Functionally distinct patterns of nucleosome remodeling at enhancers in glucocorticoid-treated acute lymphoblastic leukemia

Background

Precise nucleosome positioning is an increasingly recognized feature of promoters and enhancers, reflecting complex contributions of DNA sequence, nucleosome positioning, histone modification and transcription factor binding to enhancer activity and regulation of gene expression. Changes in nucleosome position and occupancy, histone variants and modifications, and chromatin remodeling are also critical elements of dynamic transcriptional regulation, but poorly understood at enhancers. We investigated glucocorticoid receptor-associated (GR) nucleosome dynamics at enhancers in acute lymphoblastic leukemia.

Results

For the first time, we demonstrate functionally distinct modes of nucleosome remodeling upon chromatin binding by GR, which we term central, non-central, phased, and minimal. Central and non-central remodeling reflect nucleosome eviction by GR and cofactors, respectively. Phased remodeling involves nucleosome repositioning and is associated with rapidly activated enhancers and induction of gene expression. Minimal remodeling sites initially have low levels of enhancer-associated histone modification, but the majority of these regions gain H3K4me2 or H3K27Ac to become de novo enhancers. Minimal remodeling regions are associated with gene ontologies specific to decreased B cell number and mTOR inhibition and may make unique contributions to glucocorticoid-induced leukemia cell death.

Conclusions

Our findings form a novel framework for understanding the dynamic interplay between transcription factor binding, nucleosome remodeling, enhancer function, and gene expression in the leukemia response to glucocorticoids.

Electronic supplementary material

The online version of this article (doi:10.1186/s13072-015-0046-0) contains supplementary material, which is available to authorized users.

Active nucleosome positioning beyond intrinsic biophysics is revealed by in vitro reconstitution

Genome-wide nucleosome maps revealed well-positioned nucleosomes as a major theme in eukaryotic genome organization. Promoter regions often show a conserved pattern with an NDR (nucleosome-depleted region) from which regular nucleosomal arrays emanate. Three mechanistic contributions to such NDR-array-organization and nucleosome positioning in general are discussed: DNA sequence, DNA binders and DNA-templated processes. Especially, intrinsic biophysics of DNA sequence preferences for nucleosome formation was prominently suggested to explain the majority of nucleosome positions ('genomic code for nucleosome positioning'). Nonetheless, non-histone factors that bind DNA with high or low specificity, such as transcription factors or remodelling enzymes respectively and processes such as replication, transcription and the so-called 'statistical positioning' may be involved too. Recently, these models were tested for yeast by genome-wide reconstitution. DNA sequence preferences as probed by SGD (salt gradient dialysis) reconstitution generated many NDRs, but only few individual nucleosomes, at their proper positions, and no arrays. Addition of a yeast extract and ATP led to dramatically more in vivo-like nucleosome positioning, including regular arrays for the first time. This improvement depended essentially on the extract and ATP but not on transcription or replication. Nucleosome occupancy and close spacing were maintained around promoters, even at lower histone density, arguing for active packing of nucleosomes against the 5' ends of genes rather than statistical positioning. A first extract fractionation identified a direct, specific, necessary, but not sufficient role for the RSC (remodels the structure of chromatin) remodelling enzyme. Collectively, nucleosome positioning in yeast is actively determined by factors beyond intrinsic biophysics, and in steady-state rather than at equilibrium.

A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast

Nucleosomes play an important role in gene regulation. Molecular studies observed that nucleosome binding in promoters tends to be repressive. In contrast, genomic studies have delivered conflicting results: An analysis of yeast grown on diverse carbon sources reported that nucleosome occupancies remain largely unchanged between conditions, whereas a study of the heat-shock response suggested that nucleosomes get evicted at promoters of genes with increased expression. Consequently, there are few general principles that capture the relationship between chromatin organization and transcriptional regulation. Here, we present a qualitative model for nucleosome positioning in Saccharomyces cerevisiae that helps explain important properties of gene expression. By integrating publicly available data sets, we observe that promoter-bound nucleosomes assume one of four discrete configurations that determine the active and silent transcriptional states of a gene, but not its expression level. In TATA-box-containing promoters, nucleosome architecture indicates the amount of transcriptional noise. We show that >20% of genes switch promoter states upon changes in cellular conditions. The data suggest that DNA-binding transcription factors together with chromatin-remodeling enzymes are primarily responsible for the nucleosome architecture. Our model for promoter nucleosome architecture reconciles genome-scale findings with molecular studies; in doing so, we establish principles for nucleosome positioning and gene expression that apply not only to individual genes, but across the entire genome. The study provides a stepping stone for future models of transcriptional regulation that encompass the intricate interplay between cis- and trans-acting factors, chromatin, and the core transcriptional machinery.

Variety of genomic DNA patterns for nucleosome positioning

Precise positioning of nucleosomes along DNA is important for a variety of gene regulatory processes. Among the factors directing nucleosome positioning, the DNA sequence is highly important. Two main classes of nucleosome positioning sequence (NPS) patterns have previously been described. In the first class, AA, TT, and other WW dinucleotides (where W is A or T) tend to occur together (in-phase) in the major groove of DNA closest to the histone octamer surface, while SS dinucleotides (where S is G or C) are predominantly positioned in the major groove facing outward. In the second class, AA and TT are structurally separated (AA backbone near the histone octamer, and TT backbone further away), but grouped with other RR (where R is purine A or G) and YY (where Y is pyrimidine C or T) dinucleotides. As a result, the RR/YY pattern includes counter-phase AA/TT distributions. We describe here anti-NPS patterns, which are inverse to the conventional NPS patterns: WW runs inverse to SS, and RR inverse to YY. Evidence for the biological relevance of anti-NPS patterns is presented.

Chromatin remodelers clear nucleosomes from intrinsically unfavorable sites to establish nucleosome-depleted regions at promoters

Most promoters in yeast contain a nucleosome-depleted region (NDR), but the mechanisms by which NDRs are established and maintained in vivo are currently unclear. We have examined how genome-wide nucleosome placement is altered in the absence of two distinct types of nucleosome remodeling activity. In mutants of both SNF2, which encodes the ATPase component of the Swi/Snf remodeling complex, and ASF1, which encodes a histone chaperone, distinct sets of gene promoters carry excess nucleosomes in their NDRs relative to wild-type. In snf2 mutants, excess promoter nucleosomes correlate with reduced gene expression. In both mutants, the excess nucleosomes occupy DNA sequences that are energetically less favorable for nucleosome formation, indicating that intrinsic histone-DNA interactions are not sufficient for nucleosome positioning in vivo, and that Snf2 and Asf1 promote thermodynamic equilibration of nucleosomal arrays. Cells lacking SNF2 or ASF1 still accomplish the changes in promoter nucleosome structure associated with large-scale transcriptional reprogramming. However, chromatin reorganization in the mutants is reduced in extent compared to wild-type cells, even though transcriptional changes proceed normally. In summary, active remodeling is required for distributing nucleosomes to energetically favorable positions in vivo and for reorganizing chromatin in response to changes in transcriptional activity.

Activator-independent transcription of Snf1-dependent genes in mutants lacking histone tails

Transcriptional regulation of Snf1-dependent genes occurs in part by histone-acetylation-dependent binding of the transcription factor Adr1. Analysis of previously published microarray data indicated unscheduled transcription of a large number of Snf1- and Adr1-dependent genes when either the histone H3 or H4 tail was deleted. Quantitative real-time PCR confirmed that the tails were important to preserve stringent transcriptional repression of Snf1-dependent genes when glucose was present. The absence of the tails allowed Adr1 and RNA Polymerase II to bind promoters in normally inhibitory conditions. The promoters escaped glucose repression to a limited extent and the weak constitutive ADH2 transcription induced by deletion of the histone tails was transcription factor- and Snf1-independent. These effects were apparently due to a permissive chromatin structure that allowed transcription in the absence of repression mediated by the histone tails. Deleting REG1, and thus activating Snf1 in the H3 tail mutant enhanced transcription in repressing conditions, indicating that Snf1 and the H3 tail influence transcription independently. Deleting REG1 in the histone H4 tail mutant appeared to be lethal, even in the absence of Snf1, suggesting that Reg1 and the H4 tail have redundant functions that are important for cell viability.

The RSC chromatin remodelling enzyme has a unique role in directing the accurate positioning of nucleosomes

Nucleosomes impede access to DNA. Therefore, nucleosome positioning is fundamental to genome regulation. Nevertheless, the molecular nucleosome positioning mechanisms are poorly understood. This is partly because in vitro reconstitution of in vivo-like nucleosome positions from purified components is mostly lacking, barring biochemical studies. Using a yeast extract in vitro reconstitution system that generates in vivo-like nucleosome patterns at S. cerevisiae loci, we find that the RSC chromatin remodelling enzyme is necessary for nucleosome positioning. This was previously suggested by genome-wide in vivo studies and is confirmed here in vivo for individual loci. Beyond the limitations of conditional mutants, we show biochemically that RSC functions directly, can be sufficient, but mostly relies on other factors to properly position nucleosomes. Strikingly, RSC could not be replaced by either the closely related SWI/SNF or the Isw2 remodelling enzyme. Thus, we pinpoint that nucleosome positioning specifically depends on the unique properties of the RSC complex.

Nucleosome dynamics and epigenetic stability

Nucleosome remodelling is an essential principle to assure that the packaging of eukaryotic genomes in chromatin remains flexible and adaptable to regulatory needs. Nucleosome remodelling enzymes spend the energy of ATP to alter histone–DNA interactions, to catalyse nucleosome displacement and reassembly, on histone exchange and on the relocation of histone octamers on DNA. Despite these dynamics, chromatin structures encode ‘epigenetic’ information that governs the expression of the underlying genes. These information-bearing structures must be maintained over extended periods of time in resting cells and may be sufficiently stable to resist the turmoil of the cell cycle to be passed on to the next cell generation. Intuitively, nucleosome remodelling should antagonize the maintenance of stable structures. However, upon closer inspection it becomes evident that nucleosome remodelling is intimately involved in the assembly of stable chromatin structures that correspond to functional states. Remodellers may even contribute structural information themselves. Their involvement can be seen at several structural levels: at the levels of positioning individual nucleosomes, homoeostasis of linker histones, histone variants and non-histone proteins, as well as the differential folding of the nucleosome fibre. All of them may contribute to the assembly of heritable epigenetic structures.

Gene regulation by nucleosome positioning

To achieve high compaction, most genomic DNA in eukaryotes is incorporated into nucleosomes; however, regulatory factors and transcriptional machinery must gain access to chromatin to extract genetic information. This conflict is partially resolved by a particular arrangement of nucleosome locations on the genome. Across all eukaryotic species, promoters and other regulatory sequences are more nucleosome-depleted, whereas transcribed regions tend to be occupied with well-positioned, high-density nucleosomal arrays. This nucleosome positioning pattern, as well as its dynamic regulation, facilitates the access of transcription factors to their target sites and plays a crucial role in determining the transcription level, cell-to-cell variation and activation or repression dynamics.

Crystal structures of nucleosome core particles containing the '601' strong positioning sequence

Nucleosome positioning plays a key role in genomic regulation by defining histone-DNA context and by modulating access to specific sites. Moreover, the histone-DNA register influences the double-helix structure, which in turn can affect the association of small molecules and protein factors. Analysis of genomic and synthetic DNA has revealed sequence motifs that direct nucleosome positioning in vitro; thus, establishing the basis for the DNA sequence dependence of positioning would shed light on the mechanics of the double helix and its contribution to chromatin structure in vivo. However, acquisition of well-diffracting nucleosome core particle (NCP) crystals is extremely dependent on the DNA fragment used for assembly, and all previous NCP crystal structures have been based on human α-satellite sequences. Here, we describe the crystal structures of Xenopus NCPs containing one of the strongest known histone octamer binding and positioning sequences, the so-called '601' DNA. Two distinct 145-bp 601 crystal forms display the same histone-DNA register, which coincides with the occurrence of DNA stretching-overtwisting in both halves of the particle around five double-helical turns from the nucleosome center, giving the DNA an 'effective length' of 147 bp. As we have found previously with stretching around two turns from the nucleosome center for a centromere-based sequence, the terminal stretching observed in the 601 constructs is associated with extreme kinking into the minor groove at purine-purine (pyrimidine-pyrimidine) dinucleotide steps. In other contexts, these step types display an overall nonflexible behavior, which raises the possibility that DNA stretching in the nucleosome or extreme distortions in general have unique sequence dependency characteristics. Our findings indicate that DNA stretching is an intrinsically predisposed site-specific property of the nucleosome and suggest how NCP crystal structures with diverse DNA sequences can be obtained.

Structural insight into the sequence dependence of nucleosome positioning

Nucleosome positioning displays sequence dependency and contributes to genomic regulation in a site-specific manner. We solved the structures of nucleosome core particle composed of strong positioning TTTAA elements flanking the nucleosome center. The positioning strength of the super flexible TA dinucleotide is consistent with its observed central location within minor groove inward regions, where it can contribute maximally to energetically challenging minor groove bending, kinking and compression. The marked preference for TTTAA and positioning power of the site 1.5 double helix turns from the nucleosome center relates to a unique histone protein motif at this location, which enforces a sustained, extremely narrow minor groove via a hydrophobic "sugar clamp." Our analysis sheds light on the basis of nucleosome positioning and indicates that the histone octamer has evolved not to fully minimize sequence discrimination in DNA binding.

The DNA sequence-dependence of nucleosome positioning in vivo and in vitro

The contribution of histone-DNA interactions to nucleosome positioning in vivo is currently a matter of debate. We argue here that certain nucleosome positions, often in promoter regions, in yeast may be, at least in part, specified by the DNA sequence. In contrast other positions may be poorly specified. Positioning thus has both statistical and DNA-determined components. We further argue that the relative affinity of the octamer for different DNA sequences can vary and therefore the interaction of histones with the DNA is a 'tunable' property.

Nucleosome positioning, nucleosome spacing and the nucleosome code

Nucleosome positioning has been the subject of intense study for many years. The properties of micrococcal nuclease, the enzyme central to these studies, are discussed. The various methods used to determine nucleosome positions in vitro and in vivo are reviewed critically. These include the traditional low resolution method of indirect end-labelling, high resolution methods such as primer extension, monomer extension and nucleosome sequencing, and the high throughput methods for genome-wide analysis (microarray hybridisation and parallel sequencing). It is established that low resolution mapping yields an averaged chromatin structure, whereas high resolution mapping reveals the weighted superposition of all the chromatin states in a cell population. Mapping studies suggest that yeast DNA contains information specifying the positions of nucleosomes and that this code is made use of by the cell. It is proposed that the positioning code facilitates nucleosome spacing by encoding information for multiple alternative overlapping nucleosomal arrays. Such a code might facilitate the shunting of nucleosomes from one array to another by ATP-dependent chromatin remodelling machines.