An altered DNA conformation detected by S1 nuclease occurs at specific regions in active chick globin chromatin

Conformation of promoter DNA: fine mapping of S1-hypersensitive sites

Larsen and Weintraub showed that a feature of active (but not inactive) chromatin is the appearance of S1-nuclease-hypersensitive sites in the 5'-flanking regions of expressing genes. Such sites are also present in supercoiled, but not relaxed, plasmids carrying these gene sequences. We have developed an in vitro approach to map, at the nucleotide level, S1-hypersensitive sites in artificially generated supercoiled circles of naked DNA. In the case of the adult chicken beta-globin gene, our results correlate extremely well with the coarser in vivo mapping. These sites reside in homopurine-homopyrimidine tracts, and, despite their S1 sensitivity, they do not seem to be single-stranded.

A site and strand specific nuclease activity with analogies to topoisomerase I frames the rRNA gene of Tetrahymena

Exposure of macronuclear chromatin from Tetrahymena thermophila to sodium dodecyl sulfate causes an endogenous nuclease to cleave the extra-chromosomal rDNA at specific sites. All cuts are single-strand cleavages specific to the non-coding strand. Three cleavages map in the central non-transcribed spacer of the palindromic molecule at positions -1000, -600 and -150 bp with respect to the transcription initiation point. A fourth site is located close to the transcription termination point, while no cleavage is observed in the coding region. The position of each cleavage is in the immediate neighbourhood of DNAse I hypersensitive sites. Additionally, certain DNA sequence motifs are repeated in the region around the cleavages. Upon cleavage induction a protein becomes attached to the rDNA. Our results indicate covalent binding to the generated 3' end, in analogy to the aborted reaction of topoisomerase I.

Superhelicity induces hypersensitivity of a human polypyrimidine . polypurine DNA sequence in the human alpha 2-alpha 1 globin intergenic region to S1 nuclease digestion--high resolution mapping of the clustered cleavage sites

Supercoiled recombinant DNAs containing the human adult alpha-globin gene region have been probed with nuclease S1 in vitro. While agarose gel electrophoresis showed only one predominant, double-stranded cleavage generated by S1 within 6 kb of human DNA and 4 kb of pBR322 sequence, a high resolution gel analysis reveals that the unique S1-hypersensitive locus in the human adult alpha-globin gene region actually contains more than 15 authentic S1 cleavage sites closely spaced together. The mapping approach used here locates the specific S1 cleavage sites on both DNA strands at the nucleotide sequence level. Interestingly, most of these sites are mapped within a 90 bp stretch of GC-rich (66%) polypyrimidine . polypurine DNA that is located 1060 to 1150 bp upstream from alpha 1-globin gene. These results provide the first high resolution map of double-stranded S1-cleavage sites induced within a specific DNA sequence under supercoil strain. The distribution and relative cutting frequencies of these sites mapped are consistent with a slippage mechanism in which the simple repeating sequences are organized into base-mismatched duplex on supercoiled DNA.

Analysis of the chromatin assembled in germinal vesicles of Xenopus oocytes

We have injected circular DNA, labeled with 32P at a single restriction site, into germinal vesicles of Xenopus laevis oocytes in order to study the nucleosome arrangement on the assembled minichromosomes. Two types of genes were used in these studies, the somatic 5 S RNA gene unit of Xenopus borealis and the histone gene unit of Drosophila melanogaster. We find that injections of labeled DNA alone, at 1 ng DNA per oocyte, results in irregularly spaced nucleosomes and partially supercoiled DNA molecules. However, perfectly spaced nucleosomes are assembled and fully supercoiled DNA is recovered if 5 to 20 nanograms of cold vector DNA is coinjected with the labeled DNA. At the optimum chromatin assembly conditions, the nucleosomes are perfectly spaced with a 180 base-pair periodicity, but they are randomly positioned on the DNA. The assembly of a periodic chromatin structure is accompanied by a dramatic enhancement in the expression of the injected 5 S RNA gene.

Multiple origins of transcription in the 4.5 Kb upstream of the epsilon-globin gene

By a combination of primer extension and S1 mapping, we have identified and characterized at least nine epsilon-globin initiation sites in the 4.5 kb upstream of the canonical mRNA cap site. These occur in four regions, -65 to -250, -900, -1480, and -4500 bp from the translation initiation codon ATG. Transcripts from eight sites yield sufficient material for direct RNA analysis and in all of these instances the molecules are capped. Approximately 10%-15% of epsilon-globin transcripts originate from these upstream sites in both an erythroleukemic cell line and purified erythroblasts from first-trimester human embryos. In three established cell lines derived from adult non-erythroid tissue, low levels of transcription of the epsilon-globin gene occur, but the RNA molecules originate exclusively from one of the upstream sites identified in erythroid cells. These findings suggest modification of the current models of transcription of globin genes.

Sequences locating the 5' ends of the major simian virus 40 late mRNA forms

The 5' sequences of late mRNA specified by several constructed or naturally occurring deletion or duplication mutants of simian virus 40 were examined. The mutants included viruses with various small deletions centered about 25 nucleotides upstream from the major transcription initiation site, as well as viruses containing tandem duplications of a sequence of 50 nucleotides or less embedding the major transcription initiation site. The results show that the sequences 25 to 30 nucleotides upstream from the major initiation site in the position of the TATA box of other polymerase II promoters are not essential for the precise localization of the initiation site of late mRNA. Rather, we deduce that the major late mRNA start site is determined primarily by sequences located very close to the initiation site, and that the relative abundance of the 5' ends with this initiation site is modulated by nearby downstream sequences. Modification of six nucleotides adjacent upstream to the initiation site almost completely prevents the utilization of this site. Various deletions and substitutions of sequences 21 nucleotides or more downstream from the major initiation site causes upstream shifts in the localization of the most abundantly utilized 5' ends. The sequences immediately downstream from the major simian virus 40 initiation sites contain inverted symmetries that could give rise to secondary structures in either single-stranded DNA or RNA; the possibility that these inverted symmetries function in transcription initiation at the level of DNA structure rather than in RNA stabilization is discussed. Finally, we present additional evidence that precursor species with certain 5' termini are selectively spliced to form 19S RNA, whereas other 5' termini are preferred for forming the 16S RNA splice. We discuss the possibility that this is a consequence of the influence of leader structure on downstream splicing events.

DNaseI-hypersensitive sites at promoter-like sequences in the spacer of Xenopus laevis and Xenopus borealis ribosomal DNA

We have detected a DNAseI hypersensitive site in the ribosomal DNA spacer of Xenopus laevis and Xenopus borealis. The site is present in blood and embryonic nuclei of each species. In interspecies hybrids, however, the site is absent in unexpressed borealis rDNA, but is present normally in expressed laevis rDNA. Hypersensitive sites are located well upstream (over lkb) of the pre-ribosomal RNA promoter. Sequencing of the hypersensitive region in borealis rDNA, however, shows extensive homology with the promoter sequence, and with the hypersensitive region in X. laevis. Of two promoter-like duplications in each spacer, only the most upstream copy is associated with hypersensitivity to DNAaseI. Unlike DNAaseI, Endo R. MspI digests the rDNA of laevis blood nuclei at a domain extending downstream from the hypersensitive site to near the 40S promoter. Since the organisation of conserved sequence elements within this "proximal domain" is similar in three Xenopus species whose spacers have otherwise evolved rapidly, we conclude that this domain plays an important role in rDNA function.

Association of an S1 nuclease-sensitive structure with short direct repeats 5' of Drosophila heat shock genes

The potential for a DNA molecule to assume different tertiary structures has been suggested as a possible determinant of transcriptional regulation in eukaryotes. Such forms include cruciforms transitions from B to Z DNA in the same molecule and short unpaired stretches of DNA in an alternating copolymer. All such structures contain regions which are preferentially sensitive to S1 nuclease. We report here an additional class of S1 nuclease sensitive sites associated with short direct repeats of DNA found in the 5' flanking regions of certain Drosophila melanogaster heat shock genes.

Structure of a nuclease-sensitive region inside the immunoglobin kappa gene: evidence for a role in gene regulation

A discrete chromatin region inside the active immunoglobulin kappa gene is preferentially accessible to cleavage by nucleolytic enzymes. This region comprises 200-250 bp of DNA, and is situated within the large intron of the gene, approximately 600 bp upstream from the constant region coding sequence. The local chromatin structure of this region correlates with tissue-specific kappa gene expression: it is resistant to nucleolytic digestion in the inactive kappa genes of murine brain and liver nuclei, but becomes uniquely sensitive to cleavage by deoxyribonuclease I or by a variety of restriction endonucleases in the chromatin of kappa-producing cells. Nuclease sensitivity at this site occurs in both rearranged and unrearranged kappa alleles, and can be maintained in the absence of ongoing kappa transcription. The nucleotide sequence of the hypersensitive region has been selectively conserved in evolution, and includes both a 7 bp inverted repeat sequence and a short segment homologous to the transcriptional enhancer elements of certain eukaryotic viruses. Molecular events occurring at this locus may play a role in the regulation of kappa gene expression, perhaps by influencing the activity of promoter sequences several kilobases upstream.

Detection of an altered DNA conformation at specific sites in chromatin and supercoiled DNA

We show that bromoacetaldehyde, which reacts selectively at the N-1 and N-6 positions of unpaired adenine and at the N-3 and N-4 positions of unpaired cytosine residues reacts with chromosomal DNA in intact cells at probable regulatory sequences near active genes. A region of about 200 base pairs 5' to the chicken beta A-globin gene, which contains sites sensitive to nuclease S1, to several restriction endonucleases, and to very low levels of DNase I, also contains DNA structures that are preferentially sensitive to bromoacetaldehyde. These altered DNA structures are found at reproducible positions relative to the beta A-globin gene regardless of whether the bromoacetaldehyde is presented to intact erythrocytes, erythrocyte nuclei, or the beta A-globin gene itself carried in pBR322 as purified supercoiled DNA. The unpaired DNA 5' to the adult beta A-globin gene in adult erythrocytes is not detectable in embryonic erythrocytes that express embryonic beta-globin in contrast to adult beta A-globin. Our results suggest that well-defined regions of DNA with effectively unpaired bases occur in intact nuclei and that these structures may be important for specific recognition because they are tissue specific and are found at putative regulatory regions.

Escherichia coli single-strand binding protein stabilizes specific denatured sites in superhelical DNA

Escherichia coli single-strand binding protein relaxes supercoiled DNA molecules containing the Drosophila melanogaster histone gene repeat unit, by stabilizing denaturation bubbles that map near the boundaries of the genes, at sites that in native chromatin have been shown to be hypersensitive to nucleases. A similar process may contribute to the propagation of such hypersensitive sites after their induction on the activation of gene expression.

Nucleosome distribution on the Jk and Ck immunoglobulin gene segments of mouse liver chromatin

The chromatin structure of the transcriptionally inactive kappa immunoglobulin gene in mouse liver was investigated by mainly employing indirect endlabeling on Bsp RI restriction nuclease digestions of intact nuclei. The disclosed strong (about 85%) but not uniform protection of the Bsp RI sites by nucleosomes is inconsistent with both a uniquely sequence-oriented localization and a completely random distribution of nucleosomes in this region of the genome. Several possibly applicable models are discussed. A model with multiple phases and non-uniform linker lengths cannot be excluded; however a largely random localization with a weak superimposed organization in two confined areas was tested and found sufficient for explaining the data.

BAL 31 nuclease as a probe in concentrated salt for the B-Z DNA junction

The BAL 31 nuclease, an extracellular nuclease from A. espejiana, specifically recognizes and cleaves the salt induced conformational junction between B and Z-DNA. Short segments of (dC-dG) left-handed Z-helix, comprising approximately 1% of the total DNA, are specifically detected within two different recombinant plasmids. The BAL 31 enzyme is highly resistant to inactivation by the presence of high concentrations of a variety of electrolytes that stabilize left-handed helices, is active at physiological pH, and can be used to probe both linear and circular DNAs. Additionally, the nuclease cleaves left-handed (dC-dG)n only very poorly, if at all. Thus, the BAL 31 nuclease can be utilized as a probe for helical junctions and consequently for segments of left-handed DNA that might exist within predominantly right-handed naturally occurring genomes.

Induction of globin gene expression during erythroid cell differentiation

We can provide increasing insight, albeit still incomplete, into the changes in MELC that accompany globin gene expression induced by polar chemicals, such as DMSO, and other agents. These transformed, CFUe-like erythroid precursor cells exhibit in their uninduced state, a DNA methylation pattern and globin gene (formula; see text) chromatin configuration (DNase I sensitivity) that is compatible with actual or potential gene transcription. Such features may reflect alterations in chromatin configuration that have occurred at a stage prior to leukemic transformation, during the differentiation of earlier erythroid precursor cells and associated with the restriction in developmental potential characteristic of progression to the CFUe (or MELC) stage of erythropoiesis. Uninduced MELC display a low level of globin gene transcription, producing globin mRNA or mRNA precursors whose processing or stabilization is the target of action of hemin. The major increase in MELC globin gene transcription that is initiated by DMSO, HMBA, or butyric acid, is accompanied by, and perhaps preceded by, an increase in DNase I hypersensitivity in the regions 5' to the active globin genes. This suggests that reorganization of chromatin structure in the globin gene domains is associated with accelerated globin gene transcription and may be characteristic of a developmental transition during terminal differentiation in the erythroid cell lineage.

Hexamethylenebisacetamide-resistant murine erythroleukemia cells have altered patterns of inducer-mediated chromatin changes

We determined inducer-mediated changes in chromatin structure near the globin genes in a variant line of murine erythroleukemia cells (MELC). The variant cell line, R1, was derived from the inducer-sensitive DS19 cell line by selection for inducer-resistance. R1 cells are resistant to induction of erythroid differentiation by hexamethylenebisacetamide (HMBA) whereas the parental line is HMBA-sensitive. Uninduced MELC (both inducer-sensitive DS19 cells and inducer-resistant R1 cells) have DNase I-sensitive sites in chromatin containing the alpha 1- and beta maj-globin genes. These nuclease-sensitive regions are located within the beta maj-globin second intervening sequence (IVS2) and near the alpha 1-globin gene 5' cap site. Culture with HMBA causes changes in chromatin structure in both parental and variant cell lines. In DS19 cells, the DNase I-sensitive site within the beta maj-globin IVS2 becomes more resistant to nuclease cleavage, and a new DNase I-sensitive region develops near the beta maj-globin cap site. In addition, the nuclease-sensitive region adjacent to the cap site of the alpha 1-globin gene increases, and a novel 5' nuclease-sensitive site is also established. In R1 cells, HMBA-mediated changes in chromatin structure are incomplete. The DNase I-sensitive site within the beta maj-globin IVS2 becomes more resistant to nuclease cleavage, but the nuclease sensitivity near the beta maj-globin cap site does not increase to the extent observed in DS19 cells. The pattern of nuclease sensitivity near the alpha 1-globin gene is essentially unchanged after culture of R1 cells with HMBA. Thus, in R1 cells, resistance to HMBA-induced expression of globin genes is associated with failure to detect inducer-mediated changes in chromatin structure 5' to the cap site of the alpha 1- and beta maj-globin genes. These results also suggest that the increased nuclease resistance of a site in the beta maj-globin IVS2 does not depend on the establishment of a DNase I-sensitive region near the beta maj-globin gene cap site.

Structural perturbation in supercoiled DNA: hypersensitivity to modification by a single-strand-selective chemical reagent conferred by inverted repeat sequences

Bromoacetaldehyde, a reagent which modifies unpaired adenine residues, selectively modifies supercoiled DNA in the region of inverted repeats which are known targets for single-strand-specific nucleases. The reaction is dependent upon the topological state of the molecule, and the absolute importance of the inverted repeat has been demonstrated. Finer mapping of the distribution of the modification pattern reveals significant and interesting differences from the S1 nuclease target positions. Bromoacetaldehyde modification is distributed over a wider region covering the whole inverted repeat, with greatest extent of reaction in the regions which flank the inverted repeat. It is suggested that an altered conformation may be propagated into these sequences. These results further support the contention that inverted repeats adopt an altered conformation when negatively supercoiled, for which the principal suggestion remains the cruciform structure.

Temporal order of chromatin structural changes associated with activation of the major chicken vitellogenin gene

The major chicken vitellogenin (VTG II) gene is marked at the chromatin level in hormone-responsive cells by a set of nuclease-hypersensitive sites that exist prior to hormone-mediated expression. When the gene is transcriptionally activated in the liver by treatment with 17 beta-estradiol, three additional hypersensitive sites are induced, which map near the 5' end of the gene. Two of these sites are stable and, moreover, appear to be propagated to daughter cells after hormone is withdrawn. In contrast, the third site (located 0.7 kb upstream from the gene) is observed only during periods of hormone treatment, perhaps due to a transient interaction with hormone receptor complex at this site. Whereas none of these nuclease-hypersensitive sites is observed in erythrocytes, brain, or fibroblasts, a subset is present in differentiated oviduct cells that have estrogen receptors, but do not express VTG II.

Demonstration of an S1-nuclease sensitive site near the human beta-globin gene, and its protection by HMG 1 and 2

An S1-nuclease sensitive site exists within supercoiled plasmids containing the 5'-flanking sequences of the human beta-globin gene. This site is located approximately 540 base pairs upstream from the start of the gene within a region of 52 alternating purine-pyrimidine residues which has the potential to adopt either cruciform structures or Z-form DNA. This site is protected from specific cleavage by S1-nuclease by the high-mobility-group chromosomal proteins HMG1 and 2, which may be specifically acting to protect short sequences of single-stranded DNA.

A dominant role for DNA secondary structure in forming hypersensitive structures in chromatin

Previous work has suggested that potential information in DNA secondary structure might be used by cells to define DNAase 1- and S1-sensitive chromatin structures associated with promoter and terminator regions. To test this hypothesis, supercoiled pBR322 was cotransfected into L cells. For the majority of transfected clones supercoil-induced S1-sensitive sites in pure pBR322 DNA are also S1-sensitive in L-cell nuclei. These results suggest that the potential of certain DNA sequences to form specific secondary structures in chromatin can be a dominant characteristic. A recombinant chicken beta A-globin supercoiled plasmid was reconstituted in vitro with histones. The reconstituted chromatin also retained the ability to form S1-sensitive sites. Evidence suggests that DNA sequences capable of forming S1-sensitive sites in supercoiled plasmids may bind nucleosomes poorly after reconstitution with histones.

Transcription of DNA injected into Xenopus oocytes is influenced by template topology

We have assayed the transcription of the herpes simplex virus thymidine kinase gene on circular and linear plasmids after injection into Xenopus oocytes. The circular plasmids appear to be transcribed at least 500 times more efficiently than the linear plasmids. Moreover, when the circular templates are allowed to form functioning transcription complexes, and are then linearized in situ, the synthesis of accurate transcripts is substantially reduced.

The nuclease sensitivity of active genes

Brief micrococcal nuclease digestion of chick embryonic red blood cells results in preferential excision and solubilization of monomer nucleosomes associated with beta-globin sequences and also 5'-sequences flanking the beta-globin gene. Both regions are DNAse-I sensitive in nuclei. Such salt-soluble nucleosomes are enriched in all four major HMG proteins but HMG1 and 2 are only weakly associated. These nucleosomes appear to have lost much of the DNAse-I sensitivity of active genes. The HMG14 and 17-containing salt-soluble nucleosomes separated by electrophoresis are not DNAse-I sensitive and contain inactive gene sequences as well as active sequences. Reconstitution of HMG proteins onto bulk nucleosomes or chromatin failed to reveal an HMG-dependent sensitivity of active genes as assayed by dot-blot hybridization and it was found that the DNAse-I sensitivity of ASV proviral sequences as assayed by dot-blot hybridization was not HMG-dependent. These results indicate that higher order chromatin structures might be responsible for nuclease sensitivity of active genes.

DNase I hypersensitive regions correlate with a site-specific endogenous nuclease activity on the r-chromatin of Tetrahymena

A novel nuclease activity have been detected at three specific sites in the chromatin of the spacer region flanking the 5'-end of the ribosomal RNA gene from Tetrahymena. The endogenous nuclease does not function catalytically in vitro, but is in analogy with the DNA topoisomerases activated by strong denaturants to cleave DNA at specific sites. The endogenous cleavages have been mapped at positions +50, -650 and -1100 relative to the 5'-end of the pre-35S rRNA. The endogenous cleavage sites are associated with micrococcal nuclease hypersensitive sites and DNase I hypersensitive regions. Thus, a single well-defined micrococcal nuclease hypersensitive site is found approximately 130 bp upstream from each of the endogenous cleavages. Clusters of defined sites, the majority of which fall within the 130 bp regions defined by vicinal micrococcal nuclease and endogenous cleavages, constitute the DNase I hypersensitive regions.

Functional relationships between transcriptional control signals of the thymidine kinase gene of herpes simplex virus

Transcriptional control signals occur at three separate locations upstream from the herpes virus thymidine kinase gene. I have used two approaches to examine how these signals function in relation to one another. First, double mutants that simultaneously mutate various pairs of transcriptional signals were constructed. Analyses of the transcriptional phenotypes of such mutants suggest that the two most distally located signals may function in the same metabolic step, whereas the proximal signal appears to function in a process distinct from that of the distal signals. Second, the distances that normally separate the three transcriptional signals were systematically altered. These condensation and expansion mutants were studied to determine to what extent the spatial relationship between the signals is important to their function. The transcriptional phenotypes of these spacing-change mutants show that the amount of DNA that separates the three transcriptional signals is not rigidly fixed.

Human metallothionein genes--primary structure of the metallothionein-II gene and a related processed gene

The complete nucleotide sequence of two of the human metallothionein gene family has been compared. One is a functional metallothionein-II gene, the other a pseudogene, lacking introns, terminating in a poly(A) tail and flanked by two direct repeats. In addition, we have detected a size polymorphism associated with the processed gene in the population, examined, and we have observed a region of apparent secondary structure homology between of 5' flanking region of the functional metallothionein-II gene and that of a mouse metallothionein-I gene.

Propagation of globin DNAase I-hypersensitive sites in absence of factors required for induction: a possible mechanism for determination

We tested whether DNAase I-hypersensitive sites, once induced, can be propagated to daughter cells in the absence of the original inducer. Chicken embryo fibroblasts infected with a temperature-sensitive Rous sarcoma virus at 41 degrees C and then shifted to 36 degrees C become transformed and begin to transcribe globin RNA. DNAase I-hypersensitive sites appear in the alpha- and beta-globin chromatin domains. Neither transcription nor hypersensitive sites are detected in cells infected and maintained at 41 degrees C. Activation of the globin hypersensitive sites occurs within 30 min of a temperature shift to 36 degrees C and does not require new protein synthesis. To test for the self-propagation of these hypersensitive structures, we inactivated the v-src gene product by a shift back up to 41 degrees C, and allowed the cells to divide 20 times at 41 degrees C. Although transcription of the globin genes was minimal after this treatment, the DNAase I-hypersensitive sites remained. The same sites can be induced by NaCl shock of cells. After the cells are returned to normal medium and allowed to grow for 20 doublings, the hypersensitive sites remain. This suggests that once formed, DNAase I-hypersensitive sites have the capacity to template their own structure independent of the initial "inductive" event. The single-stranded character of these DNAase I-hypersensitive sites could explain these results.

Transcriptional control signals of a eukaryotic protein-coding gene

Transcriptional control signals of a model eukaryotic protein-coding gene have been identified by a new procedure of in vitro mutagenesis. This method allows small clusters of nucleotide residues to be substituted in a site-directed manner without causing the addition or deletion of other sequences. Transcription assays of a systematic series of these clustered point mutants have led to the identification of three distinct control signals located within the 105-nucleotide residues immediately upstream from the point where transcription begins.