Selective digestion of transcriptionally active ovalbumin genes from oviduct nuclei

Are extraordinary nucleosome structures more ordinary than we thought?

The nucleosome is a DNA-protein assembly that is the basic unit of chromatin. A nucleosome can adopt various structures. In the canonical nucleosome structure, 145-147 bp of DNA is wrapped around a histone heterooctamer. The strong histone-DNA interactions cause the DNA to be inaccessible for nuclear processes such as transcription. Therefore, the canonical nucleosome structure has to be altered into different, non-canonical structures to increase DNA accessibility. While it is recognised that non-canonical structures do exist, these structures are not well understood. In this review, we discuss both the evidence for various non-canonical nucleosome structures in the nucleus and the factors that are believed to induce these structures. The wide range of non-canonical structures is likely to regulate the amount of accessible DNA, and thus have important nuclear functions.

Chromatin structure-dependent histone incorporation revealed by a genome-wide deposition assay

In eukaryotes, histone variant distribution within the genome is the key epigenetic feature. To understand how each histone variant is targeted to the genome, we developed a new method, the RhIP (Reconstituted histone complex Incorporation into chromatin of Permeabilized cell) assay, in which epitope-tagged histone complexes are introduced into permeabilized cells and incorporated into their chromatin. Using this method, we found that H3.1 and H3.3 were incorporated into chromatin in replication-dependent and -independent manners, respectively. We further found that the incorporation of histones H2A and H2A.Z mainly occurred at less condensed chromatin (open), suggesting that condensed chromatin (closed) is a barrier for histone incorporation. To overcome this barrier, H2A, but not H2A.Z, uses a replication-coupled deposition mechanism. Our study revealed that the combination of chromatin structure and DNA replication dictates the differential histone deposition to maintain the epigenetic chromatin states.

Genome-Wide Characterization of DNase I-Hypersensitive Sites and Cold Response Regulatory Landscapes in Grasses

Deep sequencing of DNase-I treated chromatin (DNase-seq) can be used to identify DNase I-hypersensitive sites (DHSs) and facilitates genome-scale mining of de novo cis-regulatory DNA elements. Here, we adapted DNase-seq to generate genome-wide maps of DHSs using control and cold-treated leaf, stem, and root tissues of three widely studied grass species: Brachypodium distachyon, foxtail millet (Setaria italica), and sorghum (Sorghum bicolor). Functional validation demonstrated that 12 of 15 DHSs drove reporter gene expression in transiently transgenic B. distachyon protoplasts. DHSs under both normal and cold treatment substantially differed among tissues and species. Intriguingly, the putative DHS-derived transcription factors (TFs) are largely colocated among tissues and species and include 17 ubiquitous motifs covering all grass taxa and all tissues examined in this study. This feature allowed us to reconstruct a regulatory network that responds to cold stress. Ethylene-responsive TFs SHINE3, ERF2, and ERF9 occurred frequently in cold feedback loops in the tissues examined, pointing to their possible roles in the regulatory network. Overall, we provide experimental annotation of 322,713 DHSs and 93 derived cold-response TF binding motifs in multiple grasses, which could serve as a valuable resource for elucidating the transcriptional networks that function in the cold-stress response and other physiological processes.

The chromatin Remodeler CHD8 is required for activation of progesterone receptor-dependent enhancers

While the importance of gene enhancers in transcriptional regulation is well established, the mechanisms and the protein factors that determine enhancers activity have only recently begun to be unravelled. Recent studies have shown that progesterone receptor (PR) binds regions that display typical features of gene enhancers. Here, we show by ChIP-seq experiments that the chromatin remodeler CHD8 mostly binds promoters under proliferation conditions. However, upon progestin stimulation, CHD8 re-localizes to PR enhancers also enriched in p300 and H3K4me1. Consistently, CHD8 depletion severely impairs progestin-dependent gene regulation. CHD8 binding is PR-dependent but independent of the pioneering factor FOXA1. The SWI/SNF chromatin-remodelling complex is required for PR-dependent gene activation. Interestingly, we show that CHD8 interacts with the SWI/SNF complex and that depletion of BRG1 and BRM, the ATPases of SWI/SNF complex, impairs CHD8 recruitment. We also show that CHD8 is not required for H3K27 acetylation, but contributes to increase accessibility of the enhancer to DNaseI. Furthermore, CHD8 was required for RNAPII recruiting to the enhancers and for transcription of enhancer-derived RNAs (eRNAs). Taken together our data demonstrate that CHD8 is involved in late stages of PR enhancers activation.

A lot of research has been devoted during the last decades to understand the mechanisms that control gene promoters activity, however, much less is known about enhancers. Only recently, the use of genome-wide chromatin immunoprecipitation techniques has revealed the existence of more than 400,000 enhancers in the human genome. We are starting to understand the importance of these regulatory elements and how they are activated or repressed. In this work we discover that the chromatin remodeler CHD8 is recruited to Progesteron Receptor-dependent enhancers upon hormone treatment. CHD8 is required for late steps in the activation of these enhancers, including transcription of the enhancers and synthesis of eRNA (long noncoding RNAs derived form the enhancers).

Constitutive and anaerobically induced DNase-I-hypersensitive sites in the 5' region of the maize Adh1 gene

DNase-I-hypersensitive sites have been characterized in a plant gene, maize Adh1 (which encodes alcohol dehydrogenase 1). It has been generally recognized in animal genes that the chromatin of the 5' flanking region can be characterized by the accessibility of its DNA to the nuclease DNase I (EC 3.1.21.1), indicating which areas in the promoter are "open" to nuclear factors. The 5' region of the maize Adh1 gene contains two distinct DNase-I-hypersensitive regions, one constitutively present from position -160 to -700 and one that is anaerobically induced from position -35 to -150. The constitutive region contains three major hypersensitive sites, one of which corresponds in part to a region of potential Z-DNA. The induced hypersensitive region includes TATAA at -38 and CAAT at -100 as well as other potential regulatory sequences.

The chromatin of active genes is not in a permanently open conformation

Quantitative measurements of local chromatin accessibility to DNase I in 15-day chicken embryo erythrocyte nuclei have been performed using a range of nuclease concentrations and real-time TaqMan PCR to monitor the loss of short ( approximately 80 bp) amplicons. At the beta-globin locus, well-established DNase I hypersensitive sites stand out against a background in which actively transcribed gene sequences (e.g., beta-adult and beta-hatching) are no more sensitive than the nearby constitutive heterochromatin that has previously been shown to form the 30-nm fibre structure. Similar observations were made at the lysozyme locus containing the active Gas41 gene and also at the GAPDH locus. We conclude that active genes are not continuously held in an open 'beads-on-a-string' configuration, but adopt a 30-nm-type structure most of the time. This implies that the compact nucleosomal supercoil re-forms in the wake of the polymerase complex.

Higher-Order Structural Determinants for Expression of the Ovalbumin Gene Family

The ovalbumin gene and the ovalbumin-related X and Y genes are expressed in the chicken oviduct in response to steroid hormones. These three genes are linked within a 100 kb domain of DNA which is preferentially sensitive to DNase I digestion in oviduct cell nuclei. No such preferential sensitivity to DNase is observed in nuclei isolated from other chicken tissues in which these genes are not transcribed. Thus, the DNase I sensitivity observed is correlated with the capacity for these genes to be expressed in oviduct. We have asked the question: are there specific signals in the DNA which are responsible for defining this domain or for conferring upon it the active, DNase I-sensitive, conformation? We have located DNA sequences belonging to a single repetitive DNA family, termed CR1, which are preferentially located in or near the boundary regions of the 100 kb domain. Therefore, these CR1 sequences are possible candidates for such a function. We have also searched for, but have not observed, any tissue-specific rearrangements of the DNA in the boundary regions of the domain. It is therefore unlikely that DNA rearrangements are involved in establishing the DNase I-sensitive domain in oviduct cells. However, we do note that a region at the far 3' end of the domain exhibits a cytidine methylation pattern which is highly variable among different chicken tissues. In particular, this region, which is approximately 30 kb downstream from the ovalbumin gene, is undermethylated in oviduct as compared to other hen tissues, and thus could be a control region involved in domain activation.

Gene memory in neuroendocrine and behavioural systems

Several examples of sex steroid hormone actions on rat brain and behaviour show that initial hormone exposures may be followed by enduring neuronal alterations, apparent long after the hormone itself has disappeared. Precedents from non-neuronal systems led to the concept of 'gene memory'. We are studying genomic structural alterations in rat hypothalamic neurons to account for these effects. The preproenkephalin gene is turned on by oestradiol in rat brain neurons in a tissue-specific and genetic sex-specific manner. Levels of preproenkephalin mRNA in the ventromedial hypothalamus correlate tightly with oestradiol-dependent reproductive behaviour. Our results indicate a tissue-specific pattern of DNA methylation in the enkephalin promoter. Putative binding sites for several transcription factors have been described in the preproenkephalin gene promoter; a role for some of these factors in regulating expression of the gene has been demonstrated.

Domain-wide displacement of histones by activated heat shock factor occurs independently of Swi/Snf and is not correlated with RNA polymerase II density

We show that histone-DNA interactions are disrupted across entire yeast heat shock genes upon their transcriptional activation. At HSP82, nucleosomal disassembly spans a domain of approximately 3 kb, beginning upstream of the promoter and extending through the transcribed region. A kinetic analysis reveals that histone H4 loses contact with DNA within 45 s of thermal upshift. Nucleosomal reassembly, prompted by temperature downshift, is also rapid, detectable within 60 s. Prior to their eviction, promoter-associated histones are transiently hyperacetylated, while those in the coding region are not. An upstream activation sequence mutation that weakens the binding of heat shock factor obviates domain-wide remodeling, while deletion of the TATA box that nearly abolishes transcription is permissive to 5'-end remodeling. The Swi/Snf complex is rapidly recruited to HSP82 upon heat shock. Nonetheless, domain-wide remodeling occurs efficiently in Swi/Snf mutants despite a sixfold reduction in transcription; it is also seen in gcn5Delta, set1Delta, and paf1Delta mutants. Contrary to current models, we demonstrate that a high density of RNA polymerase (Pol) is insufficient to elicit histone displacement. This finding suggests that histone eviction is modulated by factors that are not linked to elongating Pol II. It further suggests that histone depletion plays a causal role in mediating vigorous transcription in vivo and is not merely a consequence of it.

Mechanisms of epigenetic silencing of the c21 gene in Y1 adrenocortical tumor cells

We utilized Y1 adrenocortical carcinoma cell line as a model system to dissect the events regulating epigenomic gene silencing in tumor cells. We show here that the chromatin structure of c21 gene is inactive in Y1 cells and that it could be reconfigured to an active form by either expressing antisense mRNA to DNA methyltransferase 1 (dnmt1) or an attenuator of Ras protooncogenic signaling hGAP. Surprisingly however, the known inducer of active chromatin structure the histone deacetylase inhibitor trichostatin A TSA fails to induce expression of c21. These results suggest that the primary cause of c21 gene silencing is independent of histone deacetylation. We present a model to explain the possible roles of the different components of the epigenome and the DNA methylation and demethylation machineries in silencing c21 gene expression.

Deoxyribonucleic acid methylation and chromatin organization in Tetrahymena thermophila

Deoxyribonucleic acid (DNA) of the transcriptionally active macronucleus of Tetrahymena thermophila is methylated at the N6 position of adenine to produce methyladenine (MeAde); approximately 1 in every 125 adenine residues (0.8 mol%) is methylated. Transcriptionally inert micronuclear DNA is not methylated (< or = 0.01 mol% MeAde; M. A. Gorovsky, S. Hattman, and G. L. Pleger, J. Cell Biol. 56:697-701, 1973). There is no detectable cytosine methylation in macronuclei in Tetrahymena DNA (< or = 0.01 mol% 5-methylcytosine). MeAde-containing DNA sequences in macronuclei are preferentially digested by both staphylococcal nuclease and pancreatic deoxyribonuclease I. In contrast, there is no preferential release of MeAde during digestion of purified DNA. These results indicate that MeAde residues are predominantly located in "linker DNA" and perhaps have a function in transcription. Pulse-chase studies showed that labeled MeAde remains preferentially in linker DNA during subsequent rounds of DNA replication; i.e., there is little, if any, movement of nucleosomes during chromatin replication. This implies that nucleosomes may be phased with respect to DNA sequence.

Structural analysis of mouse rDNA: coincidence between nuclease hypersensitive sites, DNA curvature and regulatory elements in the intergenic spacer

We have analyzed the chromatin structure of mouse ribosomal RNA genes (rDNA) by partial digestion of genomic DNA with micrococcal nuclease (MNase), DNase I and identified hypersensitive sites by indirect end-labeling. This analysis has revealed defined regions of nuclease hypersensitivity in the intergenic spacer which in turn coincide with regulatory elements. Hypersensitive sites map to the transcription initiation site, the enhancer repeats, the spacer promoter and two sequence elements which coincide with amplification-promoting sequences. Analysis of the DNA curvature by computer modeling uncovered a striking correlation between sequence-directed structural features of regulatory regions and the position of nuclease hypersensitive sites. Moreover, we demonstrate that nucleosomes are specifically positioned upstream and downstream of the transcription start site. In vitro studies using chromatin assembled in the presence of Drosophila embryo extracts show that binding of the transcription termination factor TTF-I to the upstream terminator mediates this specific nucleosome positioning at the rDNA promoter in an ATP- dependent fashion.

DNA exposure and condensation in the X and 21 chromosomes

Fluorescence in situ hybridization (FISH) whole chromosome painting probe studies have been carried out with X and 21 chromosomes on normal human fibroblasts grown in tissue culture. The majority of the cells were in G1 phase (including G0). The X chromosome, which exhibits differential inactivation, displays an active form which is most commonly in the nuclear periphery, is diffused over a large area with dark regions interspersed with bright regions, and exhibits punctate bright spots at its edges. The inactive X, which contains a small fraction of active genes, is also most often at the nuclear periphery, is highly condensed and also exhibits punctate labeling around its outer edge. Occasional nuclei exhibit X chromosomal material adjacent to a nucleolus. These observations fit the pattern proposed by the genome exposure theory in which inactive gene regions are sequestered by chromosome condensation, and become exposed by decondensation into a condition invisible by the video-imaging technique employed. Such exposed genes can then be activated by appropriate molecular messengers. In accordance with this theory, the total fluorescence observed from the active X is appreciably less than that of the inactive. The FISH pattern from chromosome 21 is very different, displaying two fluorescent bodies usually connected with the nucleoli. Both bodies contain condensed and decondensed regions, and both are much more similar in their degree of decondensation than was the case with the X chromosomes, although a small difference cannot be ruled out. Use of DNase I treatment of nuclei reveals the existence of exposed DNA. The use of FISH as demonstrated here can indicate sequestered DNA. Together the two techniques promise elucidation of gene regions of various chromosomes which are active and inactive in particular tissues and in normal and pathologic conditions.

Multiple protein-DNA interactions over the yeast HSC82 heat shock gene promoter

We have utilized DNase I and micrococcal nuclease (MNase) to map the chromatin structure of the HSC82 heat shock gene of Saccharomyces cerevisiae. The gene is expressed at a high basal level which is enhanced 2-3-fold by thermal stress. A single, heat-shock invariant DNase I hypersensitive domain is found within the HSC82 chromosomal locus; it maps to the gene's 5' end and spans 250 bp of promoter sequence. DNase I genomic footprinting reveals that within this hypersensitive region are four constitutive protein-DNA interactions. These map to the transcription initiation site, the TATA box, the promoter-distal heat shock element (HSE1) and a consensus GRF2 (REB1/Factor Y) sequence. However, two other potential regulatory sites, the promoter-proximal heat shock element (HSE0) and a consensus upstream repressor sequence (URS1), are not detectably occupied under either transcriptional state. In contrast to its sensitivity to DNAase I, the nucleosome-free promoter region is relatively protected from MNase; the enzyme excises a stable nucleoprotein fragment of approximately 210 bp. As detected by MNase, there are at least two sequence-positioned nucleosomes arrayed 5' of the promoter; regularly spaced nucleosomes exhibiting an average repeat length of 160-170 bp span several kilobases of both upstream and downstream regions. Similarly, the body of the gene, which exhibits heightened sensitivity to DNase I, displays a nucleosomal organization under both basal and induced states, but these nucleosomes are not detectably positioned with respect to the underlying DNA sequence and may be irregularly spaced and/or structurally altered. We present a model of the chromatin structure of HSC82 and compare it to one previously derived for the closely related, but differentially regulated, HSP82 heat shock gene.

Dynamic chromatin: the regulatory domain organization of eukaryotic gene loci

It is hypothesized that nuclear DNA is organized in topologically constrained loop domains defining basic units of higher order chromatin structure. Our studies are performed in order to investigate the functional relevance of this structural subdivision of eukaryotic chromatin for the control of gene expression. We used the chicken lysozyme gene locus as a model to examine the relation between chromatin structure and gene function. Several structural features of the lysozyme locus are known: the extension of the region of general DNAasel sensitivity of the active gene, the location of DNA-sequences with high affinity for the nuclear matrix in vitro, and the position of DNAasel hypersensitive chromatin sites (DHSs). The pattern of DHSs changes depending on the transcriptional status of the gene. Functional studies demonstrated that DHSs mark the position of cis-acting regulatory elements. Additionally, we discovered a novel cis-activity of the border regions of the DNAasel sensitive domain (A-elements). By eliminating the position effect on gene expression usually observed when genes are randomly integrated into the genome after transfection, A-elements possibly serve as punctuation marks for a regulatory chromatin domain. Experiments using transgenic mice confirmed that the complete structurally defined lysozyme gene domain behaves as an independent regulatory unit, expressing the gene in a tissue specific and position independent manner. These expression features were lost in transgenic mice carrying a construct, in which the A-elements as well as an upstream enhancer region were deleted, indicating the lack of a locus activation function on this construct. Experiments are designed in order to uncover possible hierarchical relationships between the different cis-acting regulatory elements for stepwise gene activation during cell differentiation. We are aiming at the definition of the basic structural and functional requirements for position independent and high level gene expression. The result of these experiments will have important consequences for random gene transfer with predictable and reproducible expression of transgenes.

Confocal microscopy of genome exposure in normal, cancer, and reverse-transformed cells

Genome exposure studies were carried out on malignant CHO-K1 and C6 rat glioma cells and their respective, phenotypically normal counterparts (reverse-transformed CHO-K1, and both reverse-transformed C6 glioma and normal rat fibroblasts). Cells were subjected to the nick-translation technique previously developed to make visible the exposed (i.e., DNase I-sensitive) nuclear DNA, and examined by both epifluorescence and confocal microscopy. The confocal microscopy, by permitting examination of sections throughout the nucleus, made possible clearer identification of the regions of exposed and sequestered DNA in the cells studied. A peripheral shell of exposed DNA with some discontinuities was displayed in the great majority of the cells with normal phenotype, but in none of the cancer cells. Both types of cells displayed regions of exposed DNA in the nuclear interior, particularly surrounding the nucleoli. In accordance with previous theoretical proposals we postulate: the peripheral nuclear shell of exposed DNA contains differentiation-specific genes that include the specific growth-control genes and that are functional in normal cells but not in cancer; the exposed genes surrounding the nucleoli may represent housekeeping genes active in both normal and cancer cells; and the DNase I-resistant DNA in the interior of the nucleus we postulate to consist for the most part of genes specific to alternative differentiation states and to be sequestered and inactive. Previous differences in evaluation of roles of peripheral and internal DNA sensitivity to DNAse I hydrolysis appear to be reconciled by this formulation. Identification of exposed DNA may be useful in cancer diagnosis.

DNase I-sensitive sites within the nuclear architecture visualized by immunoelectron microscopy

Nick-translation using mild digestion with DNase I allows preferential labeling of actively transcribing or potentially active genes, as compared with inactive genes. We have adapted this method to the level of electron microscopy to see the DNase I-sensitive regions in situ in Ehrlich tumor cells. In interphase cells treated with very low concentrations of DNase I, labeled sequences are found at the borders and in the close vicinity of condensed chromatin blocks. Labeling of condensed areas of chromatin requires higher DNase I concentrations and longer incubation in the nick-translation medium. In the nucleolus, the first sites to be nick-translated are the fibrillar centers and the interstices surrounding them, whereas the dense fibrillar component never contains labeled sequences. When cells are pretreated with actinomycin D, only a few perinucleolar clumps of condensed chromatin are labeled under the same conditions. This method provides a new tool for studying the functional organization of chromatin within a cell. The precise location of nick-translated sites in nucleolar components observed could change classical views concerning the functional organization of the nucleolus.

The spatial distribution of exposed nuclear DNA in normal, cancer, and reverse-transformed cells

The malignant CHO-K1 cell is reverse-transformed by cAMP, regaining the phenotype of a normal fibroblast. During this reaction, much of its DNA re-acquires sensitivity to hydrolysis by DNase I in a way characteristic of the normal fibroblast. Exposed DNA forms a rim about the nucleus in both the normal and reverse-transformed cell but not in the malignant CHO-K1. Reacquisition of the nuclear rim requires an organized cytoskeleton. Sequestered DNA forms families of different degrees of sequestration. In accordance with previous theoretical developments it is proposed that (i) genes specific to a given differentiation state are stored in the nuclear rim, whereas genes specific to other states are sequestered within the nucleus; (ii) only exposed genes are active, and their activity is modulated by regulatory molecules in the fluid medium; (iii) exposure and sequestration are regulated by cytoskeletal and nuclear protein structures; (iv) in at least several types of cancer the regulatory defect lies in the genome exposure process so that the specific DNA sequences and their associated growth regulatory loci have been transferred from the exposed to the sequestered condition with consequent loss of the nuclear rim of exposed DNA. The methodology described should be generally applicable to examining the accessibility state of subsets of DNA during various physiological modulations of cell function.

Genome regulation in mammalian cells

A theory is presented proposing that genetic regulation in mammalian cells is at least a two-tiered effect; that one level of regulation involves the transition between gene exposure and sequestration; that normal differentiation requires a different spectrum of genes to be exposed in each separate state of differentiation; that the fiber systems of the cell cytoskeleton and the nuclear matrix together control the degree of gene exposure; that specific phosphorylation of these elements causes them to assume a different organizational network and to impose a different pattern of sequestration and exposure on the elements of the genome; that the varied gene phosphorylation mechanisms in the cell are integrated in this function; that attachment of this network system to specific parts of the chromosomes brings about sequestration or exposure of the genes in their neighborhood in a fashion similar to that observed when microtubule elements attach through the kinetochore to the centromeric DNA; that one function of repetitive sequences is to serve as elements for the final attachment of this fibrous network to the specific chromosomal loci; and that at least an important part of the calcium manifestation as a metabolic trigger of different differentiation states involves its acting as a binding agent to centers of electronegativity, in particular proteins and especially phosphorylated groups, so as to change the conformation of the fiber network that ultimately controls gene exposure in the mammalian cell. It would appear essential to determine what abnormal gene exposures and sequestrations are characteristic of each type of cancer; which agonists, if any, will bring about reverse transformation; and whether these considerations can be used in therapy.

On the biological role of histone acetylation

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Hormonal regulation of phosphoenolpyruvate carboxykinase gene expression is mediated through modulation of an already disrupted chromatin structure

We used indirect end labeling to identify a series of five hypersensitive (HS) sites in the phosphoenolpyruvate carboxykinase (PEPCK) gene in H4IIE rat hepatoma cells. These sites were found at -4800 base pairs (bp) (site A), at -1300 bp (site B), over a broad domain between -400 and -30 bp (site C), at +4650 bp (site D), and at +6200 bp (site E). Sites A to D were detected only in cells capable of expressing the PEPCK gene, whereas site E was present in all of the cells examined thus far. The HS sites were present in H4IIE cells even when transcriptional activity was reduced to a minimum by treatment with insulin. Stimulation of transcription by a cyclic AMP analog to a 40-fold increase over the insulin-repressed level did not affect the main features of the HS sites. Furthermore, increased transcription did not disrupt the nucleosomal arrangement of the coding region of the gene, nor did it affect the immediate 5' region (site C), which is always nucleosome-free. In HTC cells, a rat hepatoma line that is hormonally responsive but unable to synthesize PEPCK mRNA, the four expression-specific HS sites were totally absent. Our experimental results also showed that, although there is a general correlation between lack of DNA methylation and transcriptional competence of the PEPCK gene, the role, if any, of methylation in the regulation of PEPCK gene activity is likely to be exerted at very specific sites.

Structural alteration from non-B to B-form could reflect DNase I hypersensitivity

Preferential cleavage of active genes by DNase I has been correlated with a structurally altered conformation of DNA at the hypersensitive site in chromatin. To have a better understanding of the structural requirements for gene activation as probed by DNase I action, digestability by DNase I of synthetic polynucleotides having the ability to adopt B and non-B conformation (like Z-form) was studied which indicated a marked higher digestability of the B-form of DNA. Left handed Z form present within a natural sequence in supercoiled plasmid also showed marked resistance towards DNase I digestion. We show that alternating purine-pyrimidine sequences adopting Z-conformation exhibit DNAse I foot printing even in a protein free system. The logical deductions from the results indicate that 1) altered structure like Z-DNA is not a favourable substrate for DNase I, 2) both the ends of the alternating purine-pyrimidine insert showed hypersensitivity, 3) B-form with a minor groove of 12-13 A is a more favourable substrate for DNase I than an altered structure, 4) any structure of DNA deviating largely from B form with a capacity to flip over to the B-form are potential targets for the DNase I enzymic probes in naked DNA.

Isolation and distribution of a Drosophila protein preferentially associated with active regions of the genome

A non-histone chromosomal protein of Mr = 75,000 was isolated from Drosophila embryos. The distribution pattern of this protein was determined by indirect immunofluorescence on salivary gland chromosomes of Drosophila melanogaster third instar larvae and compared with the distribution pattern of RNA polymerase II. Despite its preferential association with transcriptionally active regions of the chromosomes there was in many cases an almost inverse correlation with the RNA polymerase II content of a given locus. We postulate a function of the Mr = 75,000 protein in posttranscriptional regulation of gene expression by storing the newly synthesized RNA.

Hormonal regulation of phosphoenolpyruvate carboxykinase gene expression is mediated through modulation of an already disrupted chromatin structure

We used indirect end labeling to identify a series of five hypersensitive (HS) sites in the phosphoenolpyruvate carboxykinase (PEPCK) gene in H4IIE rat hepatoma cells. These sites were found at -4800 base pairs (bp) (site A), at -1300 bp (site B), over a broad domain between -400 and -30 bp (site C), at +4650 bp (site D), and at +6200 bp (site E). Sites A to D were detected only in cells capable of expressing the PEPCK gene, whereas site E was present in all of the cells examined thus far. The HS sites were present in H4IIE cells even when transcriptional activity was reduced to a minimum by treatment with insulin. Stimulation of transcription by a cyclic AMP analog to a 40-fold increase over the insulin-repressed level did not affect the main features of the HS sites. Furthermore, increased transcription did not disrupt the nucleosomal arrangement of the coding region of the gene, nor did it affect the immediate 5' region (site C), which is always nucleosome-free. In HTC cells, a rat hepatoma line that is hormonally responsive but unable to synthesize PEPCK mRNA, the four expression-specific HS sites were totally absent. Our experimental results also showed that, although there is a general correlation between lack of DNA methylation and transcriptional competence of the PEPCK gene, the role, if any, of methylation in the regulation of PEPCK gene activity is likely to be exerted at very specific sites.

Specificity of the cAMP-induced gene exposure reaction in CHO cells

Previous studies demonstrated that in the transformed CHO (Chinese hamster ovary) cell a substantial part of the genome behaves as though its genes are sequestered from effective contact with soluble constituents of the intracellular fluid. The reverse transformation reaction, initiated by cAMP derivatives, causes this cell to regain the morphology, growth regulation, surface characteristics, and sensitivity of its DNA to digestion by DNase I that are characteristic of normal fibroblasts. In this paper we show that this action of cAMP is gene specific. In examination of 47 different genetic loci, some, like ribosomal RNA genes, are found to be sensitive to DNase I hydrolysis both in the absence and in the presence of cAMP; some are resistant under both conditions; and some are resistant in the untreated cell but become sensitive after cAMP treatment. Unlike other gene exposure reactions, which are irreversible and connected with differentiation phenomena, that produced by cAMP is readily reversed when the reagent is removed. A sequence of events is observed after cAMP treatment, the first of which is reorganization of the cytoskeleton. Afterwards, metabolic changes occur over periods as long as 72 hr. The cAMP-induced cytoskeleton-mediated gene exposure reaction appears to be an important genetic regulatory mechanism in mammalian cells and to have special implications for cancer.

Butyrate-induced changes in nuclease sensitivity of chromatin cannot be correlated with transcriptional activation

We examined in the H4IIE rat hepatoma cell line the relationship between butyrate-induced changes in the nuclease sensitivity of chromatin and changes in transcriptional activity of specific genes. The butyrate-inducible metallothionein I (MT-I) gene underwent a dramatic increase in DNase I sensitivity after 3 h of butyrate treatment. However, genes not transcribed in H4IIE cells underwent the same changes in DNase I sensitivity. Thus, butyrate-induced increases in DNase I sensitivity are not sufficient for the transcriptional activation of a gene. Butyrate treatment has also been reported to alter the sensitivity of sequences to micrococcal nuclease (MNase) in a manner reflecting their tissue-specific expression. Butyrate exposure caused increased digestion of the MT-I gene by MNase. However, butyrate-induced MNase sensitivity also occurred for genes which are neither transcribed in untreated cells nor butyrate inducible. Moreover, cadmium, a potent transcriptional activator of the MT-I gene, does not alter the sensitivity of the MT-I gene to MNase. Thus, the butyrate-induced alterations in MNase sensitivity are neither sufficient for, necessary for, nor indicative of transcriptional activation.

Treatment with sodium butyrate inhibits the complete condensation of interphase chromatin

The effects of histone hyperacetylation on chromatin fiber structure were studied using direct observations with the electron microscope. Histone hyperacetylation was induced in HeLa cells by treatment with sodium butyrate, and the ultrastructure of control and of acetylated chromatin fibers examined after fixation at different stages of compaction. No differences between control and acetylated chromatin were seen when the fibers were partially unfolded (10 mM NaCl, 20 mM NaCl, 50 mM NaCl), but in 100 mM NaCl, control chromatin showed further compaction to the "30 nm" fiber, while hyperacetylated chromatin failed to undergo this final compaction step. These results strongly suggest that histone acetylation causes a moderate "relaxation" rather than complete decondensation of interphase chromatin fibers. The relationship of these findings to the increased DNase I sensitivity of acetylated chromatin, and to transcription and replication, is discussed.

Isolation and distribution of a Drosophila protein preferentially associated with inactive regions of the genome

The distribution patterns of chromosomal proteins from Drosophila can be observed by immunofluorescent staining of the polytene chromosomes from larval salivary glands. We have purified a non-histone chromosomal protein of Mr = 69,000 molecular weight which has a high affinity for DNA with little sequence specificity. Immunofluorescent staining indicates that this protein is preferentially associated with the inactive portions of the genome, including the centric heterochromatin and the condensed bands within the euchromatic arms of the chromosomes. Observation of both the heat shock loci 87A and 87C and the developmentally regulated loci 74EF and 75B shows an inverse correlation between immunofluorescent staining for the Mr = 69,000 protein and for RNA polymerase. The presence of this protein appears to be correlated with the packaging of the chromatin in an inactive form.

Characterization of DNA binding proteins released from sarcoma-180 chromatin during brief digestion with DNase-I

Brief digestion of sarcoma-180 chromatin (less than or equal to 5%) by pancreatic DNase-I releases six non-histone proteins with Mol. wt. 21.5K, 26K, 72.5K, 77K, 90K and 120K dalton and pI values ranging from 4.7 to 12.4. The protein of Mol. wt. 77K dalton was obtained at high alkaline range of pH = 12.4. The antibodies against these proteins induce dose dependent inhibition in transcription of native chromatin. Results suggest a role of these proteins in positive control of gene transcription in sarcoma-180 cells.

Butyrate-induced changes in nuclease sensitivity of chromatin cannot be correlated with transcriptional activation

We examined in the H4IIE rat hepatoma cell line the relationship between butyrate-induced changes in the nuclease sensitivity of chromatin and changes in transcriptional activity of specific genes. The butyrate-inducible metallothionein I (MT-I) gene underwent a dramatic increase in DNase I sensitivity after 3 h of butyrate treatment. However, genes not transcribed in H4IIE cells underwent the same changes in DNase I sensitivity. Thus, butyrate-induced increases in DNase I sensitivity are not sufficient for the transcriptional activation of a gene. Butyrate treatment has also been reported to alter the sensitivity of sequences to micrococcal nuclease (MNase) in a manner reflecting their tissue-specific expression. Butyrate exposure caused increased digestion of the MT-I gene by MNase. However, butyrate-induced MNase sensitivity also occurred for genes which are neither transcribed in untreated cells nor butyrate inducible. Moreover, cadmium, a potent transcriptional activator of the MT-I gene, does not alter the sensitivity of the MT-I gene to MNase. Thus, the butyrate-induced alterations in MNase sensitivity are neither sufficient for, necessary for, nor indicative of transcriptional activation.

Assessment of preferential cleavage of an actively transcribed retroviral hybrid gene in murine cells by deoxyribonuclease I, bleomycin, neocarzinostatin, or ionizing radiation

Preferential cleavage induced by bleomycin, neocarzinostatin, or ionizing radiation in a transcribed cellular gene was evaluated through comparisons with deoxyribonuclease I. The glucocorticoid-inducible LTL gene (a hybrid viral gene derived from mouse mammary tumor virus DNA) previously described [Zaret, K. S., & Yamamoto, K. R. (1984) Cell (Cambridge, Mass.) 38, 29-38] served as the specific DNA target. A Southern blot analysis was used to specifically assess cleavage of the LTL gene in nuclei isolated from cells either treated or untreated with the synthetic glucocorticoid dexamethasone. Hypersensitivity of the gene to bleomycin or neocarzinostatin, which paralleled deoxyribonuclease I hypersensitivity, was evident only in nuclei isolated from dexamethasone-treated cells. Like deoxyribonuclease I, sites of dexamethasone-inducible drug hypersensitivity were coincident with the binding region for the glucocorticoid receptor found within the regulatory sequences of the LTL gene. In contrast, no hypersensitivity to ionizing radiation was evident. Although bleomycin and neocarzinostatin showed qualitatively similar preferences for the transcribed LTL gene, quantitative evaluations of damage to total cellular DNA by filter elution showed that the relative specificity of bleomycin for the hypersensitive region was much less than that of either deoxyribonuclease I or neocarzinostatin.

Transcription of adenovirus 2 major late and peptide IX genes under conditions of in vitro nucleosome assembly

Plasmid DNA containing adenovirus 2 major late and peptide IX genes was assembled into nucleosomes in vitro, and the assembled nucleosomes were used as a template to study the regulatory mechanism of transcription initiation under these conditions. Neither the major late nor peptide IX genes was transcribed on the already-assembled nucleosomes. However, the major late gene, but not the peptide IX gene, was transcribed efficiently when the DNA was incubated with HeLa cell extracts prior to assembly into nucleosomes. These results indicate that prebinding of some component in the cell extracts to DNA is essential to activate transcription of the major late gene on nucleosomes assembled under the conditions used here. Since gene IX on the nucleosomes was not transcriptionally active regardless of preincubation of DNA with the extracts, some other component or another, different template structure which is not able to be identified in an in vitro system with deproteinized DNA template might be required for activation of peptide IX gene transcription. To know the function of the upstream sequences of the major late gene, effects of the deletion on transcription of nucleosomes were compared with that of deproteinized DNA. The result showed that depression of transcription by deleting the upstream sequences had more effect on nucleosomes than on deproteinized DNA.

Hepatoma-associated nonhistone chromosomal proteins are present in active chromatin

Recently a group of nonhistone proteins with molecular weights ranging from 180-200 K were discovered which are associated with rat hepatoma chromatin specifically (Burkhardt et al., Biochim. Biophys. Acta 781, 165-172, 1984). These hepatoma-associated nonhistone proteins appeared and increased in rats treated with a hepatocarcinogen. Two approaches were used in this study to investigate whether the hepatoma-associated nonhistone chromosomal proteins are present in actively transcribed regions. We found that the limited DNase I digestion of Morris hepatoma 7777 chromatin released antigenic proteins not detected in normal liver chromatin digests. The association of antigenic nonhistone proteins with nuclear matrices was also studied. Using immunoblot analysis of nuclear matrices and total chromatin, the antigenic nonhistone chromosomal proteins were determined. Hepatoma-associated nonhistone protein antigens were extensively concentrated in the nuclear matrices. In the present study, the transcriptionally-active alpha-fetoprotein gene and the nontranscribed beta-globin gene were used as gene markers to determine the transcriptionally active chromatin region. Data presented in this paper indicate that hepatoma-associated NHPs are localized in active chromatin.

Nuclease sensitivity of storage-protein genes in isolated nuclei of pea seeds

The chromatin structure of legumin genes in nuclei isolated from leaves and cytyledons of pea (Pisum sativum L.) was investigated. Digestions with micrococcal nuclease (EC 3.1.31.1.) showed that the nucleosomal repeat length of total chromatin (171±25 base pairs) was similar in nuclei from both tissues. The sensitivity to pancreatic deoxyribonuclease (DNase I; EC 3.1.21.1.) of the legumin genes in cotyledon nuclei was greater than that in leaf nuclei; this increase in sensitivity correlated with transcriptional activity of the genes. No DNase-I-hypersensitive sites were detected in these genes in either tissue.

Significance of DNase I-hypersensitive sites in the long terminal repeats of a Moloney murine leukemia virus vector

A Moloney murine leukemia virus-derived retroviral vector (N4) carrying the bacterial neomycin resistance gene (neo) was used to study the chromatin configuration of integrated proviral DNA in NIH 3T3-derived cell lines containing one copy of the vector DNA per cell. Three independently obtained cell lines were examined. In two of these cell lines, the vector was introduced by viral infection, while in the third the construct was introduced by DNA transfection. Such transfected cell lines (including the one examined) usually express 10- to 50-fold less virus-specific RNA than do cell lines obtained by viral infection. All three cell lines exhibited similar patterns of DNase I-hypersensitive (HS) sites. Two strong DNase I HS sites were detected in the 5' long terminal repeat, which contains signals required for proper and efficient initiation of viral transcription. One of these sites was found to overlap the viral enhancer sequences, while the other site mapped very close to the start site for viral transcription. A third HS site was detected in nearby internal viral sequences. Only one HS site was found in the 3' long terminal repeat, which contains the signal(s) required for proper addition of a poly(A) tail to viral transcripts. This HS site was located in the region of the viral enhancer. Several weak DNase I HS sites were also found in the cellular sequences adjacent to the integration sites, at different locations in each cell line analyzed. No common pattern of cellular DNase I HS sites was found. These observations suggest that the 5' and 3' long terminal repeats of integrated retroviral proviruses exhibit different chromatin conformations, possibly reflecting the different functions encoded by the otherwise identical sequences, and the DNase I HS sites detected in these studies reflect only a potential for transcription and are not a reflection of the high transcriptional activity characteristic of retroviruses.

Transcription of adenovirus 2 major late and peptide IX genes under conditions of in vitro nucleosome assembly

Plasmid DNA containing adenovirus 2 major late and peptide IX genes was assembled into nucleosomes in vitro, and the assembled nucleosomes were used as a template to study the regulatory mechanism of transcription initiation under these conditions. Neither the major late nor peptide IX genes was transcribed on the already-assembled nucleosomes. However, the major late gene, but not the peptide IX gene, was transcribed efficiently when the DNA was incubated with HeLa cell extracts prior to assembly into nucleosomes. These results indicate that prebinding of some component in the cell extracts to DNA is essential to activate transcription of the major late gene on nucleosomes assembled under the conditions used here. Since gene IX on the nucleosomes was not transcriptionally active regardless of preincubation of DNA with the extracts, some other component or another, different template structure which is not able to be identified in an in vitro system with deproteinized DNA template might be required for activation of peptide IX gene transcription. To know the function of the upstream sequences of the major late gene, effects of the deletion on transcription of nucleosomes were compared with that of deproteinized DNA. The result showed that depression of transcription by deleting the upstream sequences had more effect on nucleosomes than on deproteinized DNA.

Chromatin structure of integrated T-DNA in crown gall tumors

We have investigated the chromatin structure of the integrated T-DNA in two N. tabacum crown gall tumor lines, and compared the results to those obtained in a previous study of the methylation patterns of these same integrated DNA sequences (Gelvin et al., Nucleic Acids Res. 11:159-174, 1983). The E9 octopine-type tumor contains a single copy of TL, whose transcription is essential for tumor maintenance, and 15-30 copies of TR, a non-essential region. The HT37#15 nopaline type teratoma contains a single copy of the nopaline T-DNA. All these integrated sequences can be found associated with nucleosomes, although the diffuse nature of the nucleosome bands on Southern transfers implies an 'open' chromatin conformation. In addition, all the sequences are more sensitive to digestion with deoxyribonuclease I than the bulk of the chromatin. We present evidence suggesting that, despite the previously published data that the majority of copies of the TR-DNA are highly methylated at the sequence CCGG whereas the TL-DNA is not, the majority of copies of the TR-DNA in the E9 tumor line are in the same chromatin conformation as TL. These data therefore suggest that most of the copies of TR-DNA are likely to be transcriptionally competent.

Developmental acquisition of DNase I sensitivity of the phosphoenolpyruvate carboxykinase (GTP) gene in rat liver

The sensitivity to DNase I digestion of the gene encoding rat phosphoenolpyruvate carboxykinase (GTP) (EC 4.1.1.32) was assessed during development and prior to the onset of expression. This gene is resistant to DNase I digestion in nuclei isolated from livers of 19-day rat fetuses. Gradual acquisition of sensitivity of the phosphoenolpyruvate carboxykinase gene, which starts later than the 19th day of gestation and is completed by the 21st day, occurs before initiation of gene expression. As transcription of the phosphoenolpyruvate carboxykinase gene is not detected until birth, the events observed may represent a shift from a dormant to an active gene. Injection of N6,O2-dibutyryladenosine 3',5'-cyclic monophosphate into fetuses on the 19th day of gestation induces gene expression and sensitivity to DNase I digestion within 3 hr of treatment. While this short treatment does not affect the methylation pattern of the gene, longer treatment of fetuses (2 days) with dibutyryl-cAMP results in premature hypomethylation of the gene. A hierarchy of modifications of the phosphoenolpyruvate carboxykinase gene during development is discussed.

Subnuclear localization of proteins encoded by the oncogene v-myb and its cellular homolog c-myb

The retroviral transforming gene v-myb encodes a 45,000-Mr nuclear transforming protein (p45v-myb). p45v-myb is a truncated and mutated version of a 75,000-Mr protein encoded by the chicken c-myb gene (p75c-myb). Like its viral counterpart, p75c-myb is located in the cell nucleus. As a first step in identifying nuclear targets involved in cellular transformation by v-myb and in c-myb function, we determined the subnuclear locations of p45v-myb and p75c-myb. Approximately 80 to 90% of the total p45v-myb and p75c-myb present in nuclei was released from nuclei at low salt concentrations, exhibited DNA-binding activity, and was attached to nucleoprotein particles when released from the nuclei after digestion with nuclease. A minor portion of approximately 10 to 20% of the total p45v-myb and p75c-myb remained tightly associated with the nuclei even in the presence of 2 M NaCl. These observations suggest that both proteins are associated with two nuclear substructures tentatively identified as the chromatin and the nuclear matrix. The function of myb proteins may therefore depend on interactions with several nuclear targets.

Chicken histone genes retain nuclear matrix association throughout the cell cycle

The association between histone genes and the nuclear matrix (NM) during periods of high (S-phase) and low (non-S-phase) transcriptional activity has been investigated with synchronized cells from a chicken erythroid cell line (abbreviated ts34). By DNase I and restriction enzyme analysis, these studies reveal that both core and linker histone genes (represented by H2A and H1 genes respectively) are attached to the NM independent of their transcriptional activity during the cell-cycle. The tissue-specific histone gene H5, expressed constitutively, is nuclear matrix (NM)-associated in ts34 cells but is found in the supernatant (S/N) fractions of a non-erythroid T-cell line. Furthermore, we show that DNA sequences necessary for NM-attachment of the H5 gene lie within a 780 base pair region spanning part of the coding and 5' non-translated region. Of the three non-histone genes investigated, beta-actin sequences are expressed and are NM-attached, feather keratin genes are not expressed and predominate in the S/N, and beta-globin genes although not expressed in the ts34 cell line used were found in the NM fraction. In this case the association may be fortuitous or may reflect an early event prior to transcription of globin genes in differentiating erythroid cells. These results generally support the notion that actively transcribed genes are NM-attached, but that attachment per se is not synonymous with transcription.

Conservation and variation in the large scale organisation of the globin gene domains of duck and chicken

The genomic DNA of cloned recombinants containing the duck globin genes was compared to that of the analogous domains of the chicken. A 36 kb insert including the three alpha-type globin genes was isolated from a newly prepared duck genomic library in the cosmid PJB8; another recombinant contained a 45 kb insert with the four beta globin genes. In the alpha globin gene domain, the relative positions of genes, of repetitive sequences, and of the A + T-rich segments (AT-rich linkers, ATRLs) which frame the gene cluster (Moreau et al. 1982), were found to be closely maintained between duck and chicken. Although ATRLs and repetitive sequences also frame the gene cluster in the beta globin domains of duck and chicken, there is more genetic drift in their relative positions than in the alpha domain. It is of interest that several repetitive DNA segments were detected in the chicken beta globin domain which do not exist in corresponding positions in the duck. In view of the strict conservation in both species of genes and their relative positions in the cluster, this observation seems to exclude a simple function of repetitive sequences in the control of individual genes. The data are discussed with regard to the possible significance of repetitive and AT-rich DNA segments in genome organisation and function.