ATP-dependent Chromatin Remodeling Complexes Research Articles

Integrated Analysis Of Genomic and Gene Expression Profiles In Follicular Lymphoma Reveals Subsets and Driver Genes Of Potential Microenvironmental Importance

BackgroundThe immune microenvironment in follicular lymphoma (FL) impacts its clinical course, but the interaction between FL cells and host immune cells is poorly understood, and may be influenced by large genetic abnormalities in FL cells. Regions of copy number variation (CNV) and copy-neutral loss of heterozygosity (cnLOH) are detectable by single nucleotide polymorphism (SNP) arrays and frequently found in FL, but the critical “driver genes” within them are largely unidentified. MethodsCell suspensions from tumor biopsies of 66 untreated FL patients were sorted into “B cell” and non-B fractions by immunomagnetic depletion targeting CD3 or CD19 and CD20 respectively. High-resolution Illumina Omni5 SNP arrays were used to profile genomic DNA from B cell fractions and germline DNA (from non-B fractions or peripheral blood cells). Nexus Copy Number software (BioDiscovery) compared paired profiles to determine tumor-specific CNV and cnLOH abnormalities of each patient. Genes within overlapping recurrently-altered regions were identified by the JISTIC algorithm (PMID: 20398270). For 43 of these patients, whole-genome gene expression profiling (GEP) of both fractions was done on Illumina HT12v4 arrays. CONEXIC module network analysis (PMID: 21129771) identified candidate driver genes, based on correlation of their expression in B-cell fractions with that of modules of genes in B-cell or non-B fractions. ResultsComparing tumor vs. germline profiles in SNP array analysis clarified the detection of tumor-specific CNV, and enabled the detection of cnLOH. The aggregate genomic profile of regions affected by CNV in our 66 FL samples was highly similar to results of previous FL studies. Most frequent (each in 25-35% of samples) were deletions of 1p36 or a large part of 6q, amplifications of 1q, 7p/q, 12q, 17q, or 18p/q, and cnLOH at 16p. The distribution of these abnormalities suggested that FL can be divided into subgroups based on several large mutually-exclusive genomic aberrations: -10q, -16p, +12q, and, less clearly, -1p/1q+. Novel analysis combining copy number values with corresponding SNP frequencies also identified abnormalities of lower frequency within samples, suggestive of tumor subclones with potential growth advantages, notably including deletions at 13q14 and 19p12 and amplification of 16p13.JISTIC identified 715 expressed genes within amplified regions and 413 expressed genes within deleted regions (329 genes) or regions of cnLOH (84 genes). CONEXIC identified 62 and 68 of these genes as candidate drivers regulating expression of gene modules in tumor B cells and infiltrating immune cells, respectively. Several regulators of B-cell modules were already described in FL or other hematological malignancies: MDM2 (12q15, amplified in 26%), an E3 ubiquitin ligase whose targets include TP53; NME1 (17q21.33, amplified in 21%), part of the nucleoside diphosphate kinase complex, overexpressed and correlated with poor prognosis in AML; or B-cell receptor-associated CD79B (17q23.3, amplified in 21%), mutated and functionally significant in diffuse large B-cell lymphoma. Validating MDM2 as a driver gene, Gene Set Enrichment Analysis showed strong positive association between expression of MDM2 and that of proliferation signatures in B cells, including signatures of genes downregulated by TP53.Genes affecting the interaction between tumor B cells and the FL microenvironment plausibly regulate module expression in both B cells and non-B cells. Such dual candidate driver genes included PHIP (6q14.1, deleted in 27%), a binding partner of insulin receptor substrate-1, overexpressed in melanoma and linked to its metastasis and progression; SMARCC2 (12q13.2, amplified in 25%), part of the ATP-dependent chromatin remodeling complex SNF/SWI, mutated in some carcinomas; SFR1 (10q25.1, deleted in 18%), involved in DNA homologous recombination; and BUD31(7q22.1, amplified in 21%), a homolog of a yeast protein involved in pre-mRNA splicing. ConclusionsCNV and cnLOH abnormalities are frequent in FL, and may identify subgroups within FL. Integrated analysis finds known candidate driver genes within recurrently-altered regions, appearing to regulate expression of gene modules in B cells. Novel candidate driver genes that appear to regulate modules in both B and non-B cells may shape the FL microenvironment in important ways, and are being investigated experimentally. Disclosures:No relevant conflicts of interest to declare.

Tumor suppressor role of chromatin-remodeling factor ARID1A

The mammalian SWI/SNF complex is one of ATP-dependent chromatin-remodeling complexes, which plays important roles in cell proliferation, differentiation, development and tumor suppression. ARID1A (AT-rich interactive domain-containing protein 1A) is a large subunit of SWI/SNF complex, and also an ARID family member with non- sequence-specific DNA binding activity. ARID1A is a tumor suppressor gene which is frequently mutated in many cancers, such as ovarian, bladder and gastric cancers. ARID1A can suppress cell proliferation through the up-regulation of p21 and the down-regulation of E2F-responsive genes. These findings on ARID1A and its role of tumor suppression contribute to understanding the mechanism of cancer development and developing new therapy for cancer.It is introduced in the review that ARID1A basic characteristic, related to cancer development, and biological role for full understanding of ARID1A.

Molecular Architecture of the ATP-Dependent Chromatin-Remodeling Complex SWR1

SummaryThe ATP-dependent chromatin-remodeling complex SWR1 exchanges a variant histone H2A.Z/H2B dimer for a canonical H2A/H2B dimer at nucleosomes flanking histone-depleted regions, such as promoters. This localization of H2A.Z is conserved throughout eukaryotes. SWR1 is a 1 megadalton complex containing 14 different polypeptides, including the AAA+ ATPases Rvb1 and Rvb2. Using electron microscopy, we obtained the three-dimensional structure of SWR1 and mapped its major functional components. Our data show that SWR1 contains a single heterohexameric Rvb1/Rvb2 ring that, together with the catalytic subunit Swr1, brackets two independently assembled multisubunit modules. We also show that SWR1 undergoes a large conformational change upon engaging a limited region of the nucleosome core particle. Our work suggests an important structural role for the Rvbs and a distinct substrate-handling mode by SWR1, thereby providing a structural framework for understanding the complex dimer-exchange reaction.

Epigenetic control of cell fate in mouse blastocysts: The role of covalent histone modifications and chromatin remodeling

The first cell-fate decision in mammalian preimplantation embryos is the segregation of the inner cell mass (ICM) and trophectoderm (TE) cell lineages. The ICM develops into the embryo proper, whereas the TE ensures embryo implantation and is the source of the extra-embryonic trophoblast cell lineages, which contribute to the functional components of the placenta. The development of a totipotent zygote into a multi-lineage blastocyst is associated with the generation of distinct transcriptional programs. Several key transcription factors participate in the ICM and TE-specific transcriptional networks, and recent studies indicate that post-translational histone modifications as well as ATP-dependent chromatin remodeling complexes converge with these transcriptional networks to regulate ICM and TE lineage specification. This review will discuss our current understanding and future perspectives related to transcriptional and epigenetic regulatory mechanisms that are implicated in the initial mammalian lineage commitment steps, with a focus on events in mice.

The ATP-dependent Chromatin Remodeling Enzyme Fun30 Represses Transcription by Sliding Promoter-proximal Nucleosomes

The evolutionarily conserved ATP-dependent chromatin remodeling enzyme Fun30 has recently been shown to play important roles in heterochromatin silencing and DNA repair. However, how Fun30 remodels nucleosomes is not clear. Here we report a nucleosome sliding activity of Fun30 and its role in transcriptional repression. We observed that Fun30 repressed the expression of genes involved in amino acid and carbohydrate metabolism, the stress response, and meiosis. In addition, Fun30 was localized at the 5' and 3' ends of genes and within the open reading frames of its targets. Consistent with its role in gene repression, we observed that Fun30 target genes lacked histone modifications often associated with gene activation and showed an increased level of ubiquitinated histone H2B. Furthermore, a genome-wide nucleosome mapping analysis revealed that the length of the nucleosome-free region at the 5' end of a subset of genes was changed in Fun30-depleted cells. In addition, the positions of the -1, +2, and +3 nucleosomes at the 5' end of target genes were shifted significantly, whereas the position of the +1 nucleosome remained largely unchanged in the fun30Δ mutant. Finally, we demonstrated that affinity-purified, single-component Fun30 exhibited a nucleosome sliding activity in an ATP-dependent manner. These results define a role for Fun30 in the regulation of transcription and indicate that Fun30 remodels chromatin at the 5' end of genes by sliding promoter-proximal nucleosomes.

Coffin–Siris syndrome is a SWI/SNF complex disorder

Coffin-Siris syndrome (CSS) is a congenital disorder characterized by intellectual disability, growth deficiency, microcephaly, coarse facial features, and hypoplastic or absent fifth fingernails and/or toenails. We previously reported that five genes are mutated in CSS, all of which encode subunits of the switch/sucrose non-fermenting (SWI/SNF) ATP-dependent chromatin-remodeling complex: SMARCB1, SMARCA4, SMARCE1, ARID1A, and ARID1B. In this study, we examined 49 newly recruited CSS-suspected patients, and re-examined three patients who did not show any mutations (using high-resolution melting analysis) in the previous study, by whole-exome sequencing or targeted resequencing. We found that SMARCB1, SMARCA4, or ARID1B were mutated in 20 patients. By examining available parental samples, we ascertained that 17 occurred de novo. All mutations in SMARCB1 and SMARCA4 were non-truncating (missense or in-frame deletion) whereas those in ARID1B were all truncating (nonsense or frameshift deletion/insertion) in this study as in our previous study. Our data further support that CSS is a SWI/SNF complex disorder.

Isw1a does not have strict limitations on the length of extranucleosomal DNAs for mobilization of nucleosomes assembled with HeLa cell histones

The Saccharomyces cerevisiae Isw1a and Isw2 ATP-dependent chromatin-remodeling complexes have important roles in vivo in the regulation of nucleosome positioning and modulation of gene activity. We studied the ability of the Isw1a- and Isw2-remodeling enzymes to reposition nucleosomes in mono- and dinucleosomes templates with variably positioned histone octamers (in the center or at the ends of the DNA fragment). To compare the Isw1a and Isw2 nucleosome-mobilizing activities, we utilized mono- and dinucleosome templates reconstituted with purified HeLa cell histones and DNA containing one or two copies of the “601” nucleosome high-affinity sequence used to specifically position nucleosomes on the DNA. The obtained data suggest that Isw1a is able to mobilize HeLa cell histone-assembled mononucleosomes with long (more than 30 bp) extranucleosomal DNAs protruding from both sides, which contrasts to the previously reported inability of Isw1 to mobilize similar nucleosomes assembled with recombinant yeast histones. The results also suggest that Isw1a and Isw2 can mobilize nucleosomes with unfavorably short linker DNA lengths, and the presence of internucleosomal interactions promotes mobilization of nucleosomes even when the linkers are short.

Placing the HIRA Histone Chaperone Complex in the Chromatin Landscape

The HIRA chaperone complex, comprised of HIRA, UBN1, and CABIN1, collaborates with histone-binding protein ASF1a to incorporate histone variant H3.3 into chromatin in a DNA replication-independent manner. To better understand HIRA's function and mechanism, we integrated HIRA, UBN1, ASF1a, and histone H3.3 chromatin immunoprecipitation sequencing and gene expression analyses. Most HIRA-binding sites colocalize with UBN1, ASF1a, and H3.3 at active promoters and active and weak/poised enhancers. At promoters, binding of HIRA/UBN1/ASF1a correlates with the level of gene expression. HIRA is required for deposition of histone H3.3 at its binding sites. There are marked differences in nucleosome and coregulator composition at different classes of HIRA-bound regulatory sites. Underscoring this, we report physical interactions between the HIRA complex and transcription factors, a chromatin insulator and an ATP-dependent chromatin-remodeling complex. Our results map the distribution of the HIRA chaperone across the chromatin landscape and point to different interacting partners at functionally distinct regulatory sites.

Brg1-dependent epigenetic control of vascular smooth muscle cell proliferation by hydrogen sulfide

Hydrogen sulfide (H2S) can modulate the proliferation of vascular smooth muscle cells. This study was designed to investigate the epigenetic control of vascular smooth muscle cell proliferation in response to H2S. Microarray analysis indicated that Brahma-related gene 1 (Brg1) and proliferation-related genes including proliferating cell nuclear antigen (Pcna), neurotrophin 3 (Ntf3) and platelet-derived growth factor subunit A (Pdgfα) were significantly downregulated by H2S in endothelin-1-stimulated proliferative vascular smooth muscle cells. Brg1 is the central catalytic subunit of the SWI/SNF apparatus (an ATP-dependent chromatin remodeling complex). Overexpression and knockdown of Brg1 confirmed that Brg1 was crucial for H2S-induced inhibition of vascular smooth muscle cell proliferation. A luciferase reporter assay, real-time PCR and Western blotting demonstrated that H2S inhibited Brg1 transcription and expression. A DNase I hypersensitivity assay revealed that H2S reversed endothelin-1-stimulated Pcna, Ntf3 and Pdgfα chromatin remodeling and vascular smooth muscle cell proliferation. A chromatin immunoprecipitation assay indicated that H2S inhibited the recruitment of Brg1 to the Pcna, Ntf3 and Pdgfα promoters. The results of this study indicate that H2S inhibits vascular smooth muscle cell proliferation via an epigenetic mechanism involving the inhibition of Brg1 transcription and expression, and by reducing the recruitment of Brg1 to the Pcna, Ntf3 and Pdgfα promoter regions.

S-nitrosylation of HDAC2 regulates the expression of the chromatin-remodeling factor Brm during radial neuron migration.

Dynamic epigenetic modifications play a key role in mediating the expression of genes required for neuronal development. We previously identified nitric oxide (NO) as a signaling molecule that mediates S-nitrosylation of histone deacetylase 2 (HDAC2) and epigenetic changes in neurons. Here, we show that HDAC2 nitrosylation regulates neuronal radial migration during cortical development. Bead-array analysis performed in the developing cortex revealed that brahma (Brm), a subunit of the ATP-dependent chromatin-remodeling complex BRG/brahma-associated factor, is one of the genes regulated by S-nitrosylation of HDAC2. In the cortex, expression of a mutant form of HDAC2 that cannot be nitrosylated dramatically inhibits Brm expression. Our study identifies NO and HDAC2 nitrosylation as part of a signaling pathway that regulates cortical development and the expression of Brm in neurons.

Interactions of Nuclear Actin-Related Proteins with SWI/SNF Chromatin-Remodeling Complexes

ATP-dependent chromatin-remodeling complexes (remodelers) modulate chromatin structure and thus play important roles in transcription, DNA replication, and DNA repair. Nuclear actin and actin-related proteins (Arps) are subunits of several such complexes, where they are commonly found in pairs. However, the role of actin/Arps and the mechanism through which they bind the catalytic subunits of their host complexes are unknown. Here, we investigated how budding yeast Arp7 and Arp9 are incorporated into SWI/SNF-family chromatin-remodeling complexes. We present the first biochemical evidence that Arp7 and Arp9 must heterodimerize to bind ATP and interact with the catalytic subunits of the SWI/SNF and RSC complexes. In addition, we present ITC data, which define the remodeler region that interacts with Arp7/9, thus providing a mechanistic framework for understanding how actin/Arps are selectively loaded into their host remodelers.

A SWI/SNF Chromatin-Remodeling Complex Acts in Noncoding RNA-Mediated Transcriptional Silencing

SummaryRNA-mediated transcriptional silencing prevents deleterious effects of transposon activity and controls the expression of protein-coding genes. It involves long noncoding RNAs (lncRNAs). In Arabidopsis thaliana, some of those lncRNAs are produced by a specialized RNA Polymerase V (Pol V). The mechanism by which lncRNAs affect chromatin structure and mRNA production remains mostly unknown. Here we identify the SWI/SNF ATP-dependent nucleosome-remodeling complex as a component of the RNA-mediated transcriptional silencing pathway. We found that SWI3B, an essential subunit of the SWI/SNF complex, physically interacts with a lncRNA-binding protein, IDN2. SWI/SNF subunits contribute to lncRNA-mediated transcriptional silencing. Moreover, Pol V mediates stabilization of nucleosomes on silenced regions. We propose that Pol V-produced lncRNAs mediate transcriptional silencing by guiding the SWI/SNF complex and establishing positioned nucleosomes on specific genomic loci. We further propose that guiding ATP-dependent chromatin-remodeling complexes may be a more general function of lncRNAs.

1662P - MCPH1 (BRIT1) and Outcome to Erlotinib in Non-Small-Cell Lung Cancer (NSCLC) Patients (P) Harboring EGFR Mutations

ABSTRACT Background Progression-free survival (PFS) in EGFR-mutant NSCLC p treated with erlotinib can range from a few months (m) to more than two years, but genetic influences on the duration of response remain unclear. The cytotoxic effect of erlotinib has been related to several proteins that regulate DNA damage response (eg, BRCA1, BRCA2). MCPH1 contains 3 BRCT domains which are conserved in important molecules involved in DNA damage signaling, including BRCA1, MDC1 and 53BP1. MCPH1 binds to BRCA2 and regulates the localization of BRCA2 and Rad51 at sites of DNA damage. MCPH1 also regulates the ATP-dependent SWI-SNF chromatin remodeling complex during DNA repair. Methods We used the NanoString nCounter gene expression system, which captures and counts individual mRNA transcripts, to analyze the expression of 44 selected genes, many of which are involved in DNA damage response, in 55 erlotinib-treated NSCLC p. We identified MCPH1 and correlated expression levels with clinical outcomes. Results p characteristics: 16 males, 39 females (70.9%); 39 never-smokers (70.9%), 12 former smokers, 4 current smokers; 34 with EGFR deletion in exon 19 (61.8%), 21 with L858R mutation (38.2%). PFS was not reached for patients with high MCPH1, while it was 19 m for those with intermediate levels and 9 m for those with low levels (P = 0.01). Median survival was 31 m for p with high levels, not reached for p with intermediate levels and 17 m for p with low levels (P = 0.004). Conclusions The enhanced effect of erlotinib in the presence of elevated MCPH1 could be due to the fact that MCPH1 can interfere with the function of MDC1 and 53BP1. The role of MCPH1 merits validation as a predictive marker of erlotinib response. Disclosure All authors have declared no conflicts of interest.

Molecular mechanisms of chromatin transcription by RNA polymerase III. Part 1

Chromatin provides for the dense packing of DNA in eukaryotic cell nuclei and its proper functioning. The present review describes mechanisms of chromatin transcription by RNA polymerase III (RNAP III). This mechanism is characteristic of eukaryotic RNAP III, some bacteriophage RNAPs, and many ATP-dependent chromatin remodeling complexes. During the remodeling of chromatin according to this mechanism, nucleosomes move along the DNA molecule without octamer release into the liquid phase.

Rsf-1/HBXAP overexpression is independent of gene amplification and is associated with poor outcome in patients with urinary bladder urothelial carcinoma

BackgroundsUrothelial carcinoma of the urinary bladder (UCUB) is prevalent in developed countries. It often shows genetic instability and is associated with amplification (or gain) of various oncogenic genes or suppressive...

New transcription regulatory mechanisms of latent HIV LTR

Despite the effectiveness of antiretroviral medication, the HIV virus persists in resting memory T cells of infected patients in a latent state, providing the main impediment to eradication of the virus. We are interested in identifying the molecular mechanism responsible for the establishment and maintenance of HIV latency and its re-activation. We recently used a cell system reflecting HIV latency in my lab to determine the high resolution nucleosomal landscape of the latent HIV LTR and examine its dynamic changes upon re-activation (Rafati et al., Nov 2011 PLoS Biology). We combined mathematical predictions of nucleosome positioning with a combinatorial biochemical approach based on formaldehyde crosslinking of latent and activated HIV infected cells (using FAIRE, ChIP and high resolution MNase nucleosomal mapping) to define LTR nucleosome positioning and regulation during active and latent HIV infections. We found that BAF, an ATP-dependent chromatin remodelling complex generates a chromatin structure at the LTR that is energetically unfavorable to its intrinsic histone-DNA sequence preferences. Specifically, we find that BAF positions a repressive nucleosome immediately downstream of the HIV transcription start site, abrogating transcription, and in this way contributes to the establishment and maintenance of HIV latency. Our data describe a novel molecular mechanism for the establishment and maintenance of HIV latency, and we identify the catalytic subunit of BAF, the enzyme BRG1, as a putative molecular target to deplete the latent reservoir in infected patients. We will also present preliminary data addressing the role of a novel signalling pathway in de-repression of latent HIV, and the effect of small molecules and ligands, which activate this pathway to study reactivation of latent HIV. We anticipate these experiments will further our understanding of HIV transcription regulation and identify both novel cofactors for targeting and molecules with potential to purge HIV latency.

Chromatin-remodeling complex specificity and embryonic vascular development

Vascular development is a dynamic process that relies on the coordinated expression of numerous genes, but the factors that regulate gene expression during blood vessel development are not well defined. ATP-dependent chromatin-remodeling complexes are gaining attention for their specific temporal and spatial effects on gene expression during vascular development. Genetic mutations in chromatin-remodeling complex subunits are revealing roles for the complexes in vascular signaling pathways at discrete developmental time points. Phenotypic analysis of these models at various stages of vascular development will continue to expand our understanding of how chromatin remodeling impacts new blood vessel growth. Such research could also provide novel therapeutic targets for the treatment of vascular pathologies.

MCPH1 (BRIT1) and outcome to erlotinib in non-small cell lung cancer (NSCLC) patients (p) harboring EGFR mutations.

e18131 Background: Progression-free survival (PFS) in EGFR-mutant NSCLC p treated with erlotinib can range from a few months (m) to more than two years, but genetic influences on the duration of response remain unclear. The cytotoxic effect of erlotinib has been related to several proteins that regulate DNA damage response (eg, BRCA1, BRCA2). MCPH1 contains 3 BRCT domains which are conserved in important molecules involved in DNA damage signaling, including BRCA1, MDC1 and 53BP1. MCPH1 binds to BRCA2 and regulates the localization of BRCA2 and Rad51 at sites of DNA damage. MCPH1 also regulates the ATP-dependent SWI-SNF chromatin remodeling complex during DNA repair. Methods: We used the NanoString nCounter gene expression system, which captures and counts individual mRNA transcripts, to analyze the expression of 44 selected genes, many of which are involved in DNA damage response, in 55 erlotinib-treated NSCLC p. We identified MCPH1 and correlated expression levels with clinical outcomes. Results: p characteristics: 16 males, 39 females (70.9%); 39 never-smokers (70.9%), 12 former smokers, 4 current smokers; 34 with EGFR deletion in exon 19 (61.8%), 21 with L858R mutation (38.2%). PFS was not reached for patients with high MCPH1, while it was 19 m for those with intermediate levels and 9 m for those with low levels (P=0.01). Median survival was 31 m for p with high levels, not reached for p with intermediate levels and 17 m for p with low levels (P=0.004). Conclusions: The enhanced effect of erlotinib in the presence of elevated MCPH1 could be due to the fact that MCPH1 can interfere with the function of MDC1 and 53BP1. The role of MCPH1 merits validation as a predictive marker of erlotinib response.

MiR-124-regulated RhoG reduces neuronal process complexity via ELMO/Dock180/Rac1 and Cdc42 signalling

The small GTPase RhoG plays a central role in actin remodelling during diverse biological processes such as neurite outgrowth, cell migration, phagocytosis of apoptotic cells, and the invasion of pathogenic bacteria. Although it is known that RhoG stimulates neurite outgrowth in the rat pheochromocytoma PC12 cell line, neither the physiological function nor the regulation of this GTPase in neuronal differentiation is clear. Here, we identify RhoG as an inhibitor of neuronal process complexity, which is regulated by the microRNA miR-124. We find that RhoG inhibits dendritic branching in hippocampal neurons in vitro and in vivo. RhoG also inhibits axonal branching, acting via an ELMO/Dock180/Rac1 signalling pathway. However, RhoG inhibits dendritic branching dependent on the small GTPase Cdc42. Finally, we show that the expression of RhoG in neurons is suppressed by the CNS-specific microRNA miR-124 and connect the regulation of RhoG expression by miR-124 to the stimulation of neuronal process complexity. Thus, RhoG emerges as a cellular conductor of Rac1 and Cdc42 activity, in turn regulated by miR-124 to control axonal and dendritic branching.

The chromatin remodeling complex NuRD establishes the poised state of rRNA genes characterized by bivalent histone modifications and altered nucleosome positions

rRNA genes (rDNA) exist in two distinct epigenetic states, active promoters being unmethylated and marked by euchromatic histone modifications, whereas silent ones are methylated and exhibit heterochromatic features. Here we show that the nucleosome remodeling and deacetylation (NuRD) complex establishes a specific chromatin structure at rRNA genes that are poised for transcription activation. The promoter of poised rRNA genes is unmethylated, associated with components of the preinitiation complex, marked by bivalent histone modifications and covered by a nucleosome in the "off" position, which is refractory to transcription initiation. Repression of rDNA transcription in growth-arrested and differentiated cells correlates with elevated association of NuRD and increased levels of poised rRNA genes. Reactivation of transcription requires resetting the promoter-bound nucleosome into the "on" position by the DNA-dependent ATPase CSB (Cockayne syndrome protein B). The results uncover a unique mechanism by which ATP-dependent chromatin remodeling complexes with opposing activities establish a specific chromatin state and regulate transcription.