to resulting biological phenotypes. The framework takes into account multiple partially assembled states of the nucleosome at the atomic resolution. The framework is validated against experimentally known nucleosome stability changes due to the acetylation of specific lysines, and their effect on transcription. The predicted effect of charge-altering PTMs on DNA accessibility can vary dramatically, from virtually none to a strong, region-dependent increase in accessibility of the nucleosomal DNA; in some cases, e.g., H4K44, H2AK75, and H2BK57, the effect is significantly stronger than that of the extensively studied acetylation sites such H3K56, H3K115 or H3K122. Proximity to the DNA is suggestive of the strength of the PTM effect, but there are many exceptions. For the vast majority of charge-altering PTMs, the predicted increase in the DNA accessibility should be large enough to result in a measurable modulation of transcription. However, a few possible PTMs, such as acetylation of H4K77, counterintuitively decrease the DNA accessibility, suggestive of the repressed chromatin. A structural explanation for the phenomenon is provided. For the majority of charge-altering PTMs, the effect on DNA accessibility is simply additive (noncooperative), but there are exceptions, e.g., simultaneous acetylation of H4K79 and H3K122, where the combined effect is amplified. The amplification is a direct consequence of the nucleosome–DNA complex having more than two structural states. The effect of individual PTMs is classified based on changes in the accessibility of various regions throughout the nucleosomal DNA. The PTM’s resulting imprint on the DNA accessibility, “PTMprint,” is used to predict effects of many yet unexplored PTMs. For example, acetylation of H4K44 yields a PTMprint similar to the PTMprint of H3K56, and thus acetylation of H4K44 is predicted to lead to a wide range of strong biological effects.ConclusionCharge-altering post-translational modifications in the relatively unexplored globular histone core may provide a precision mechanism for controlling accessibility to the nucleosomal DNA.

The role of DNA sequence in nucleosome breathing

.Roughly 3/4 of human genomes are sequestered by nucleosomes, DNA spools with a protein core, dictating a broad range of biological processes, ranging from gene regulation, recombination, and replication, to chromosome condensation. Nucleosomes are dynamical structures and temporarily expose wrapped DNA through spontaneous unspooling from either end, a process called site exposure or nucleosome breathing. Here we ask how this process is influenced by the mechanical properties of the wrapped DNA, which is known to depend on the underlying base pair sequence. Using a coarse-grained nucleosome model we calculate the accessibility profiles for site exposure. We find that the process is very sensitive to sequence effects, so that evolution could potentially tune the accessibility of nucleosomal DNA and would only need a small number of mutations to do so.Graphical abstract

Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction.

Activation of transcription requires alteration of chromatin by complexes that increase the accessibility of nucleosomal DNA. Removing nucleosomes from regulatory sequences has been proposed to play a significant role in activation. We tested whether changes in nucleosome occupancy occurred on the set of genes that is activated by the unfolded protein response (UPR). We observed no decrease in occupancy on most promoters, gene bodies, and enhancers. Instead, there was an increase in the accessibility of nucleosomes, as measured by micrococcal nuclease (MNase) digestion and ATAC-seq (assay for transposase-accessible chromatin [ATAC] using sequencing), that did not result from removal of the nucleosome. Thus, changes in nucleosome accessibility predominate over changes in nucleosome occupancy during rapid transcriptional induction during the UPR.

Large-scale ATP-independent nucleosome unfolding by a histone chaperone.

DNA accessibility to regulatory proteins is substantially influenced by nucleosome structure and dynamics. The facilitates chromatin transcription (FACT) complex increases the accessibility of nucleosomal DNA, but the mechanism and extent of its nucleosome reorganization activity are unknown. Here we determined the effects of FACT from the yeast Saccharomyces cerevisiae on single nucleosomes by using single-particle Förster resonance energy transfer (spFRET) microscopy. FACT binding results in dramatic ATP-independent, symmetrical and reversible DNA uncoiling that affects at least 70% of the DNA within a nucleosome, occurs without apparent loss of histones and proceeds via an 'all-or-none' mechanism. A mutated version of FACT is defective in uncoiling, and a histone mutation that suppresses phenotypes caused by this FACT mutation in vivo restores the uncoiling activity in vitro. Thus, FACT-dependent nucleosome unfolding modulates the accessibility of nucleosomal DNA, and this activity is an important function of FACT in vivo.

Nucleosome breathing and remodeling constrain CRISPR-Cas9 function.

The CRISPR-Cas9 bacterial surveillance system has become a versatile tool for genome editing and gene regulation in eukaryotic cells, yet how CRISPR-Cas9 contends with the barriers presented by eukaryotic chromatin is poorly understood. Here we investigate how the smallest unit of chromatin, a nucleosome, constrains the activity of the CRISPR-Cas9 system. We find that nucleosomes assembled on native DNA sequences are permissive to Cas9 action. However, the accessibility of nucleosomal DNA to Cas9 is variable over several orders of magnitude depending on dynamic properties of the DNA sequence and the distance of the PAM site from the nucleosome dyad. We further find that chromatin remodeling enzymes stimulate Cas9 activity on nucleosomal templates. Our findings imply that the spontaneous breathing of nucleosomal DNA together with the action of chromatin remodelers allow Cas9 to effectively act on chromatin in vivo.

Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability.

Cytosine can undergo modifications, forming 5-methylcytosine (5-mC) and its oxidized products 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC) and 5-carboxylcytosine (5-caC). Despite their importance as epigenetic markers and as central players in cellular processes, it is not well understood how these modifications influence physical properties of DNA and chromatin. Here we report a comprehensive survey of the effect of cytosine modifications on DNA flexibility. We find that even a single copy of 5-fC increases DNA flexibility markedly. 5-mC reduces and 5-hmC enhances flexibility, and 5-caC does not have a measurable effect. Molecular dynamics simulations show that these modifications promote or dampen structural fluctuations, likely through competing effects of base polarity and steric hindrance, without changing the average structure. The increase in DNA flexibility increases the mechanical stability of the nucleosome and vice versa, suggesting a gene regulation mechanism where cytosine modifications change the accessibility of nucleosomal DNA through their effects on DNA flexibility.

The effect of DNA supercoiling on nucleosome structure and stability

Nucleosomes have to open to allow access to DNA in transcription, replication, and DNA damage repair. Changes in DNA torsional strain (e.g. during transcription elongation) influence the accessibility of nucleosomal DNA. Here we investigated the effect of DNA supercoiling-induced torsional strain on nucleosome structure and stability by scanning force microscopy (SFM) and fluorescence correlation spectroscopy (FCS). Nucleosomes were reconstituted onto 2.7 kb DNA plasmids with varying superhelical densities. The SFM results show a clear dependence of the amount of DNA wrapped around the nucleosome core on the strength and type of supercoiling. Negative supercoiling led to smaller nucleosome opening angles as compared to relaxed or positively supercoiled DNA. FCS experiments show that nucleosomes reconstituted on negatively superhelical DNA are more resistant to salt-induced destabilization, as seen by reduced H2A–H2B dimer eviction from the nucleosome. Our results show that changes in DNA topology, e.g. during transcription elongation, affect the accessibility of nucleosomal DNA.

SpFRET reveals changes in nucleosome breathing by neighboring nucleosomes

Chromatin, the structure in which DNA is compacted in eukaryotic cells, plays a key role in regulating DNA accessibility. FRET experiments on single nucleosomes, the basic units in chromatin, have revealed a dynamic nucleosome where spontaneous DNA unwrapping from the ends provides access to the nucleosomal DNA. Here we investigated how this DNA breathing is affected by extension of the linker DNA and by the presence of a neighboring nucleosome. We found that both electrostatic interactions between the entering and exiting linker DNA and nucleosome–nucleosome interactions increase unwrapping. Interactions between neighboring nucleosomes are more likely in dinucleosomes spaced by 55 bp of linker DNA than in dinucleosomes spaced by 50 bp of linker DNA. Such increased unwrapping may not only increase the accessibility of nucleosomal DNA in chromatin fibers, it may also be key to folding of nucleosomes into higher order structures.

Acetylation of Histone H3 Lysine 56 Abolishes Linker Histone Regulation of Transcription Factor Binding

The linker histone H1 is an ubiquitous regulator of chromatin structure and dynamics. These linker histones are highly abundant in metazoan somatic cells with almost one linker histone per nucleosome, and regulate gene expression during development and within somatic cells. We used fluorescence resonance energy transfer (FRET) to detect changes to nucleosome wrapping, which is sensitive to both H1 binding and transcription factor binding within the nucleosome. H1 binding induces an increase in nucleosome wrapping and FRET, while transcription factor binding within the nucleosome decreases nucleosome wrapping and FRET. We find that H1 suppresses but does not abolish TF binding suggesting that H1 dynamically regulates nucleosomal DNA accessibility to TF binding. We then prepared nucleosomes with histone H3 acetylated at lysine 56 (H3K56ac). This modification is involved transcriptional regulation and increases DNA unwrapping. We find that this modification abolishes H1 suppression of TF binding within the nucleosome. This result suggests that H3K56ac can encode, within a nucleosome, H1 regulation of DNA accessibility and provides a mechanism by which H1 regulation of DNA accessibility is targeted through the genome.