DNase I sensitivity of ribosomal genes in isolated nucleosome core particles

Genome-wide codon usage bias analysis in Beauveria bassiana

Codon usage bias analysis allows in identifying the factors that are influencing and contributing to shape the evolution of the organisms. Therefore, it is of interest to analyze 10363 gene sequences from Beauveria bassiana. The GC content with 51.50% is higher than the AT content (48.50%) in B. bassiana. The fungal nuclear genes tend to be GC rich and predominantly G/C ending. Codon usage bias exhibited by B. bassiana is based on the Relative Synonymous Codon Usage (RSCU) values of 61 sense codons, of which 28 codons are with RSCU value larger than 1. Other factors like Nucleotide composition, mutational pressure and selection also has a role in shaping the codon usage bias. We identified 24 optimal codons that end with G or C. Correlation analysis suggests existence of translational efficiency of amino acids. Based on the GC3s distribution evolution of the B. bassiana genes is by the contribution of mutation pressure. ENC may be the major factor in shaping the codon usage bias. This study provides insights into the compositional selection pressure of the genes in B. bassiana.

Chromatin states at ribosomal DNA loci

Eukaryotic transcription of ribosomal RNAs (rRNAs) by RNA polymerase I can account for more than half of the total cellular transcripts depending on organism and growth condition. To support this level of expression, eukaryotic rRNA genes are present in multiple copies. Interestingly, these genes co-exist in different chromatin states that may differ significantly in their nucleosome content and generally correlate well with transcriptional activity. Here we review how these chromatin states have been discovered and characterized focusing particularly on their structural protein components. The establishment and maintenance of rRNA gene chromatin states and their impact on rRNA synthesis are discussed. This article is part of a Special Issue entitled: Transcription by Odd Pols.

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.

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.

The DNA of ciliated protozoa

Ciliates contain two types of nuclei: a micronucleus and a macronucleus. The micronucleus serves as the germ line nucleus but does not express its genes. The macronucleus provides the nuclear RNA for vegetative growth. Mating cells exchange haploid micronuclei, and a new macronucleus develops from a new diploid micronucleus. The old macronucleus is destroyed. This conversion consists of amplification, elimination, fragmentation, and splicing of DNA sequences on a massive scale. Fragmentation produces subchromosomal molecules in Tetrahymena and Paramecium cells and much smaller, gene-sized molecules in hypotrichous ciliates to which telomere sequences are added. These molecules are then amplified, some to higher copy numbers than others. rDNA is differentially amplified to thousands of copies per macronucleus. Eliminated sequences include transposonlike elements and sequences called internal eliminated sequences that interrupt gene coding regions in the micronuclear genome. Some, perhaps all, of these are excised as circular molecules and destroyed. In at least some hypotrichs, segments of some micronuclear genes are scrambled in a nonfunctional order and are recorded during macronuclear development. Vegetatively growing ciliates appear to possess a mechanism for adjusting copy numbers of individual genes, which corrects gene imbalances resulting from random distribution of DNA molecules during amitosis of the macronucleus. Other distinctive features of ciliate DNA include an altered use of the conventional stop codons.

Independent evolutionary origin of histone H3.3-like variants of animals and Tetrahymena

All three genes encoding histone H3 proteins were cloned and sequenced from Tetrahymena thermophila. Two of these genes encode a major H3 protein identical to that of T. pyriformis and 87% identical to the major H3 of vertebrates. The third gene encodes hv2, a quantitatively minor replication independent (replacement) variant. The sequence of hv2 is only 85% identical to the animal replacement variant H3.3 and is the most divergent H3 replacement variant described. Phylogenetic analysis of 73 H3 protein sequences suggests that hv2, H3.3, and the plant replacement variant H3.III evolved independently, and that H3.3 is not the ancestral H3 gene, as was previously suggested (Wells, D., Bains, W., and Kedes, L. 1986, J. Mol. Evol., 23: 224-241). These results suggest it is the replication independence and not the particular protein sequence that is important in the function of H3 replacement variants.

Ribosomal DNA sequences attached to the nuclear matrix

The organization of rat liver ribosomal DNA (rDNA) as matrix-attached DNA loops was examined using a protocol which fractionates chromatin from discrete regions of DNA loops. Southern blot analysis of matrix-attached and solubilized chromatin DNA fragments demonstrated that rDNA is associated with the matrix via its 5' and 3' nontranscribed spacer sequences (NTS). Although the 45 S rRNA coding sequences were approximately threefold enriched in matrix preparations, the recovery of this DNA (unlike the NTS) was dependent on the extent of nuclease digest and proportional to the length of the matrix-attached DNA fragments. The data suggest that rDNA is organized as matrix-attached DNA loops and only the NTS are directly involved in matrix binding. Further, we demonstrated that while the kinetics and extent of nuclease digestion were similar in all regions of the DNA loops, the nuclease digestion pattern of bulk nuclear and matrix DNA showed a typical nucleosome organization, but the rDNA fragments retained with the nuclear matrix did not.

Affinity chromatographic purification of nucleosomes containing transcriptionally active DNA sequences

The unfolding of nucleosome cores in transcriptionally active chromatin uncovers the sulfhydryl groups of histone H3, making them accessible to SH-reagents. This has suggested that nucleosomes from active genes could be retained selectively on organomercurial/agarose columns. When nucleosomes released from rat liver nuclei by limited digestion with micrococcal nuclease were passed through an Hg affinity column, a run-off fraction of compact, beaded nucleosomes was separated from a retained nucleosome fraction. Although both contained monomer-length DNA and a full complement of core histones, histones in the retained fraction were hyperacetylated. Dot blot hybridizations showed the Hg-bound nucleosome fraction to be enriched in DNA sequences transcribed by hepatocytes (serum albumin and transferrin genes), while a brain-specific gene (preproenkephalin) was not retained, but appeared in the nucleosomes of the run-off fraction. The results are discussed in light of other evidence linking hyperacetylation of histones H3 and H4 to conformational changes at the middle of the nucleosome core.

An intervening sequence in an unusual histone H1 gene of Tetrahymena thermophila

An intervening sequence of 254 base pairs interrupts the coding region of the single gene for macronuclear histone H1 of the ciliated protozoan, Tetrahymena thermophila. The intervening sequence has splice junctions similar to those found in RNA polymerase II genes of other organisms. No obvious similarities are observed between this intron and the self-splicing intervening sequence of the Tetrahymena ribosomal gene. The derived amino acid sequence describes a small extremely basic H1 protein missing most of the central hydrophobic domain that is conserved in all other H1 proteins. Macronuclei divide amitotically, without chromosome condensation, suggesting the conserved globular domain of H1 plays a role in higher-order chromatin structure.

Localization of specific rDNA spacer sequences to the mouse L-cell nucleolar matrix

Mouse L-cell nucleoli were isolated from sonicated nuclei by centrifugation and extensively treated with pancreatic DNase or micrococcal nuclease to obtain "core nucleoli." Core nucleoli still contained the precursors to rRNA and about 1% of the total nuclear DNA, which remained tightly bound even after the removal of some chromatin proteins with 2 M NaCl. The core nucleolar DNA electrophoresed in a series of discrete bands, 20 to about 200 base pairs in length. Hybridization tests with specific DNA probes showed that the DNA was devoid of sequences complementary to mouse satellite, mouse Alu-like, and 5S RNA sequences. It also lacked sequences coding for cytoplasmic rRNA species, since it did not hybridize to the 18S to 28S portion of rDNA in Northern blot analyses and none of it was protected by hybridization to a 100-fold excess of total cytoplasmic RNA in S1 nuclease assays. However, the core nucleolar DNA did hybridize to nontranscribed and external transcribed spacer rDNA sequences. We infer that specific portions of rDNA are protected from DNase action by a tight association with nucleolar structural proteins.

Eukaryotic ternary transcription complexes: transcription complexes of RNA polymerase II are associated with histone-containing, nucleosome-like particles in vivo

Using a psoralen crosslinking, radioactive labelling technique, we have previously been able to study ternary transcription complexes containing DNA-dependent RNA polymerases I and II which are released from rat liver nuclei by endogenous nuclease digestion [Sargan and Butterworth, refs 1 and 2]. Although the DNA component of these complexes was found to have a 'nucleosome-like' size profile and although the experimental conditions for autodigestion were designed to minimise histone rearrangement, it is necessary to provide further evidence that the periodicity of nuclease cutting around these transcription complexes is conferred by histones. Studies using secondary nuclease digestion of the released transcription complexes now show a digestion barrier characteristic of that conferred by nucleosomal histones which is lost if histones are removed from the complexes. Furthermore, antibodies raised against histones are effective in precipitating transcription complexes of RNA polymerase II and, to a lesser extent, of RNA polymerase I. The data suggest that, in rat hepatic tissue, transcription complexes are in very close proximity (within a few hundred base pairs) of histone-containing, nucleosome-like particles in vivo.

Localization of specific rDNA spacer sequences to the mouse L-cell nucleolar matrix

Mouse L-cell nucleoli were isolated from sonicated nuclei by centrifugation and extensively treated with pancreatic DNase or micrococcal nuclease to obtain "core nucleoli." Core nucleoli still contained the precursors to rRNA and about 1% of the total nuclear DNA, which remained tightly bound even after the removal of some chromatin proteins with 2 M NaCl. The core nucleolar DNA electrophoresed in a series of discrete bands, 20 to about 200 base pairs in length. Hybridization tests with specific DNA probes showed that the DNA was devoid of sequences complementary to mouse satellite, mouse Alu-like, and 5S RNA sequences. It also lacked sequences coding for cytoplasmic rRNA species, since it did not hybridize to the 18S to 28S portion of rDNA in Northern blot analyses and none of it was protected by hybridization to a 100-fold excess of total cytoplasmic RNA in S1 nuclease assays. However, the core nucleolar DNA did hybridize to nontranscribed and external transcribed spacer rDNA sequences. We infer that specific portions of rDNA are protected from DNase action by a tight association with nucleolar structural proteins.

Compact structure of ribosomal chromatin in Xenopus laevis

Micrococcal nuclease digestion was used as a tool to study the organization of the ribosomal chromatin in liver, blood and embryo cells of X. laevis. It was found that in liver and blood cells, ribosomal DNA is efficiently protected from nuclease attack in comparison to bulk chromatin. Although ribosomal chromatin is fragmented in a typical nucleosomal pattern, a considerable portion of ribosomal DNA retains a high molecular weight even after extensive digestion. A greater accessibility of the coding region in comparison to the non-coding spacer was found. In embryos, when ribosomal DNA is fully transcribed, these genes are even more highly protected than in adult tissues: in fact, the nucleosomal ladder can hardly be detected and rDNA is preserved in high molecular weight. Treatment of chromatin with 0.8 M NaCl abolishes the specific resistance of the ribosomal chromatin to digestion. The ribosomal chromatin, particularly in its active state, seems to be therefore tightly complexed with chromosomal proteins which protect its DNA from nuclease degradation.

Varigated chromatin structures of mouse ribosomal RNA genes

We have employed a chromatin fractionation procedure on micrococcal nuclease-digested nuclei to examine the chromatin structure of mouse ribosomal RNA genes in two systems that differ by at least 14-fold in the level of ribosomal RNA transcription. In a cultured cell line enriched in transcriptionally active ribosomal chromatin, most ribosomal sequences are preferentially sensitive to digestion by micrococcal nuclease, reside in an insoluble chromatin fraction, and lack typical nucleosomal packaging; only minor amounts of ribosomal sequences are packaged into soluble, nucleosomal chromatin. By contrast, in adult liver, which is enriched in transcriptionally inactive ribosomal chromatin, the majority of ribosomal genes are packaged into soluble, nucleosomal chromatin. However, a significant fraction of liver ribosomal chromatin is insoluble and possesses a non-nucleosomal structure. Therefore, within a single cell population or tissue, mouse ribosomal RNA genes are organized into both nucleosomal and non-nucleosomal chromatin structures. We suggest that these structures have functional significance.

Chromatin structure along the ribosomal DNA of Dictyostelium. Regional differences and changes accompanying cell differentiation

The ribosomal genes of Dictyostelium discoideum are extrachromosomal palindromic DNA molecules situated in the nucleolus. Each molecule comprises ribosomal RNA coding regions and non-transcribed spacer regions. We used both biochemical and electron microscopic approaches to investigate the structure of transcribing and non-transcribing chromatin. Nucleoli from exponentially growing cells were digested with micrococcal nuclease, and the resulting DNA fragments were separated by gel electrophoresis and transferred to DBM paper. They were hybridized with cloned EcoRI fragments derived from different parts of the ribosomal gene. Probes of the coding region showed a smear, while probes of the non-transcribed regions gave pronounced banding patterns more complex than typical nucleosome repeats, but not due solely to sequence-specific cutting by micrococcal nuclease. The DNA of the coding region was digested more quickly than that of the non-transcribed ones. When nucleoli were digested with restriction enzymes, sites within the coding region were accessible and sites in the non-transcribed region were protected. The structure of ribosomal chromatin in differentiating cells, in which the rate of ribosomal RNA synthesis is reduced, was examined using essentially the same methods. The coding region, probed by hybridization to micrococcal digests, then showed a typical DNA repeat pattern indicating that this region had become condensed into nucleosomes, and its accessibility to restriction enzymes was very much reduced. On electron micrographs of lysed nucleoli from exponentially growing cells, two types of chromatin were observed, one with a beaded nucleosomal appearance, the other with putative RNA polymerase molecules attached to fibres indistinguishable from free DNA adsorbed to the same grid. The combined results suggest that whereas regions that are not transcribed are packaged with proteins that protect them from nuclease digestion, actively transcribing ribosomal genes are associated with few macromolecular constituents apart from those required for transcription and its regulation.

DNase I sensitivity of transcriptionally active genes in intact nuclei and isolated chromatin of plants

We have investigated the DNase I sensitivity of transcriptionally active DNA sequences in intact nuclei and isolated chromatin from embryos of wheat (Triticum aestivum L.). Nuclei or isolated chromatin was incubated with DNase I, and the extent of DNA digestion was monitored as percentage acid solubility. The resistant DNA and DNA from sham-digested controls were used to drive reassociation reactions with cDNA populations corresponding to either total poly(A)+RNA from unimbibed wheat embryos or polysomal poly(A)+RNA from embryos that had imbibed for 3 hr. Sequences complementary to either probe were depleted in DNase I-resistant DNA from nuclei and from chromatin isolated under low-ionic-strength conditions. This indicates that transcriptionally active sequences are preferentially DNase I sensitive in plants. In chromatin isolated at higher ionic strength, cDNA complementary sequences were not preferentially depleted by DNase I treatment. Therefore, the chromatin structure that confers preferential DNase I sensitivity to transcriptionally active genes appears to be lost when the higher-ionic-strength method of preparation is used. Treatment of wheat nuclei with DNase I causes the release of four prominent nonhistone chromosomal proteins that comigrate with wheat high mobility group proteins on NaDodSO4 gels.

Correlation of nitrosourea murine bone marrow toxicity with deoxyribonucleic acid alkylation and chromatin binding sites

All of the clinically available nitrosourea antitumor agents produce serious treatment-limiting bone marrow toxicity. A reduction in this toxicity can be achieved by attaching the chloroethylnitrosourea cytotoxic group to C2 (chlorozotocin) or C1 (1-(2-chloroethyl)-3-(beta-D-glucopyranosyl)-1-nitrosourea, GANU) of glucose. Both glucose analogs are less myelotoxic in mice than 1-(2-chloroethyl)-3-cyclohepyl-1-nitrosourea (CCNU) or 1-(4-amino-2-methylpyrimidin-5-yl)methyl-3-(2-chloroethyl)-3-nitrosourea (ACNU), while retaining comparable antitumor activity against the murine L1210 leukemia. To define the nuclear mechanisms for this reduced myelotoxicity, alkylation of L1210 and murine bone marrow DNA was quantitated. With the use of the endonuclease micrococcal nuclease and DNase I, the sites of alkylation within the chromatin substructure were determined. Experiments were performed on L1210 leukemia or bone marrow cells that had been incubated in vitro for 2 hr with 0.1 mM [14C]chloroethyl drug. The quantitative alkylation of DNA by GANU was 1.3-fold greater in L1210, as compared to bone marrow, cells. This ratio of DNA alkylation is comparable to the 1.3 ratio we previously reported for chlorozotocin [L. C. Panasci, D. Green and P. S. Schein, J. clin. Invest. 64, 1103 (1979)]. In contrast, the ratio of alkylation (L1210:bone marrow DNA) for the myelotoxic ACNU was 0.66, similar to 0.59 for CCNU. Nuclease digestion experiments demonstrated that chlorozotocin and GANU preferentially alkylated internucleosomal linker regions of bone marrow chromatin, while nucleosome core particles were the preferred targets of CCNU and ACNU. The reduced myelotoxicity of chlorozotocin and GANU may be correlated with the advantageous ratio of L1210:bone marrow DNA alkylation and preferential alkylation of internucleosomal regions of bone marrow chromatin.

Photoaffinity labeling of chromatin. Synthesis and properties of arylazido derivatives of 9-aminoacridine: potential photolabels for chromatin studies

The syntheses and properties of potential photoaffinity labels for the proteins in chromatin studies are described. One compound, N,N'-bis-(9-acridinyl)-4-aza-4-(4-azidobenzoyl)-1,7-diaminoheptane dihydrochloride, has been studied more closely. This photolabel shows high affinity towards DNA (Ka approximately 3 x 10(5) M-1) and photoreacts with histones at wavelengths in the range 260-450 nm. The photoreaction was monitored fluorimetrically, and labeling of histones H1, H2A/H2B and H3 was observed. When chromatin was photolabeled, labeling of H1 was exclusively quenched by NaCl at concentrations which are known to cause dissociation of this histone from the DNA. It is inferred that only DNA-associated proteins are photolabeled by the reagent.

Characterization of rat liver oligonucleosomes enriched in transcriptionally active genes: evidence for altered base composition and a shortened nucleosome repeat

A transcriptionally active chromatin fraction of oligonucleosome size has been separated and isolated by a modified micrococcal nuclease fractionation procedure. After mild enzymatic digestion, rat liver nuclei were lysed, and the chromatin was separated by centrifugation on linear sucrose gradients. Fractions from four regions of the gradient were pooled and labeled, from the top to the bottom, A, B, C, and D, respectively. Fraction A, which contained 20% or less of the total DNA, was determined to have a mean size of a hexanucleosome. By hybridization with [3H]cDNA transcribed from total cytoplasmic poly(A) mRNA, DNA from fraction A was shown to be 10-15-fold enriched in transcribing genes when compared with total DNA. This fraction also has a somewhat higher concentration of AT base sequences. Significant differences were observed in nucleosome phasing. Fraction A has the shortest repeat length, fractions B and C are intermediate, and fraction D, which is depleted in transcribing DNA sequences, has the longest. Thus, we have isolated a chromatin fraction of oligonucleosome size enriched in transcribing genes and organized with reduced nucleosome spacing.

Nuclease sensitivity of chromatin containing active genes: kinetic analyses utilizing continuous elution of digestion products from an ultrafiltration cell

Methods have been developed to analyze the kinetics of digestion of chromatin by nucleases. Radioactively labeled nuclei were incubated with enzyme in an ultrafiltration apparatus and digestion rates of different chromatin samples were computed employing a least-squares curve fitting technique to fit the data to zero-order and/or first-order kinetic models. These methods allow detailed kinetic analyses on small amounts of chromatin. Two biological systems were studied. 1) Tetrahymena thermophila macronuclei and micronuclei were compared; these nuclei differ in their transcriptional activities. 2) Ribosomal DNA (rDNA) of Tetrahymena pyriformis, approximately 60% of which codes for rRNA, can be preferentially labeled during starvation-refeeding; its digestion kinetics relative to bulk chromatin were studied. DNase I digested 20-40% of the macromolecular DNA about 3 times faster than bulk macronuclear or micronuclear DNA, and 60-80% of ribosomal gene-containing chromatin about 5 times faster than bulk chromatin. Filter hybridization studies of the DNAase I sensitivity of tRNA, 5S RNA, and ribosomal genes yielded similar results. These data are consistent with the observation that transcribed genes are especially sensitive to attach by DNase I and suggest that activated chromatin structure as probed by extensive DNase I digestion is the same in higher and lower eucaryotes for genes transcribed by all three RNA polymerases. Digestion kinetics of micrococcal nuclease were found to depend on the digestion conditions employed. These two biological systems and the methods we have developed should facilitate analyses of the factors responsible for maintaining an active chromatin structure.

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.

Nuclease-sensitive regions on the extrachromosomal r-chromatin from Tetrahymena pyriformis

The extrachromosomal DNA coding for the ribosomal precursor in Tetrahymena contains a transcribed region with a size of 6 x 10(3) base pairs plus non-transcribed central and distal spacers. In the present study the chromatin structure of the transcribed region and the terminal spacer have been compared. Micrococcal nuclease and DNase I were used to investigate the nucleosomal and the higher order structures. The specific DNA fragments were visualized by gel electrophoresis, Southern blotting onto nitrocellulose sheets and hybridization with specific 32P-labelled RNA probes. Investigations of the cleavage patterns demonstrate the presence of a defined nucleosomal structure in the non-transcribed region, while there is no indication of a nucleosomal pattern in the transcribed region. Specific regions on the r-chromatin are hypersensitive to DNase I. The first cleavage occurs in the non-transcribed central spacer region, while the second cleavage takes place in a region near the 3' end. The hypersensitivity of the central part of r-chromatin is also found by autodigestion in isolated nucleoli.

Structure of nucleosome core particles containing uH2A (A24)

We have purified uH2A (A24) and reconstituted it, in place of H2A, into high molecular weight nucleohistone containing the core histones and DNA. uH2A-containing core particles were then prepared by nuclease digestion and studies on these particles were carried out. We show that two uH2A molecules can be accommodated within a core particle. We also show that the presence of two uH2A molecules in a core particle does not alter significantly either the pattern or the rate of DNase I digestion as compared to both reconstituted and native core particles. Finally, we show that HMG proteins 14 and 17 can bind to uH2A-containing core particles. We conclude that uH2A has little influence on structure at the level of individual nucleosomes.

Selective release of HMG nonhistone proteins during DNase digestion of Tetrahymena chromatin at different stages of the cell cycle

The possible role of LG-1, a Tetrahymena specific HMG protein found in the macronuclear chromatin (Hamana, K. and Iwai, K. (1979) J. Biochem. 86, 789-794), was examined in relation to the chromatin structure. The chromatin isolated from cells synchronized at different stages of the cell cycle contained about one molecule of LG-1 per nucleosome. Limited digestion of the chromatin with DNase I or micrococcal nuclease selectively released LG-1 with the nucleosomal core histones and H1 remained insoluble, bound to the resistant DNA. Depending on the cell stages several types of chromatin structure were distinguished by their nuclease sensitivity. However, the chromatin at different stages exhibited the similar behavior of the LG-1 release with the nucleases as a function of the degree of chromatin solubilization. The results suggest that LG-1 proteins play a role in the chromatin organization which is rather independent of the cell stages.

The roles of H1, the histone core and DNA length in the unfolding of nucleosomes at low ionic strength

Calf thymus nucleosomes exhibit two different and independent hydrodynamic responses to diminishing salt concentration. One change is gradual over the range 40 to 0.2 mM Na+ and is accompanied by decreases in contact-site cross-linking efficiency. The other change is abrupt, being centered between 1 and 2 mM Na+. We found only one abrupt change in sedimentation rate for particles ranging in DNA content fom 144 to 230 base pairs. This response to decreasing ionic strength is similar for particles of both 169 and 230 base pairs. Core particles (144 base pairs) exhibit a somewhat diminished response. The abrupt change is blocked by formaldehyde or dimethylsuberimidate cross-linking. The blockage by dimethylsuberimidate demonstrates that the abrupt conformational change requires the participation of the core histones. H1 completely blocks the abrupt but not the gradual conformational change. Thus H1 uncouples the different responses to low ionic strength and exerts an important constraint on the conformational states available to the nucleosome core.

Heat shock, deciliation and release from anoxia induce the synthesis of the same set of polypeptides in starved T. pyriformis

Heat shock, deciliation and release from anoxia result in similar alterations in the pattern of protein synthesis in starved Tetrahymena pyriformis. In each case, synthesis of the same set of (at least) 16 polypeptides is induced, and many of these polypeptides accumulate in stainable amounts within 50 min. The molecular weights of these proteins, which we refer to as stress proteins (sp), are very similar to those of the heat shock polypeptides of Drosophila. Heat shock and deciliation also lead to similar changes in proteins associated with isolated nuclei. One stress-induced polypeptide, designated sp29c, is highly enriched in the nucleus. This protein is undetectable in control cells but is synthesized in response to stress and accumulates in the nucleus in stainable amounts within 50 min. It is not released by staphylococcal nuclease digestion, suggesting that it is not chromatin-associated. Three other stress-induced proteins, sp73 and sp75a and b, are also present in nuclei isolated from stressed cells but, unlike sp29c, are not enriched in this compartment. Another protein, which is present in stainable quantities in the cytoplasm of control cells, appears to be translocated to the nucleus after stress.