Chromatin structure and gene activity: the role of nonhistone chromosomal proteins

Correlation between DNase I hypersensitive sites and putative regulatory sequences in human immunoglobulin genes of the kappa light chain type

The human lymphoid cell lines Walker and Daudi constitute a particularly suitable system for studies on the chromatin structure of K light chain genes (see preceding paper). The rearranged and non-rearranged alleles of Walker cells were found to be about equally sensitive towards digestion with DNAase I. A DNAase I hypersensitive site was mapped 0.13 kb upstream of the leader segment of the rearranged VK genes; it comprises a region in which promoter-like regulatory elements were discovered recently. Additional hypersensitive sites are located further upstream. A hypersensitive site in the JK-CK intron coincides with a putative tissue specific enhancer element. A hypersensitive region down-stream of CK overlaps with the cleavage/polyadenylation recognition signal which is flanked by sequences related to the above mentioned putative regulatory sequences. The coincidence between DNAase I hypersensitive sites and those sequences may be functionally significant.

A model chromatin assembly system. Factors affecting nucleosome spacing

Poly[d(A-T)].poly[d(A-T)], when reconstituted with chicken erythrocyte core histones and subsequently incubated with sufficient histone H5 in a solution containing polyglutamic acid, forms structures resembling chromatin. H5 induces nucleosome alignment in about two hours at physiological ionic strength and 37 degrees C. The nucleosome spacing and apparent linker heterogeneity in the assembled nucleoprotein are very similar to those in chicken erythrocyte chromatin. Also, condensed chromatin-like fibers on the polynucleotide can be visualized. The binding of one mole of H5 per mole of core octamer is necessary to generate the physiological nucleosome spacing, which remains constant with the addition of more H5. The nucleosome repeat length is not a function of the core histone to poly[d(A-T)] ratio for values lower than the physiological ratio. With increasing ratios, in excess of the physiological value, nucleosome spacing first becomes non-uniform, and then takes on the close packing limit of approximately 165 base-pairs. In addition to eliminating possible base sequence effects on nucleosome positioning, poly[d(A-T)] allows nucleosomes to slide more readily than does DNA, thereby facilitating alignment. Evidence is presented that polyglutamic acid facilitates the nucleosome spacing activity of histone H5, primarily by keeping the nucleoprotein soluble. This model system should be useful for understanding how different repeat lengths arise in chromatin.

Alternative sets of DNase I-hypersensitive sites characterize the various functional states of the chicken lysozyme gene

The structural organization of chromatin is thought to determine the state of differentiation and activity of eukaryotic genes. Local interruptions of the regular nucleosomal array, the so-called DNase-hypersensitive sites, may indicate regions of the genome which play a critical part in regulation of differential gene activity. We present here two new observations on the chromatin structure of the chicken lysozyme gene, which strongly support a regulatory function for these sites. First, different sets of DNase I-hypersensitive sites have been found upstream from the promoter, depending on whether the gene is constitutively expressed (cultured macrophages) or in the steroid hormone-controlled state (oviduct). It seems, therefore, that diverse modes of regulation of the same gene are associated with discrete patterns of DNase I hypersensitivity. Second, one of the DNase I-hypersensitive sites in the oviduct chromatin disappears and reappears on steroid hormone withdrawal and secondary induction. These reversible changes in a narrow chromatin region reflect the transition from the potentially active to the active state of the lysozyme gene.

Transcriptionally active chromatin

Eukaryotic chromatin has a dynamic, complex hierarchical structure. Active gene transcription takes place on only a small proportion of it at a time. While many workers have tried to characterize active chromatin, we are still far from understanding all the biochemical, morphological and compositional features that distinguish it from inactive nuclear material. Active genes are apparently packaged in an altered nucleosome structure and are associated with domains of chromatin that are less condensed or more open than inactive domains. Active genes are more sensitive to nuclease digestions and probably contain specific nonhistone proteins which may establish and/or maintain the active state. Variant or modified histones as well as altered configurations or modifications of the DNA itself may likewise be involved. Practically nothing is known about the mechanisms that control these nuclear characteristics. However, controlled accessibility to regions of chromatin and specific sequences of DNA may be one of the primary regulatory mechanisms by which higher cells establish potentially active chromatin domains. Another control mechanism may be compartmentalization of active chromatin to certain regions within the nucleus, perhaps to the nuclear matrix. Topological constraints and DNA supercoiling may influence the active regions of chromatin and be involved in eukaryotic genomic functions. Further, the chromatin structure of various DNA regulatory sequences, such as promoters, terminators and enhancers, appears to partially regulate transcriptional activity.

Origin of replication in episomal bovine papilloma virus type 1 DNA isolated from transformed cells

The origin of replication of bovine papilloma virus type 1 (BPV-1) has been determined by isolating replicative intermediates (RI) of BPV-transformed hamster embryo fibroblasts (HEF-BPV). These RI were treated with single cut restriction enzymes to determine the start-position (origin) of the extending replication eyes using electron microscopic techniques. 'Cairns'-type RI molecules were shown to contain one replication eye in monomeric as well as in dimeric molecules. The position of this eye was localized at 6940 +/- 5% bp in the physical map. In a second set of experiments BPV-1 DNA fragments cloned in pBR322 were tested for transient episomal replication. Transfected cells were harvested after increasing periods of time and screened for replication with isoschizomeric restriction enzymes to differentiate between input and replicated DNA. The part of the BPV genome harboring the replication origin spans the BPV ClaI-C restriction fragment corresponding to the non-coding region of the BPV genome and coincides with the DNase I-hypersensitive control region in the chromatin, isolated from transformed cells.

Nuclease digestion of circular TRP1ARS1 chromatin reveals positioned nucleosomes separated by nuclease-sensitive regions

TRP1ARS1 is a circular yeast DNA of 1453 base-pairs that contains the N-5'phosphoribosyl anthranilate isomerase (TRP1) gene and a sequence important for autonomous replication (ARS1). It exists extrachromosomally in 100 to 200 copies/cell and is presumably packed in nucleosomes. TRP1ARS1 has been partially purified as chromatin from lysed spheroplasts of yeast using gel filtration. A structural analysis of mapping micrococcal nuclease and DNAase I cutting sites with an accuracy of +/- 20 base-pairs is presented. Comparison of nuclease cleavage sites in chromatin and in purified DNA reveals that regions which are protected against nuclease attack are not distributed randomly. These regions are big enough to accommodate nucleosome cores. Three nucleosomes are positioned in the so-called ARS sequences, and are stable at low and high levels of digestion. The TRP1 gene region is covered by four nucleosomes, but they are neither randomly arranged nor precisely positioned. They are not stable and rearrange or disintegrate during digestion. The nucleosomal regions are separated by two segments of DNA (A, B), each about 180 base-pairs long, which are very sensitive to DNAase I and micrococcal nuclease and therefore presumably not packed in nucleosomes. Region B is found 5' to the TRP1 gene and might be related to transcription, whereas region A is centered around the termination codon of the TRP1 gene and the putative origin of replication.

DNA replication and chromatin structure of simian virus 40 insertion mutants

Insertion of DNA segments into the nuclease-sensitive region of simian virus 40 alters both replication efficiency and chromatin structure. Mutants containing large insertions between the simian virus 40 origin of replication (ori site) and the 21-base-pair repeated sequences replicated poorly when assayed by transfection into COS-1 cells. Replication of mutants with shorter insertions was moderately reduced. This effect was cis-acting and independent of the nucleotide sequence of the insert. The nuclease-sensitive chromatin structure was retained in these mutants, but the pattern of cleavage sites was displaced in the late direction from the ori site. New cleavage sites appeared within the inserted sequences, suggesting that information specifying the nuclease-sensitive chromatin structure is located on the late side of the inserts. Accessibility to BglI (which cleaves within the ori site) was reduced in the larger insertion mutants. These results support the conclusion that efficient function of the viral origin of replication is correlated with its proximity to an altered chromatin structure.

Structural properties of barley nucleosomes

The structural properties of barley oligonucleosomes are investigated and compared to those of rat liver oligomers. Extraction of barley chromatin was performed using mild nuclease digestion of isolated nuclei leading to a low ionic strength soluble fraction. Oligonucleosomes were fractionated on sucrose gradients and characterized for DNA and histone content. Physico-chemical studies (sedimentation, circular dichroism and electric birefringence) showed that barley oligonucleosomes exhibit properties very close to those of the H1-depleted rat liver counterparts. Moreover, in situ, barley linker DNA was more sensitive to micrococcal nuclease digestion than that of rat liver. These results suggest that barley oligonucleosomes show a less compact structure than their rat liver counterparts and appear to be in contradiction with the very condensed organization of barley chromatin previously suggested.

Differences of supranucleosomal organization in different kinds of chromatin: cell type-specific globular subunits containing different numbers of nucleosomes

Fractions of homogeneously-sized supranucleosomal particles can be obtained in high yield and purity from various types of cells by brief micrococcal nuclease digestion (10 or 20 s) of condensed chromatin in 100 mM NaCl followed by sucrose gradient centrifugation and agarose gel electrophoresis. These chromatin particles, which contain only DNA and histones, differed according to cell type. Sea urchin spermatozoa (Paracentrotus lividus) gave rise to heavy particles (ca. 260 S) with a mean diameter (48 nm). These resembled the unit chromatin fibrils fixed in situ, which contain an average of 48 nucleosomes, as determined both by electron microscopy after unraveling in low salt buffer and gel electrophoresis. In contrast, higher order particles from chicken erythrocyte chromatin were smaller (105 S; 36-nm diam) and contained approximately 20 nucleosomes. The smallest type of supranucleosomal particle was obtained from chicken and rat liver (39 S; 32-nm diam; eight nucleosomes). Oligomeric chains of such granular particles could be recognized in regions of higher sucrose density, indicating that distinct supranucleosomal particles of globular shape are not an artifact of exposure to low salt concentrations but can be obtained at near-physiological ionic strength. The demonstration of different particle sizes in chromatin from different types of nuclei is contrary to the view that such granular particles are produced by artificial breakdown into "detached turns" from a uniform and general solenoid structure of approximately six nucleosomes per turn. Our observations indicate that the higher order packing of the nucleosomal chain can differ greatly in different types of nuclei and the supranucleosomal organization of chromatin differs between cell types and is related to the specific state of cell differentiation.

Barriers to nuclease Bal31 digestion across specific sites in simian virus 40 chromatin

A portion of the nucleoprotein containing viral DNA extracted from cells infected by simian virus (SV40) is preferentially cleaved by endonucleases in a region of the genome encompassing the origin of replication and early and late promoters. To explore this nuclease-sensitive structure, we cleaved SV40 chromatin molecules with restriction enzymes and digested the exposed termini with nuclease Bal31. Digestion proceeded only a short distance in the late direction from the MspI site, but some molecules were degraded 400 to 500 base pairs in the early direction. By comparison, BglI-cleaved chromatin was digested for only a short distance in the early direction, but some molecules were degraded 400 to 450 base pairs in the late direction. These barriers to Bal31 digestion (bracketing the BglI and the MspI sites) define the borders of the same open region in SV40 chromatin that is preferentially digested by DNase I and other endonucleases. In a portion of the SV40 chromatin, Bal31 could not digest through the nuclease-sensitive region and reached barriers after digesting only 50 to 100 base pairs from one end or the other. Chromatin molecules that contain barriers in the BglI to MspI region are physically distinct from molecules that are open in this region as evidenced by partial separation of the two populations on sucrose density gradients.

Nucleosomes are positioned on mouse satellite DNA in multiple highly specific frames that are correlated with a diverged subrepeat of nine base-pairs

Nucleosome phasing on highly repetitive DNA was investigated using a novel strategy. Nucleosome cores were prepared from mouse liver nuclei with micrococcal nuclease, exonuclease III and nuclease S1. The core DNA population that contains satellite sequences was then purified from total core DNA by denaturation of the DNA, reassociation to a low Cot value and hydroxyapatite chromatography to separate the renatured satellite fraction. After end-labeling, the termini of the satellite core DNA fragments were mapped with an accuracy of +/- 1 base-pair relative to known restriction sites on the satellite DNA. Sixteen dominant nucleosome positions were detected. There is a striking correlation between these nucleosome frames and an internal highly diverged 9 base-pair subrepeat of the satellite DNA. The results are consistent with a sequence-dependent association of histone octamers with the satellite DNA. Our finding that histone octamers can interact with a given DNA in a number of different defined frames has important implications for the possible biological significance of nucleosome phasing.

Positioning of nucleosomes in satellite I-containing chromatin of rat liver

The location of nucleosomes on rat satellite I DNA has been investigated using a new approach. Nucleosome cores were prepared from rat liver nuclei with micrococcal nuclease, exonuclease III and nucleases S1. From the total population of core DNA fragments the satellite-containing fragments were isolated by molecular cloning and the complete sequence of 50 clones was determined. The location of nucleosomes along the satellite sequence was found to be non-random. Our results show that nucleosomes occupy a number of positions on satellite I DNA. About 35 to 50% of all nucleosomes are positioned in two corresponding major sites, the remainder in about 16 less preferred sites. The major nucleosome positions are apparently strictly defined with the precision of a single base-pair. These results were confirmed by other approaches, including restriction nuclease digestion experiments. There are good indications of a defined long-range organization of the satellite chromatin fiber in two or more oligonucleosomal arrays with distinct nucleosome configurations.

Nuclear localization and phosphorylation of three 25-kilodalton rat stress proteins

The nuclear localization and phosphorylation of three 25-kilodalton rat myoblast stress proteins were examined. Data obtained in these analyses led to the following conclusions: (i) all three proteins become localized in the nucleus of stressed cells, (ii) two of the proteins are modified by phosphorylation, and (iii) phosphorylation occurs exclusively on serine residues.

Fractionation of the gene-size macronuclear chromatin fragments of the binucleated eukaryote Oxytricha

The macronuclear chromatin of Oxytrichia nova consists of chromatin fragments which are fully soluble in 0.2 mM EDTA and whose DNA length varies from 500-25 000 bp. The DNA migrates electrophoretically as a series of discrete bands, with specific genes present in only one or a few bands. The chromatin fragments are composed of nucleosomes and migrate electrophoretically in proportion to their DNA length. These results suggest schemes for the fractionation of undigested chromatin in order to enrich for specific genes, facilitating analysis of changes in chromatin structure associated with changes in gene expression.

Two human colon tumor cell lines with similar nuclease sensitivities have different ethidium bromide binding characteristics

Chromatin from two human colon adenocarcinoma cell lines (HT-29 and LoVo) showed similar digestion kinetics when sensitivities to DNase I and micrococcal nuclease were examined. Chromatin conformations were probed by examining the binding of ethidium bromide. A Scatchard plot revealed that both chromatins bound the same amount of ethidium bromide per mole of DNA, but the DNA from LoVo cells was more accessible to the intercalator. The results indicate that differences in chromatin conformation are not necessarily accompanied by different nuclease sensitivities.

Barriers to nuclease Bal31 digestion across specific sites in simian virus 40 chromatin

A portion of the nucleoprotein containing viral DNA extracted from cells infected by simian virus (SV40) is preferentially cleaved by endonucleases in a region of the genome encompassing the origin of replication and early and late promoters. To explore this nuclease-sensitive structure, we cleaved SV40 chromatin molecules with restriction enzymes and digested the exposed termini with nuclease Bal31. Digestion proceeded only a short distance in the late direction from the MspI site, but some molecules were degraded 400 to 500 base pairs in the early direction. By comparison, BglI-cleaved chromatin was digested for only a short distance in the early direction, but some molecules were degraded 400 to 450 base pairs in the late direction. These barriers to Bal31 digestion (bracketing the BglI and the MspI sites) define the borders of the same open region in SV40 chromatin that is preferentially digested by DNase I and other endonucleases. In a portion of the SV40 chromatin, Bal31 could not digest through the nuclease-sensitive region and reached barriers after digesting only 50 to 100 base pairs from one end or the other. Chromatin molecules that contain barriers in the BglI to MspI region are physically distinct from molecules that are open in this region as evidenced by partial separation of the two populations on sucrose density gradients.

Gene control by phosphoproteins: a theoretical model for eukarotic DNA regulation

Although gene regulatory mechanisms in eukaryotic cells are complex, some progress is being made in understanding them. Chromosomal proteins may play a significant role in genome function and gene control. More specifically, a central role may be played by the nuclear nonhistone proteins. It appears that both viral transformation and steroid hormone action may be associated with the phosphorylation of these proteins. Recent studies have revealed that some oncogenic viruses are capable of producing viral transforming proteins with protein kinase activity. This suggests how they may subvert normal gene regulatory mechanisms. Furthermore, the effects of the steroid-receptor complex on nuclear nonhistone proteins may be similar to the effects of these viral transforming proteins, but in a controlled sense. A model of gene-regulatory, nuclear phosphorylation reactions is formulated which suggests how some oncogenic viruses may control normal gene regulatory mechanisms and how steroid hormones may interact with these same mechanisms. Such a model may reveal how disruption of these same mechanisms leads to carcinogenesis.

Nuclear localization and phosphorylation of three 25-kilodalton rat stress proteins

The nuclear localization and phosphorylation of three 25-kilodalton rat myoblast stress proteins were examined. Data obtained in these analyses led to the following conclusions: (i) all three proteins become localized in the nucleus of stressed cells, (ii) two of the proteins are modified by phosphorylation, and (iii) phosphorylation occurs exclusively on serine residues.

Nucleotide sequence-directed mapping of the nucleosomes of SV40 chromatin

In our previous work we have shown by comparison of experimental and computational data that the positions of the histone octamers bound to the DNA molecule appear to be completely sequence-dependent. This provides a convenient and quick method for locating the nucleosomes along the DNA molecule, as soon as the nucleotide sequence is known. Using this computational approach, the complete nucleosomal map of the SV40 minichromosome has been constructed. The map consists of 25 nucleosomes, with their coordinates (centers) being specified with high accuracy. The map is found to be in remarkable agreement with available experimental data.

Induction of altered chromatin structures by simian virus 40 enhancer and promoter elements

Two simian virus 40 transcriptional promoter elements, the 72-base pair (bp) repeat and the 21-bp repeat region, induce chromatin structures of increased DNase I sensitivity when transposed elsewhere in the viral genome. The induction of a sufficiently long stretch of DNase I-sensitive chromatin leads to the appearance of a visible nucleosome-free region.

Chromatin structure of hsp 70 genes, activated by heat shock: selective removal of histones from the coding region and their absence from the 5' region

The presence of histones in hsp 70 genes was studied by "protein-image" hybridization technique after crosslinking histones to DNA. With increasing transcription of the genes, the coding region was demonstrated to be depleted first of H1 and then of all histones. This probably accounts for unraveling the 25 nm silent chromatin fiber to moderately and actively transcribed 10 nm fiber and linearized DNA. No histones were found in the 5'-terminal DNAase I-hypersensitive region, which may be a prerequisite to gene activation. The absence of histones on DNA correlates well with the high nuclease sensitivity and disappearance of the regular pattern in micrococcal nuclease digests of chromatin.

Gene control by phosphoproteins: a theoretical model for eukaryotic DNA regulation

Although gene regulatory mechanisms in eukaryotic cells are complex, some progress is being made in understanding them. Chromosomal proteins may play a significant role in genome function and gene control. More specifically, a central role may be played by the nuclear nonhistone proteins. It appears that both viral transformation and steroid hormone action may be associated with the phosphorylation of these proteins. Recent studies have revealed that some oncogenic viruses are capable of producing viral transforming proteins with protein kinase activity. This suggests how they may subvert normal gene regulatory mechanisms. Furthermore, the effects of the steroid-receptor complex on nuclear nonhistone proteins may be similar to the effects of these viral transforming proteins, but in a controlled sense. A model of gene-regulatory, nuclear phosphorylation reactions is formulated which suggests how some oncogenic viruses may control normal gene regulatory mechanisms and how steroid hormones may interact with these same mechanisms. Such a model may reveal how disruption of these same mechanisms leads to carcinogenesis.

Selective unfolding of erythroid chromatin in the region of the active beta-globin gene

Globin gene expression, which occurs exclusively in the erythroid cell lineage, is controlled at the level of transcription. It is thus of some considerable interest to compare the chromatin structure of this gene with that of inactive genes in erythroid cell nuclei and to compare the chromatin structure of the globin gene in its active and inactive states in nuclei of different cell types. Other workers have observed that globin genes in erythroid cell nuclei exhibit the enhanced overall sensitivity to nucleases and the hypersensitive site in the 5'-flanking sequence typical of many active genes. The nature of the structural changes giving rise to nuclease sensitivity are however obscure. We have investigated the local higher order structure of chromatin in the region of unique genes in chicken by sucrose gradient sedimentation of chromatin restriction fragments. We find that ovalbumin and alpha 2-collagen gene fragments in erythrocyte chromatin and an adult beta-globin gene fragment in spleen chromatin sediment with bulk chromatin fragments of the same DNA size, whereas the beta-globin gene fragment in erythrocyte chromatin sediments more slowly than bulk fragments of equivalent size. The simplest interpretation of the results is that the solenoid structure in the region of the globin gene is selectively and permanently unfolded on gene activation.

Ultraviolet radiation-induced metallothionein-I gene activation is associated with extensive DNA demethylation

Ultraviolet irradiation (UV) of cadmium-sensitive S49 mouse cells induces a large increase in cadmium-resistant variants. About 30%-40% of these variants make metallothionein (MT)-I mRNA while S49 cells do not. S49 cells contain two copies of the MT-I gene; both alleles are heavily methylated but can be conveniently distinguished by the methylation status of a single Hpa II site. In lines expressing MT-I, one allele becomes completely demethylated at all methylation-sensitive restriction sites examined over at least a 2.5 kb region spanning the MT-I gene. Activation of a quiescent gene by UV has implications for understanding the initiation of carcinogenesis.

Nuclear proteins associated with gene expression in mouse plasmacytoma cell lines

Nucleoplasmic and non-histone chromatin proteins from two unrelated and four related mouse plasmacytoma cell lines have been analysed by biosynthetic labelling with [35S]-methionine followed by one- and two-dimensional polyacrylamide gel electrophoresis. We have attempted to find a relationship between the patterns of nuclear proteins and gene expression in mutant plasmacytoma cell lines. The majority of nuclear proteins are common to all of the cell lines studied as would be expected if the majority of nuclear proteins are concerned with functions common to all plasma cells. There are, however, both qualitative and quantitative differences in the nuclear protein patterns of mutant and parent cell lines which appear to correlate with differences in gene expression. The turnover of nuclear proteins in two of the cell lines, MOPC 315.40 (IgA producer) and MOPC 315.32 (lambda 2 chain producer) was studied using pulse-chase techniques.

Eight different highly specific nucleosome phases on alpha-satellite DNA in the African green monkey

The question of nucleosome phasing on African Green Monkey (AGM) alpha-satellite DNA has been addressed by employing a new approach. Nucleosome cores were prepared from AGM nuclei with micrococcal nuclease, exonuclease III and nuclease S1. The core DNA population derived from alpha-satellite DNA containing chromatin was purified from total core DNA by denaturation of the DNA, reassociation to a low Cot value, and hydroxyapatite chromatography to separate the renatured satellite fraction. After end-labeling the termini of the alpha-satellite containing core DNA fragments were mapped by high resolution gel electrophoresis relative to known restriction sites along the 172 bp repeat unit of the satellite DNA. The results show that nucleosomes occupy eight strictly defined positions on the alpha-satellite DNA which could be determined with an accuracy of +/- 1 base pair. Approximately 35% of all nucleosomes are organized in one of these frames while the other seven registers contribute about 10% each.

Role of histones H1 and H3 in the maintenance of chromatin in a compact conformation. Study with an immobilized enzyme

Chromatin polynucleosomes have been digested with trypsin immobilized on collagen membranes. This method allows the mild removal of the most accessible histone fragments simply by dipping the enzymatic membrane into the chromatin solution, without modification of its ionic and chemical composition. These results demonstrate that the removal of H1 does not affect the higher-order structure of chromatin and that only the elimination of the terminal regions of H3 leads to the unfolding of H1-depleted fibres. This observation suggests that structural changes reported in many previous works were not due to only the removal of H1 but to a concomitant unbinding from DNA of the N-terminal domain of H3.

Cleavage of chromatin with methidiumpropyl-EDTA . iron(II)

Methidiumpropyl-EDTA . iron(II) [MPE . Fe (II)] cleaves double-helical DNA with considerably lower sequence specificity than micrococcal nuclease. Moreover, digestions with MPE . Fe(II) can be performed in the presence of certain metal chelators, which will minimize the action of many endogenous nucleases. Because of these properties MPE . Fe(II) would appear to be a superior tool for probing chromatin structure. We have compared the patterns generated from the 1.688 g/cm3 complex satellite, 5S ribosomal RNA, and histone gene sequences of Drosophila melanogaster chromatin and protein-free DNA by MPE . Fe(II) and micrococcal nuclease cleavage. MPE . Fe(II) at low concentrations recognizes the nucleosome array, efficiently introducing a regular series of single-stranded (and some double-stranded) cleavages in chromatin DNA. Subsequent S1 nuclease digestion of the purified DNA produces a typical extended oligonucleosome pattern, with a repeating unit of ca. 190 base pairs. Under suitable conditions, relatively little other nicking is observed. Unlike micrococcal nuclease, which has a noticeable sequence preference in introducing cleavages, MPE . Fe(II) cleaves protein-free tandemly repetitive satellite and 5S DNA sequences in a near-random fashion. The spacing of cleavage sites in chromatin, however, bears a direct relationship to the length of the respective sequence repeats. In the case of the histone gene sequences a faint, but detectable, MPE . Fe(II) cleavage pattern is observed on DNA, in some regions similar to and in some regions different from the strong chromatin-specified pattern. The results indicate that MPE . Fe(II) will be very useful in the analysis of chromatin structure.

Correlation of patterns of nuclear protein synthesis with differentiation of mitogen-stimulated B-lymphocytes

Nuclear proteins synthesised by mouse lymphocytes stimulated by the B-lymphocyte mitogen lipopolysaccharide have been analysed by 2-dimensional polyacrylamide gel electrophoresis. It has been shown that the rate of synthesis of both nucleoplasmic proteins and nonhistone chromatin proteins is stimulated dramatically by LPS and many nuclear proteins are synthesised that were undetectable in resting lymphocytes. The majority of these proteins are synthesised by lymphoblasts and plasma cells, the lymphocytes that remain small after LPS stimulation synthesizing relatively few proteins. Two chromatin proteins that have previously been shown to appear in the nucleus within 4h of mitogen stimulation exhibit a continuous increase in their rate of synthesis during lymphocyte differentiation. The possible roles of these proteins in differentiating lymphocytes are discussed.