Nucleosome remodeling by the human SWI/SNF complex requires transient global disruption of histone-DNA interactions

Emerging Themes in Mechanisms of Tumorigenesis by SWI/SNF Subunit Mutation

The SWI/SNF chromatin remodeling complex uses the energy of ATP hydrolysis to alter contacts between DNA and nucleosomes, allowing regions of the genome to become accessible for biological processes such as transcription. The SWI/SNF chromatin remodeler is also one of the most frequently altered protein complexes in cancer, with upwards of 20% of all cancers carrying mutations in a SWI/SNF subunit. Intense studies over the last decade have probed the molecular events associated with SWI/SNF dysfunction in cancer and common themes are beginning to emerge in how tumor-associated SWI/SNF mutations promote malignancy. In this review, we summarize current understanding of SWI/SNF complexes, their alterations in cancer, and what is known about the impact of these mutations on tumor-relevant transcriptional events. We discuss how enhancer dysregulation is a common theme in SWI/SNF mutant cancers and describe how resultant alterations in enhancer and super-enhancer activity conspire to block development and differentiation while promoting stemness and self-renewal. We also identify a second emerging theme in which SWI/SNF perturbations intersect with potent oncoprotein transcription factors AP-1 and MYC to drive malignant transcriptional programs.

Generating specificity in genome regulation through transcription factor sensitivity to chromatin

Cell type-specific gene expression relies on transcription factors (TFs) binding DNA sequence motifs embedded in chromatin. Understanding how motifs are accessed in chromatin is crucial to comprehend differential transcriptional responses and the phenotypic impact of sequence variation. Chromatin obstacles to TF binding range from DNA methylation to restriction of DNA access by nucleosomes depending on their position, composition and modification. In vivo and in vitro approaches now enable the study of TF binding in chromatin at unprecedented resolution. Emerging insights suggest that TFs vary in their ability to navigate chromatin states. However, it remains challenging to link binding and transcriptional outcomes to molecular characteristics of TFs or the local chromatin substrate. Here, we discuss our current understanding of how TFs access DNA in chromatin and novel techniques and directions towards a better understanding of this critical step in genome regulation.

Reb1, Cbf1, and Pho4 bias histone sliding and deposition away from their binding sites

In transcriptionally active genes, nucleosome positions in promoters are regulated by nucleosome displacing factors (NDFs) and chromatin remodeling enzymes. Depletion of NDFs or the RSC chromatin remodeler shrinks or abolishes the nucleosome depleted regions (NDRs) in promoters, which can suppress gene activation and result in cryptic transcription. Despite their vital cellular functions, how the action of chromatin remodelers may be directly affected by site-specific binding factors like NDFs is poorly understood. Here we demonstrate that two NDFs, Reb1 and Cbf1, can direct both Chd1 and RSC chromatin remodeling enzymes in vitro, stimulating repositioning of the histone core away from their binding sites. Interestingly, although the Pho4 transcription factor had a much weaker effect on nucleosome positioning, both NDFs and Pho4 were able to similarly redirect positioning of hexasomes. In chaperone-mediated nucleosome assembly assays, Reb1 but not Pho4 showed an ability to block deposition of the histone H3/H4 tetramer, but Reb1 did not block addition of the H2A/H2B dimer to hexasomes. Our in vitro results show that NDFs bias the action of remodelers to increase the length of the free DNA in the vicinity of their binding sites. These results suggest that NDFs could directly affect NDR architecture through chromatin remodelers.

High precision FRET studies reveal reversible transitions in nucleosomes between microseconds and minutes

Nucleosomes play a dual role in compacting the genome and regulating the access to DNA. To unravel the underlying mechanism, we study fluorescently labeled mononucleosomes by multi-parameter FRET measurements and characterize their structural and dynamic heterogeneity upon NaCl-induced destabilization. Species-selective fluorescence lifetime analysis and dynamic photon distribution analysis reveal intermediates during nucleosome opening and lead to a coherent structural and kinetic model. In dynamic octasomes and hexasomes the interface between the H2A-H2B dimers and the (H3-H4)₂ tetramer opens asymmetrically by an angle of ≈20° on a 50 and 15 µs time scale, respectively. This is followed by a slower stepwise release of the dimers coupled with DNA unwrapping. A mutation (H2A-R81A) at the interface between H2A and H3 facilitates initial opening, confirming the central role of the dimer:tetramer interface for nucleosome stability. Partially opened states such as those described here might serve as convenient nucleation sites for DNA-recognizing proteins.

Mechanisms of ATP-Dependent Chromatin Remodeling Motors

Chromatin remodeling motors play essential roles in all DNA-based processes. These motors catalyze diverse outcomes ranging from sliding the smallest units of chromatin, known as nucleosomes, to completely disassembling chromatin. The broad range of actions carried out by these motors on the complex template presented by chromatin raises many stimulating mechanistic questions. Other well-studied nucleic acid motors provide examples of the depth of mechanistic understanding that is achievable from detailed biophysical studies. We use these studies as a guiding framework to discuss the current state of knowledge of chromatin remodeling mechanisms and highlight exciting open questions that would continue to benefit from biophysical analyses.

Stepwise nucleosome translocation by RSC remodeling complexes

The SWI/SNF-family remodelers regulate chromatin structure by coupling the free energy from ATP hydrolysis to the repositioning and restructuring of nucleosomes, but how the ATPase activity of these enzymes drives the motion of DNA across the nucleosome remains unclear. Here, we used single-molecule FRET to monitor the remodeling of mononucleosomes by the yeast SWI/SNF remodeler, RSC. We observed that RSC primarily translocates DNA around the nucleosome without substantial displacement of the H2A-H2B dimer. At the sites where DNA enters and exits the nucleosome, the DNA moves largely along or near its canonical wrapping path. The translocation of DNA occurs in a stepwise manner, and at both sites where DNA enters and exits the nucleosome, the step size distributions exhibit a peak at approximately 1–2 bp. These results suggest that the movement of DNA across the nucleosome is likely coupled directly to DNA translocation by the ATPase at its binding site inside the nucleosome.

DOI:http://dx.doi.org/10.7554/eLife.10051.001

Cells package their genetic information in a "complex” of proteins and DNA called chromatin. This complex is made of units called nucleosomes, each of which consist of a short stretch of DNA wrapped around proteins known as histones. These nucleosomes restrict access to the DNA wrapped around the histone proteins, and thus serve to regulate whether genes are activated and a variety of other cellular processes. Certain enzymes regulate the structure of chromatin by altering the position and structure of nucleosomes. However, it is not clear exactly how these “chromatin remodeling” enzymes alter the contacts between the DNA and histone proteins to move DNA around the nucleosome.

RSC is a chromatin-remodeling enzyme that typically helps to activate genes. Harada et al. used a technique called single molecule fluorescence resonance energy transfer (or single molecule FRET for short) to observe the movement of DNA around the histone proteins. The technique involves placing a green fluorescent dye on the histone proteins and a red fluorescent dye on the DNA. If the red dye is close to the green dye, some of the energy can be transferred from the green dye to the red dye when the green dye is excited by a laser. By looking at the ratio of green and red light emitted, it is possible to tell how far apart they are, and how this changes over time.

The experiments show that the RSC enzyme moves the DNA into and out of the nucleosome in small steps. These steps match the expected step size of DNA movements by a section of the enzyme called the ATPase domain. This suggests that the ATPase domain drives the motion of DNA across the entire nucleosome. A future challenge is to better understand how chromatin remodeling enzymes cooperate with other molecules in cells to remodel nucleosomes and chromatin.

DOI:http://dx.doi.org/10.7554/eLife.10051.002

Transcriptional Enhancers in the Regulation of T Cell Differentiation

The changes in phenotype and function that characterize the differentiation of naïve T cells to effector and memory states are underscored by large-scale, coordinated, and stable changes in gene expression. In turn, these changes are choreographed by the interplay between transcription factors and epigenetic regulators that act to restructure the genome, ultimately ensuring lineage-appropriate gene expression. Here, we focus on the mechanisms that control T cell differentiation, with a particular focus on the role of regulatory elements encoded within the genome, known as transcriptional enhancers (TEs). We discuss the central role of TEs in regulating T cell differentiation, both in health and disease.

Dynamic regulation of transcription factors by nucleosome remodeling

The chromatin landscape and promoter architecture are dominated by the interplay of nucleosome and transcription factor (TF) binding to crucial DNA sequence elements. However, it remains unclear whether nucleosomes mobilized by chromatin remodelers can influence TFs that are already present on the DNA template. In this study, we investigated the interplay between nucleosome remodeling, by either yeast ISW1a or SWI/SNF, and a bound TF. We found that a TF serves as a major barrier to ISW1a remodeling, and acts as a boundary for nucleosome repositioning. In contrast, SWI/SNF was able to slide a nucleosome past a TF, with concurrent eviction of the TF from the DNA, and the TF did not significantly impact the nucleosome positioning. Our results provide direct evidence for a novel mechanism for both nucleosome positioning regulation by bound TFs and TF regulation via dynamic repositioning of nucleosomes.

DOI:http://dx.doi.org/10.7554/eLife.06249.001

Cells contain thousands of genes that are encoded by molecules of DNA. In yeast and other eukaryotic organisms, this DNA is wrapped around proteins called histones to make structures called nucleosomes. This compacts the DNA and allows it to fit inside the tiny nucleus within the cell. The positioning of the nucleosomes influences how tightly packed the DNA is, which in turn influences the activity of genes. Less active genes tend to be found within regions of DNA that are tightly packed, while more active genes are found in less tightly packed regions.

To activate a gene, proteins called transcription factors bind to a section of DNA within the gene called the promoter. Enzymes known as ‘chromatin remodelers’ can alter the locations of nucleosomes on DNA to allow the transcription factors access to the promoters of particular genes. In yeast, the SWI/SNF family of chromatin remodelers can disassemble nucleosomes to promote gene activity, while the ISW1 family organises nucleosomes into closely spaced groups to repress gene activity. However, it is not clear if, or how, chromatin remodelers can influence transcription factors that are already bound to DNA.

Here, Li et al. studied the interactions between a transcription factor and the chromatin remodelers in yeast. The experiment used a piece of DNA that contained a bound transcription factor and a single nucleosome. Li et al. used a technique called ‘single molecule DNA unzipping’, which enabled them to precisely locate the position of the nucleosome and transcription factor before and after the nucleosome was remodeled. The experiments found that a chromatin remodeler called ISW1a moved the nucleosome away from the transcription factor, while a SWI/SNF chromatin remodeler moved the nucleosome towards it.

Significantly, Li et al. also found that a transcription factor is a major barrier to ISW1a's remodeling activity, suggesting that ISW1a may use transcription factors as reference points to position nucleosomes. In contrast, SWI/SNF was able to slide a nucleosome past the transcription factor, which led to the transcription factor falling off the DNA. Therefore, SWI/SNF is able to move transcription factors out of the way to deactivate genes.

Li et al. propose a new model for how chromatin remodelers can move nucleosomes and regulate transcription factors to alter gene activity. A future challenge will be to observe these types of activities in living cells.

DOI:http://dx.doi.org/10.7554/eLife.06249.002

ATP-Dependent Chromatin Remodeling

In the eukaryotic nucleus, processes of DNA metabolism such as transcription, DNA replication, and repair occur in the context of DNA packaged into nucleosomes and higher order chromatin structures. In order to overcome the barrier presented by chromatin structures to the protein machinery carrying out these processes, the cell relies on a class of enzymes called chromatin remodeling complexes which catalyze ATP-dependent restructuring and repositioning of nucleosomes. Chromatin remodelers are large multi-subunit complexes which all share a common SF2 helicase ATPase domain in their catalytic subunit, and are classified into four different families-SWI/SNF, ISWI, CHD, INO80-based on the arrangement of other domains in their catalytic subunit as well as their non-catalytic subunit composition. A large body of structural, biochemical, and biophysical evidence suggests chromatin remodelers operate as histone octamer-anchored directional DNA translocases in order to disrupt DNA-histone interactions and catalyze nucleosome sliding. Remodeling mechanisms are family-specific and depend on factors such as how the enzyme engages with nucleosomal and linker DNA, features of DNA loop intermediates, specificity for mono- or oligonucleosomal substrates, and ability to remove histones and exchange histone variants. Ultimately, the biological function of chromatin remodelers and their genomic targeting in vivo is regulated by each complex's subunit composition, association with chromatin modifiers and histone chaperones, and affinity for chromatin signals such as histone posttranslational modifications.

Defining the molecular blueprint that drives CD8(+) T cell differentiation in response to infection

A cardinal feature of adaptive, cytotoxic T lymphocyte (CTL)-mediated immunity is the ability of naïve CTLs to undergo a program of differentiation and proliferation upon activation resulting in the acquisition of lineage-specific T cell functions and eventual establishment of immunological memory. In this review, we examine the molecular factors that shape both the acquisition and maintenance of lineage-specific effector function in virus-specific CTL during both the effector and memory phases of immunity.

SWI/SNF- and RSC-catalyzed nucleosome mobilization requires internal DNA loop translocation within nucleosomes

The multisubunit SWI/SNF and RSC complexes utilize energy derived from ATP hydrolysis to mobilize nucleosomes and render the DNA accessible for various nuclear processes. Here we test the idea that remodeling involves intermediates with mobile DNA bulges or loops within the nucleosome by cross-linking the H2A N- or C-terminal tails together to generate protein "loops" that constrict separation of the DNA from the histone surface. Analyses indicate that this intranucleosomal cross-linking causes little or no change in remodeling-dependent exposure of DNA sequences within the nucleosome to restriction enzymes. However, cross-linking inhibits nucleosome mobilization and blocks complete movement of nucleosomes to extreme end positions on the DNA fragments. These results are consistent with evidence that nucleosome remodeling involves intermediates with DNA loops on the nucleosome surface but indicate that such loops do not freely diffuse about the surface of the histone octamer. We propose a threading model for movement of DNA loops around the perimeter of the nucleosome core.

Activity of FEN1 endonuclease on nucleosome substrates is dependent upon DNA sequence but not flap orientation

We demonstrated previously that human FEN1 endonuclease, an enzyme involved in excising single-stranded DNA flaps that arise during Okazaki fragment processing and base excision repair, cleaves model flap substrates assembled into nucleosomes. Here we explore the effect of flap orientation with respect to the surface of the histone octamer on nucleosome structure and FEN1 activity in vitro. We find that orienting the flap substrate toward the histone octamer does not significantly alter the rotational orientation of two different nucleosome positioning sequences on the surface of the histone octamer but does cause minor perturbation of nucleosome structure. Surprisingly, flaps oriented toward the nucleosome surface are accessible to FEN1 cleavage in nucleosomes containing the Xenopus 5S positioning sequence. In contrast, neither flaps oriented toward nor away from the nucleosome surface are cleaved by the enzyme in nucleosomes containing the high-affinity 601 nucleosome positioning sequence. The data are consistent with a model in which sequence-dependent motility of DNA on the nucleosome is a major determinant of FEN1 activity. The implications of these findings for the activity of FEN1 in vivo are discussed.

Histone tyrosine phosphorylation comes of age

Histones were discovered over a century ago and have since been found to be the most extensively posttranslationally modified proteins, although tyrosine phosphorylation of histones had remained elusive until recently. The year 2009 proved to be a landmark year for histone tyrosine (Y) phosphorylation as five research groups independently discovered this modification. Three groups describe phosphorylation of Y142 in the variant histone H2A.X, where it may be involved in the cellular decision making process to either undergo DNA repair or apoptosis in response to DNA damage. Further, one group suggests that phosphorylation of histone H3 on Y99 is crucial for its regulated proteolysis in yeast, while another found that Y41 phosphorylation modulates chromatin architecture and oncogenesis in mammalian cells. These pioneering studies provide the initial conceptual framework for further analyses of the diverse roles of tyrosine phosphorylation on different histones, with far reaching implications for human health and disease.

Mechanism(s) of SWI/SNF-induced nucleosome mobilization

Impediments to DNA access due to assembly of the eukaryotic genome into chromatin are in part overcome by the activity of ATP-dependent chromatin-remodeling complexes. These complexes employ energy derived from ATP hydrolysis to destabilize histone-DNA interactions and alter nucleosome positions, thereby increasing the accessibility of DNA-binding factors to their targets. However, the mechanism by which theses complexes accomplish this task remains unresolved. We review aspects of nucleosome alteration by the SWI/SNF complex, the archetypal remodeling enzyme. We focus on experiments that provide insights into how SWI/SNF induces nucleosome movement along DNA. Numerous biochemical activities have been characterized for this complex, all likely providing clues as to the molecular mechanism of translocation.

Chromatin remodeling in silico: a stochastic model for SWI/SNF

Beside their contribution in DNA packaging, histone-core particles modulate the transcription machinery access to the DNA through dynamic chromatin structure. Chromatin remodeling complexes perturb such modulations through diverse mechanisms. SWI/SNF is a well-studied highly conserved chromatin remodeling complex that is ubiquitous across eukaryotes. Rigorous study of experimental observations suggests randomness in dynamics of SWI/SNF in cis chromatin remodeling process. In this work we propose a stochastic computational model that captures such fluctuations. We incorporate the physiological properties of the process through parametric microevents. Each microevent is then associated with a stochastic model that couples its random temporal and spatial dynamics with the energy landscape of the remodeling process. We further show that DNA sequence stacks and friction force have negligible effect on chromatin remodeling. Our approach shows a promising approximation to the force impinged on the DNA by the SWI/SNF complex. We validate our model predictions with several experimental data sets. The proposed model suggest that the in cis translocation rate of histone-core particle follows a Gamma distribution. By carefully analyzing the simulation results we conjecture that SWI/SNF chromatin remodeling has low energy efficiency (<0.30). We use our model to recapitulate the dynamics of the parallel remodeling processes that occur in close proximity across a typical eukaryotic genome. Our results suggest that the orchestrated chromatin remodeling makes few kilobase-pairs of the DNA accessible to the transcription machinery in a timely manner.

Transcription dynamics

All aspects of transcription and its regulation involve dynamic events. The basal transcription machinery and regulatory components are dynamically recruited to their target genes, and dynamic interactions of transcription factors with chromatin--and with each other--play a key role in RNA polymerase assembly, initiation, and elongation. These short-term binding dynamics of transcription factors are superimposed by long-term cyclical behavior of chromatin opening and transcription factor-binding events. Its dynamic nature is not only a fundamental property of the transcription machinery, but it is emerging as an important modulator of physiological processes, particularly in differentiation and development.

Transcription dynamics

All aspects of transcription and its regulation involve dynamic events. The basal transcription machinery and regulatory components are dynamically recruited to their target genes, and dynamic interactions of transcription factors with chromatin--and with each other--play a key role in RNA polymerase assembly, initiation, and elongation. These short-term binding dynamics of transcription factors are superimposed by long-term cyclical behavior of chromatin opening and transcription factor-binding events. Its dynamic nature is not only a fundamental property of the transcription machinery, but it is emerging as an important modulator of physiological processes, particularly in differentiation and development.

Human SWI/SNF directs sequence-specific chromatin changes on promoter polynucleosomes

Studies in humans and other species have revealed that a surprisingly large fraction of nucleosomes adopt specific positions on promoters, and that these positions appear to be determined by nucleosome positioning DNA sequences (NPSs). Recent studies by our lab, using minicircles containing only one nucleosome, indicated that the human SWI/SNF complex (hSWI/SNF) prefers to relocate nucleosomes away from NPSs. We now make use of novel mapping techniques to examine the hSWI/SNF sequence preference for nucleosome movement in the context of polynucleosomal chromatin, where adjacent nucleosomes can limit movement and where hSWI/SNF forms altered dinucleosomal structures. Using two NPS templates (5S rDNA and 601) and two hSWI/SNF target promoter templates (c-myc and UGT1A1), we observed hSWI/SNF-driven depletion of normal mononucleosomes from almost all positions that were strongly favored by assembly. In some cases, these mononucleosomes were moved to hSWI/SNF-preferred sequences. In the majority of other cases, one repositioned mononucleosome appeared to combine with an unmoved mononucleosome forming a specifically localized altered or normal dinucleosome. These effects result in dramatic, template-specific changes in nucleosomal distribution. Taken together, these studies indicate hSWI/SNF is likely to activate or repress transcription of its target genes by generating promoter sequence-specific changes in chromatin configuration.

Marking time: the dynamic role of chromatin and covalent modification in transcription

The expression of genes subject to strict regulation can be a highly dynamic, cyclical process that sequentially achieves and then limits transcription. Kinetic investigations of the estrogen responsive pS2 (TFF1) promoter, to determine the occupancy of factors or the occurrence of covalent marks on chromatin, have provided the most comprehensive picture of the complexity of transcriptional cycling to date. Cycles are initiated by the assembly of intermediate transcription factors that in turn provoke conscription of the basal transcription machinery. These events then achieve activation of the polymerase II complex, which is subsequently followed by limitation of productivity through the action of repressive complexes. This latter phase resets the target promoter, through acting on chromatin structure, such that a subsequent cycle can be initiated. In consequence, transcription is dependent upon cis-acting elements (DNA and nucleosomes) that either interact with or are modified by trans-acting factors. Induced local structural changes to chromatin encompassing regulatory elements of gene promoters include alteration of the positional phasing of nucleosomes, substitution by variant histones, post-translational modification of nucleosomes, changes in the methylation of CpG dinucleotides and breaks in the sugar-phosphate backbone of DNA. A primary function of covalent modification of chromatin may be to drive a sequential progression of reversible interactions that achieve and regulate gene expression.

Prohibitin and the SWI/SNF ATPase subunit BRG1 are required for effective androgen antagonist-mediated transcriptional repression of androgen receptor-regulated genes

Androgen antagonists or androgen deprivation are the primary therapeutic modalities for the treatment of prostate cancer. Invariably, however, the disease becomes progressive and unresponsive to androgen ablation therapy (hormone refractory). The molecular mechanisms by which androgen antagonists inhibit prostate cancer proliferation are not fully defined. In this study, we identify two molecules which are required for effective prostate cancer cell responsiveness to androgen antagonists. We establish that androgen receptor (AR)-dependent transcriptional suppression by androgen antagonists requires the tumor suppressor prohibitin. This requirement for prohibitin was demonstrated using structurally-distinct androgen antagonists, stable and transient knockdown of prohibitin and transfected and endogenous AR-responsive genes. The SWI-SNF complex core ATPase BRG1, but not its closely-related counterpart ATPase BRM, is required for this repressive action of prohibitin on AR-responsive promoters. Androgen antagonists induce recruitment of prohibitin and BRG1 to endogenous AR-responsive promoters and induce a physical association between AR and prohibitin and BRG1. The recruitment of prohibitin to endogenous AR-responsive promoters is dependent upon antagonist-bound AR. Prohibitin binding in the prostate-specific antigen (PSA) promoter results in the recruitment of BRG1 and the dissociation of p300 from the PSA promoter. These findings suggest that prohibitin may function through BRG1-mediated local chromatin remodeling activity and the removal of p300-mediated acetylation to produce androgen antagonist-mediated transcriptional repression. Furthermore, in addition to its necessary role in AR-mediated transcriptional repression, we demonstrate that prohibitin is required for full and efficient androgen antagonist-mediated growth suppression of prostate cancer cells.

Swi3p controls SWI/SNF assembly and ATP-dependent H2A-H2B displacement

Yeast SWI/SNF is a multisubunit, 1.14-MDa ATP-dependent chromatin-remodeling enzyme required for transcription of a subset of inducible genes. Biochemical studies have demonstrated that SWI/SNF uses the energy from ATP hydrolysis to generate superhelical torsion, mobilize mononucleosomes, enhance the accessibility of nucleosomal DNA and remove H2A-H2B dimers from mononucleosomes. Here we describe the ATP-dependent activities of a SWI/SNF sub complex that is composed of only three subunits, Swi2p, Arp7p and Arp9p. Whereas this sub complex is fully functional in most remodeling assays, Swi2p-Arp7p-Arp9p is defective for ATP-dependent removal of H2A-H2B dimers. We identify the acidic N terminus of the Swi3p subunit as a novel H2A-H2B-binding domain required for ATP-dependent dimer loss. Our data indicate that H2A-H2B dimer loss is not an obligatory consequence of ATP-dependent DNA translocation, and furthermore they suggest that SWI/SNF is composed of at least four interdependent modules.

Human ACF1 alters the remodeling strategy of SNF2h

The human ACF chromatin-remodeling complex (hACF) contains the ATPase motor protein SNF2h and the non-catalytic hACF1 subunit. Here, we have compared the ability of SNF2h and a reconstituted hACF complex containing both SNF2h and hACF1 to remodel a series of nucleosomes containing different lengths of DNA overhang. Both SNF2h and hACF functioned in a manner consistent with sliding a canonical nucleosome. However, the non-catalytic subunit, hACF1, altered the remodeling properties of SNF2h by changing the nature of the requirement for a DNA overhang in the nucleosomal substrate and altering the DNA accessibility profile of the remodeled products. Surprisingly, addition of hACF1 to SNF2h increased the amount of DNA overhang needed to observe measurable amounts of DNA accessibility, but decreased the amount of overhang needed for a measurable binding interaction. We propose that these hACF1 functions might contribute to making the hACF complex more efficient at nucleosome spacing compared with SNF2h. In contrast, the SWI/SNF complex and its ATPase subunit BRG1 generated DNA accessibility profiles that were similar to each other, but different significantly from those of hACF and SNF2h. Thus, we observed divergent remodeling behaviors in these two remodeling families and found that the manner in which hACF1 alters the remodeling behavior of the ATPase is not shared by SWI/SNF subunits.

Probing SWI/SNF remodeling of the nucleosome by unzipping single DNA molecules

Chromatin-remodeling enzymes can overcome strong histone-DNA interactions within the nucleosome to regulate access of DNA-binding factors to the genetic code. By unzipping individual DNA duplexes, each containing a uniquely positioned nucleosome flanked by long segments of DNA, we directly probed histone-DNA interactions. The resulting disruption-force signatures were characteristic of the types and locations of interactions and allowed measurement of the positions of nucleosomes with 2.6-base-pair (bp) precision. Nucleosomes remodeled by yeast SWI/SNF were moved bidirectionally along the DNA, resulting in a continuous position distribution. The characteristic distance of motion was approximately 28 bp per remodeling event, and each event occurred with a catalytic efficiency of 0.4 min(-1) per nM SWI/SNF. Remodeled nucleosomes had essentially identical disruption signatures to those of unremodeled nucleosomes, indicating that their overall structure remained canonical. These results impose substantial constraints on the mechanism of SWI/SNF remodeling.

A conserved Swi2/Snf2 ATPase motif couples ATP hydrolysis to chromatin remodeling

Yeast (Saccharomyces cerevisiae) SWI/SNF is a prototype for a large family of ATP-dependent chromatin-remodeling enzymes that facilitate numerous DNA-mediated processes. Swi2/Snf2 is the catalytic subunit of SWI/SNF, and it is the founding member of a novel subfamily of the SF2 superfamily of DNA helicase/ATPases. Here we present a functional analysis of the diagnostic set of helicase/ATPase sequence motifs found within all Swi2p/Snf2p family members. Whereas many of these motifs play key roles in ATP binding and/or hydrolysis, we identify residues within conserved motif V that are specifically required to couple ATP hydrolysis to chromatin-remodeling activity. Interestingly, motif V of the human Swi2p/Snf2p homolog, Brg1p, has been shown to be a possible hot spot for mutational alterations associated with cancers.

Changes in attitude, changes in latitude: nuclear receptors remodeling chromatin to regulate transcription

Nuclear receptors (NRs) are a large family of ligand-dependent transcription factors that regulate important physiological processes. To activate or repress genes assembled naturally as chromatin, NRs recruit two distinct enzymatic activities, namely histone-modifying enzymes and ATP-dependent chromatin remodeling complexes, to alter local chromatin structure at target gene promoters. In this review, we examine the functional relationship between ATP-dependent chromatin remodeling complexes and NRs in the context of transcriptional regulation. Using the steroid-responsive mouse mammary tumor virus promoter as a model system, we discuss in detail the molecular mechanisms underlying the recruitment of these complexes and subsequent chromatin structure changes catalyzed by this group of enzymes. In addition, we extend the discussion to other NR-regulated promoters including the pS2 promoter. Finally, we summarize specific principles governing this critical relationship, identify unanswered questions and discuss the potential application of these principles in rational drug design.

Using atomic force microscopy to study nucleosome remodeling on individual nucleosomal arrays in situ

In eukaryotes, genomic processes like transcription, replication, repair, and recombination typically require alterations in nucleosome structure on specific DNA regions to operate. ATP-dependent nucleosome remodeling complexes provide a major mechanism for carrying out such alterations in vivo. To learn more about the action of these important complexes, we have utilized an atomic force microscopy in situ technique that permits comparison of the same individual molecules before and after activation of a particular process, in this case nucleosome remodeling. This direct approach was used to look for changes induced by the action of the human Swi-Snf remodeling complex on individual, single-copy mouse mammary tumor virus promoter nucleosomal arrays. Using this technique, we detect a variety of changes on remodeling. Many of these changes are larger in scale than suggested from previous studies and involve a number of DNA-mediated events, including a preference for the removal of a complete turn (80 basepairs) of nucleosomal DNA. The latter result raises the possibility of an unanticipated mode of human Swi-Snf interaction with the nucleosome, namely via the 11-nm histone surface.

Nucleosome remodeling: one mechanism, many phenomena?

The term 'nucleosome remodeling' subsumes a large number of energy-dependent alterations of canonical nucleosome structure, catalyzed by dedicated ATPases in large multiprotein complexes. The importance of these factors for gene regulation and other processes with chromatin substrate have emerged from genetic studies. Mechanistic analyses of nucleosome remodeling by different enzymes provided a diverse, almost confusing phenomenology of ATP-dependent derangement of nucleosomes in vitro, suggesting that different remodeling machines follow different strategies to disrupt histone-DNA interactions. This review explores the alternative possibility that the rich phenomenology of nucleosome remodeling may be brought about by variations of one basic remodeling reaction.

Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions

Here we describe 11 crystal structures of nucleosome core particles containing individual point mutations in the structured regions of histones H3 and H4. The mutated residues are located at the two protein-DNA interfaces flanking the nucleosomal dyad. Five of the mutations partially restore the in vivo effects of SWI/SNF inactivation in yeast. We find that even nonconservative mutations of these residues (which exhibit a distinct phenotype in vivo) have only moderate effects on global nucleosome structure. Rather, local protein-DNA interactions are disrupted and weakened in a subtle and complex manner. The number of lost protein-DNA interactions correlates directly with an increased propensity of the histone octamer to reposition with respect to the DNA, and with an overall destabilization of the nucleosome. Thus, the disruption of only two to six of the approximately 120 direct histone-DNA interactions within the nucleosome has a pronounced effect on nucleosome mobility and stability. This has implications for our understanding of how these structures are made accessible to the transcription and replication machinery in vivo.

Chromatin remodeling by ATP-dependent molecular machines

The eukaryotic genome is packaged into a periodic nucleoprotein structure termed chromatin. The repeating unit of chromatin, the nucleosome, consists of DNA that is wound nearly two times around an octamer of histone proteins. To facilitate DNA-directed processes in chromatin, it is often necessary to rearrange or to mobilize the nucleosomes. This remodeling of the nucleosomes is achieved by the action of chromatin-remodeling complexes, which are a family of ATP-dependent molecular machines. Chromatin-remodeling factors share a related ATPase subunit and participate in transcriptional regulation, DNA repair, homologous recombination and chromatin assembly. In this review, we provide an overview of chromatin-remodeling enzymes and discuss two possible mechanisms by which these factors might act to reorganize nucleosome structure.

Chromatin remodeling in vivo: evidence for a nucleosome sliding mechanism

Members of the ISWI family of chromatin remodeling factors exhibit ATP-dependent nucleosome sliding, loading, and spacing activities in vitro. However, it is unclear which of these activities are utilized by ISWI complexes to remodel chromatin in vivo. We therefore sought to identify the mechanisms of chromatin remodeling by Saccharomyces cerevisiae Isw2 complex at its known sites of action in vivo. To address this question, we developed a method of identifying intermediates of the Isw2-dependent chromatin remodeling reaction as it proceeded. We show that Isw2 complex catalyzes nucleosome sliding at two different classes of target genes in vivo, in each case sliding nucleosomes closer to the promoter regions. In contrast to its biochemical activities in vitro, nucleosome sliding by Isw2 complex in vivo is unidirectional and localized to a few nucleosomes at each site, suggesting that Isw2 activity is constrained by cellular factors.

ATP-dependent chromatin remodeling

The study of chromatin and how this dynamic structure modulates events in the eukaryotic nucleus has become an increasingly important topic in biomedical research. A large number of enzymes have been discovered that are responsible for modifying and altering chromatin structure, either globally or specifically at particular gene promoters or regions of the chromosome. This chapter provides an introduction to the structure of chromatin and then describes how special classes of enzymes modulate chromatin structure to allow access to DNA.

Dynamic properties of nucleosomes during thermal and ATP-driven mobilization

The fundamental subunit of chromatin, the nucleosome, is not a static entity but can move along DNA via either thermal or enzyme-driven movements. Here we have monitored the movements of nucleosomes following deposition at well-defined locations on mouse mammary tumor virus promoter DNA. We found that the sites to which nucleosomes are deposited during chromatin assembly differ from those favored during thermal equilibration. Taking advantage of this, we were able to track the movement of nucleosomes over 156 bp and found that this proceeds via intermediate positions spaced between 46 and 62 bp. The remodeling enzyme ISWI was found to direct the movement of nucleosomes to sites related to those observed during thermal mobilization. In contrast, nucleosome mobilization driven by the SWI/SNF and RSC complexes were found to drive nucleosomes towards sites up to 51 bp beyond DNA ends, with little respect for the sites favored during thermal repositioning. The dynamic properties of nucleosomes we describe are likely to influence their role in gene regulation.

Nucleosome sliding induced by the xMi-2 complex does not occur exclusively via a simple twist-diffusion mechanism

ATP-dependent chromatin remodeling complexes can induce the translocation (sliding) of nucleosomes in cis along DNA, but the mechanism by which sliding occurs is not well defined. We previously presented evidence that sliding induced by the human SWI/SNF complex does not occur solely via a proposed "twist-diffusion" mechanism whereby the DNA rotates about its helical axis without displacement from the surface of the nucleosome (Aoyagi, S., and Hayes, J. J. (2002) Mol. Cell. Biol. 22, 7484-7490). Here we examined whether the Xenopus Mi-2 nucleosome remodeling complex induces nucleosome sliding via a twist-diffusion mechanism with nucleosomes assembled onto DNA templates containing branched DNA structures expected to sterically hinder rotation of the DNA helix on the nucleosome surface. We find that the branched DNA-containing nucleosomes undergo xMi-2-catalyzed sliding at a rate and extent identical to that of nucleosomes assembled on native DNA fragments. These results indicate that both the hSWI/SNF and xMi-2 complexes induce nucleosome sliding via a mechanism(s) other than simple twist diffusion and are consistent with models in which the DNA largely maintains its rotational orientation with respect to the histone surface.

Mechanism of nucleosome disruption and octamer transfer by the chicken SWI/SNF-like complex

We had recently characterized SLC, a SWI/SNF-like chromatin remodelling activity, from chicken liver. The SLC efficiently disrupts nucleosomes, transfers histone octamers from nucleosomal substrates onto acceptor DNA, and slides histone octamers along DNA. Here, we present evidence that SLC is indeed a SWI/SNF homologue, and it disrupts nucleosomes by inducing extensive dynamic helical distortions in the nucleosomal DNA. Both the nucleosome disruption and octamer transfer functions are indifferent to nucleosomal histone tails. We further show that the nucleosome disruption precedes the octamer transfer and that the latter requires continuous presence of ATP. Based on these observations, we propose that a disrupted nucleosome is not a spontaneous substrate for octamer transfer; rather the nucleosome disruption and the octamer transfer are two temporally successive, ATP-dependent events during nucleosome remodelling by SLC in vitro.

Recent advances in understanding chromatin remodeling by Swi/Snf complexes

Members of the Swi/Snf family of chromatin-remodeling complexes play critical roles in transcriptional control. Recent studies have made significant advances in our understanding of the fundamental aspects of Swi/Snf complexes, including the roles of specific subunits, the repression of transcription, and the mechanism of remodeling. In addition, new findings also indicate an important role for the Swi/Snf-related complex, RSC, in controlling gene expression.

SWI/SNF unwraps, slides, and rewraps the nucleosome

The structure of the SWI/SNF-remodeled nucleosome was characterized with single base-pair resolution by mapping the contacts of specific histone fold residues with nucleosomal DNA. We demonstrate that SWI/SNF peels up to 50 bp of DNA from the edge of the nucleosome, translocates the histone octamer beyond the DNA ends via a DNA bulge propagation mechanism, and promotes the formation of an intramolecular DNA loop between the nucleosomal entry and exit sites. This stable altered nucleosome conformation also exhibits alterations in the distance between contacts of specific histone residues with DNA and higher electrophoretic and sedimentation mobility, consistent with a more compact molecular shape. SWI/SNF converts a nucleosome to the altered state in less than 1 s, hydrolyzing fewer than 10 ATPs per event.

Relationship between expression of P-glycoprotein and efficacy of chemotherapy in gastric cancer

AIM: To investigate the significance of the expression of P-glycoprotein and the relationship between its expression and the efficacy of chemotherapy in patients with gastric cancer.

METHODS: P-glycoprotein was examined by immunohistochemical staining in 101 specimens of paraffin embedded gastric cancer tissues.

RESULTS: The expression rates of P-glycoprotein in normal gastric mucosa, paracancerous tissues and gastric cancer tissues were 13%, 22% and 43%, respectively (P < 0.05). The expression rates of P-glycoprotein in the highly and moderately differentiated tumors (58% and 80%, respectively) were significantly higher than those in the lowly and poorly differentiated tumors (36% and 25%, respectively) (P < 0.01). The postoperative cumulative survival rate of the patients receiving chemotherapy was significantly higher than that of the patients without chemotherapy in P-glycoprotein-negative patients with gastric cancer (P < 0.01).

CONCLUSION: The expression of P-glycoprotein was correlated with the degree of tumor differentiation and influenced the efficacy of postoperative chemotherapy.

hSWI/SNF-catalyzed nucleosome sliding does not occur solely via a twist-diffusion mechanism

Nucleosome remodeling by the hSWI/SNF complex and other chromatin remodeling complexes can cause translocation (sliding) of the histone octamer in cis along DNA. Structural and biochemical evidence suggest that sliding involves a DNA twist-diffusion process whereby the DNA rotates about the helical axis without major displacement from the surface of the nucleosome and that this process may be driven by torsional stress within the DNA. We report that hSWI/SNF efficiently catalyzes sliding of nucleosomes containing branched DNAs as steric blocks to twist-diffusion and a nick to allow dissipation of torsional stress within the nucleosome. These results suggest that SWI/SNF-catalyzed nucleosome sliding does not occur exclusively via a simple twist-diffusion mechanism and support models in which the DNA maintains its rotational orientation to and is at least partially separated from the histone surface during nucleosome translocation.

High-resolution mapping of changes in histone-DNA contacts of nucleosomes remodeled by ISW2

The imitation switch (ISWI) complex from yeast containing the Isw2 and Itc1 proteins was shown to preferentially slide mononucleosomes with as little as 23 bp of linker DNA from the end to the center of DNA. The contacts of unique residues in the histone fold regions of H4, H2B, and H2A with DNA were determined with base pair resolution before and after chromatin remodeling by a site-specific photochemical cross-linking approach. The path of DNA and the conformation of the histone octamer in the nucleosome remodeled or slid by ISW2 were not altered, because after adjustment for the new translational position, the DNA contacts at specific sites in the histone octamer had not been changed. Maintenance of the canonical nucleosome structure after sliding was also demonstrated by DNA photoaffinity labeling of histone proteins at specific sites within the DNA template. In addition, nucleosomal DNA does not become more accessible during ISW2 remodeling, as assayed by restriction endonuclease cutting. ISW2 was also shown to have the novel capability of counteracting transcriptional activators by sliding nucleosomes through Gal4-VP16 bound initially to linker DNA and displacing the activator from DNA.

Contributions of mass spectrometry in the study of nucleic acid-binding proteins and of nucleic acid-protein interactions

Nucleic-acid-protein (NA-P) interactions play essential roles in a variety of biological processes-gene expression regulation, DNA repair, chromatin structure regulation, transcription regulation, RNA processing, and translation-to cite only a few. Such biological processes involve a broad spectrum of NA-P interactions as well as protein-protein (P-P) interactions. These interactions are dynamic, in terms of the chemical composition of the complexes involved and in terms of their mere existence, which may be restricted to a given cell-cycle phase. In this review, the contributions of mass spectrometry (MS) to the deciphering of these intricate networked interactions are described along with the numerous applications in which it has proven useful. Such applications include, for example, the identification of the partners involved in NA-P or P-P complexes, the identification of post-translational modifications that (may) regulate such complexes' activities, or even the precise molecular mapping of the interaction sites in the NA-P complex. From a biological standpoint, we felt that it was worth the reader's time to be as informative as possible about the functional significance of the analytical methods reviewed herein. From a technical standpoint, because mass spectrometry without proper sample preparation would serve no purpose, each application described in this review is detailed by duly emphasizing the sample preparation-whenever this step is considered innovative-that led to significant analytical achievements.