The level of expression of the rat growth hormone gene in liver tumor cells is at least eight orders of magnitude less than that in anterior pituitary cells

Quiescence: early evolutionary origins and universality do not imply uniformity

Cell cycle investigations have focused on relentless exponential proliferation of cells, an unsustainable situation in nature. Proliferation of cells, whether microbial or metazoan, is interrupted by periods of quiescence. The vast majority of cells in an adult metazoan lie quiescent. As disruptions in this quiescence are at the foundation of cancer, it will be important for the field to turn its attention to the mechanisms regulating quiescence. While often presented as a single topic, there are multiple forms of quiescence each with complex inputs, some of which are tied to conceptually challenging aspects of metazoan regulation such as size control. In an effort to expose the enormity of the challenge, I describe the differing biological purposes of quiescence, and the coupling of quiescence in metazoans to growth and to the structuring of tissues during development. I emphasize studies in the organism rather than in tissue culture, because these expose the diversity of regulation. While quiescence is likely to be a primitive biological process, it appears that in adapting quiescence to its many distinct biological settings, evolution has diversified it. Consideration of quiescence in different models gives us an overview of this diversity.

The pre-omics era: the early days of two-dimensional gels

I present a personal view of the beginning of two-dimensional gels and unsanctioned proteomics. I was still a young graduate student in the early 1970s when I developed methods for two-dimensional gel electrophoresis that became widely used. Though the method gave us the capacity to do things that had never been done, the value of global enumeration of proteins was not appreciated, and we were still two decades away from the invention of the term proteomics. I describe a period of exploration where, by exercising our new capability, we conducted the first proteomic type expression experiments, and made unforeseen contributions to advances in biology. Detection of single-amino acid substitutions validated genetic selections in cultured cells, and revealed a regulatory system that maintains the accuracy of protein synthesis by assuring an unbiased supply of its substrates. We documented biologic control with a dynamic range >10(8) fold, and, in a surprising turn, we identified an approach that provided a major breakthrough in recombinant DNA technology, the ability to express cloned sequences in Escherichia coli. The challenge then and now is to use a capability for global analysis to produce new insights into fundamental aspects of biology and to drive substantive technical advances.

Dynamic Chromatin Loops and the Regulation of Gene Expression

Although we have a draft sequence of the human genome, little is known about how the chromatin fiber is packed in three-dimensional (3D) space, or how packing affects function (Jackson 2003). We know packing plays a major role; the rate of transcription of a typical gene can vary over eight orders of magnitude (Ivarie et al. 1983), but deleting local elements like promoters and enhancers reduces expression by less than 5000-fold in transient transfection assays where the 3D “context” is missing. Common sense suggests the fiber cannot be packed randomly, but elucidating what any underlying order might be has proved difficult. First, the foldings of the chromatin fiber have dimensions below the resolution (≈200 nm) of the light microscope (LM) and so can only be seen by electron microscopy (EM), but then the fixation required can distort structure. Second, DNA is so long and packed so tightly it breaks and/or aggregates easily on isolation. Third, chromatin is poised in a metastable state so small charge alterations trigger changes in structure and function, and replacing the natural environment with our buffers often promotes aggregation.

Chromosome organization and chromatin modification: influence on genome function and evolution

Histone modifications of nucleosomes distinguish euchromatic from heterochromatic chromatin states, distinguish gene regulation in eukaryotes from that of prokaryotes, and appear to allow eukaryotes to focus recombination events on regions of highest gene concentrations. Four additional epigenetic mechanisms that regulate commitment of cell lineages to their differentiated states are involved in the inheritance of differentiated states, e.g., DNA methylation, RNA interference, gene repositioning between interphase compartments, and gene replication time. The number of additional mechanisms used increases with the taxon's somatic complexity. The ability of siRNA transcribed from one locus to target, in trans, RNAi-associated nucleation of heterochromatin in distal, but complementary, loci seems central to orchestration of chromatin states along chromosomes. Most genes are inactive when heterochromatic. However, genes within beta-heterochromatin actually require the heterochromatic state for their activity, a property that uniquely positions such genes as sources of siRNA to target heterochromatinization of both the source locus and distal loci. Vertebrate chromosomes are organized into permanent structures that, during S-phase, regulate simultaneous firing of replicon clusters. The late replicating clusters, seen as G-bands during metaphase and as meiotic chromomeres during meiosis, epitomize an ontological utilization of all five self-reinforcing epigenetic mechanisms to regulate the reversible chromatin state called facultative (conditional) heterochromatin. Alternating euchromatin/heterochromatin domains separated by band boundaries, and interphase repositioning of G-band genes during ontological commitment can impose constraints on both meiotic interactions and mammalian karyotype evolution.

Gene silencing by methyl-CpG-binding proteins

An important consequence of CpG methylation is the local silencing of gene expression. In part this can be mediated by direct interference of methylation with the binding of transcription factors. The major component of silencing, however, appears to be the binding of repressors that have an affinity for methyl-CpG. We have studied two proteins that bind to methylated DNA, methyl-CpG-binding protein 1 (MeCP1) and MeCP2. MeCP2 is a relatively abundant chromosomal protein whose localization in the nucleus is primarily dependent on CpG methylation. We find that MeCP2 is a potent transcriptional repressor with a genome-wide distribution. MeCP1 requires multiple methylated CpGs for binding and has previously been implicated as a methyl-CpG-dependent transcriptional repressor. Recent cloning of a candidate gene for a component of MeCP1 may provide clues to its mechanism of action.

The rat growth hormone and human cellular retinol binding protein 1 genes share homologous NF1-like binding sites that exert either positive or negative influences on gene expression in vitro

High levels of expression for the rat growth hormone (rGH) gene are restricted to the somatotroph cells of the anterior pituitary. Previously, we have shown that rGH cell-specific repression results in part from the recognition of negatively acting silencers by a number of nuclear proteins that repress basal promoter activity. Examination of these silencers revealed the presence of binding sites for proteins that belong to the NF1 family of transcription factors. Indeed, proteins from this family were shown to bind the rGH proximal silencer (designated silencer-1) in in vitro assays. Furthermore, this silencer site is capable of repressing chloramphenicol acetyltransferase (CAT) gene expression driven by an heterologous promoter (that of the mouse p12 gene), even in pituitary cells. Recently, we identified in the 5' untranslated region of the gene encoding human cellular retinol binding protein 1 (hCRBP1) a negative regulatory element (Fp1) that also bears an NF1 binding site very similar to that of rGH silencer-1. However, although deletion of Fp1 in the hCRBP1 gene yielded increased CAT activity, pointing toward a negative regulatory function exerted by this element, its insertion upstream of the p12 basal promoter results in an impressive positive stimulation of CAT gene expression. By exploiting NaDodSO4 gel protein fractionation and renaturation, we identified a 40-kD nuclear protein (designated Bp1) present in GH4C1 cells that binds very strongly to rGH silencer-1 but only weakly to hCRBP1 Fp1. Similarly, we also detected a 29-kD nuclear factor (designated Bp2) that recognizes exclusively the Fp1 element as its target site, therefore suggesting that different, but likely related, proteins bind these homologous elements to either activate or repress gene transcription. Although they bind DNA through the recognition of the NF1-like target sequence contained on these elements, competition and supershift experiments in electrophoretic mobility shift assays provided evidence that neither of these proteins belong to the NF1 family.

Gene number, noise reduction and biological complexity

Preliminary estimates suggest that gene number, and hence biological complexity, increased suddenly at two periods of macroevolutionary change (the origin of eukaryotes and the origin of vertebrates), but otherwise remained relatively constant. As the genome is in constant flux, what normally constrains the number of different genes that an organism can retain? Here, I suggest that an important limitation on gene number is the efficiency of mechanisms that reduce transcriptional background noise. The appearance of both eukaryotes and vertebrates coincided with novel mechanisms of noise reduction.

The rat growth hormone proximal silencer contains a novel DNA-binding site for multiple nuclear proteins that represses basal promoter activity

Cell-type-specific expression of the rat growth hormone (rGH) gene is determined by the interaction of both positive as well as negative regulatory proteins with cis-acting elements located upstream of the rGH mRNA start site. We have recently shown that the rat liver transcription factor NF1-L binds to the proximal rGH silencer (called silencer-1) to repress its transcriptional activity. However, this single factor proved to be insufficient by itself to confer cell-specific gene repression. We therefore attempted to identify other regulatory proteins interacting with silencer 1, which might be needed to achieve full cell-specific repression of that gene. A common recognition site for three yet uncharacterized nuclear proteins (designated as SBP1, SBP2 and SBP3) which bind a DNA sequence adjacent to the NF1-L-binding site in the rGH silencer-1 element were identified. UV crosslinking of DNA/protein complexes and nuclear protein fractionation/renaturation from SDS/polyacrylamide gels further indicated that the molecular masses for SBP1-3 are 41, 26 and 17 kDa respectively, the major species being the 26-kDa protein (SBP2) which account for 83% of the shifted SBP double-stranded oligonucleotide in gel mobility-shift assays. For this reason, most of this study focussed on the characterization of SBP2. We demonstrated that binding of NF1-L and SBP2 to their respective recognition sequence is a mutually exclusive event. Although an SBP-binding activity has been found in every non-pituitary tissue or cell line tested, no such activity could be detected in either rat pituitaries or rat pituitary GH4C1 cells. Insertion of the SBP element upstream of the basal promoter of the mouse p12 heterologous gene resulted in a consistent decrease in chloramphenicol acetyl transferase reporter gene expression following transient transfections in non-pituitary cells only, suggesting that the related SBP1-3 proteins might be involved in generally repressing gene transcription in a cell-specific manner.

RNA polymerase: structural determinant of the chromatin loop and the chromosome

Current models for RNA synthesis involve an RNA polymerase that tracks along a static template. However, research on chromatin loops suggests that the template slides past a stationary polymerase; individual polymerases tie the chromatin fibre into loops and clusters of polymerases determine the basic structure of the interphase and metaphase chromosome. RNA polymerase is then both a player and a manager of the chromosome loop.

The 30-kDa rat liver transcription factor nuclear factor 1 binds the rat growth-hormone proximal silencer

Transcription of the gene encoding rat growth hormone is under the influence of cis-acting negative regulatory elements termed silencers. We showed previously that one such element, designated the rat growth hormone proximal silencer-1 site, binds a nuclear protein, the nuclear-factor-1-like protein that is probably a member of the CAAT transcription factor/nuclear-factor-1 (CTF/NF-I) family of transcription factors. This nuclear protein possesses DNA-binding activity as well as biochemical properties similar to those reported for the 30-kDa rat liver form of nuclear factor 1 (NF1-L). Results from both gel mobility supershift assays and Western-blot analyses, performed in combination with a polyclonal antibody directed against the DNA-binding domain of NF1-L, indicated that rat liver nuclear factor 1 might indeed correspond to one of the transcription factors interacting with the rat growth-hormone proximal silencer element. Further experiments using gel mobility shift assays also indicated that, as for NF1-L, multiple proteins among the 52-66-kDa CTF/NF-I isoforms from human HeLa cells also possess the ability to bind the rat growth-hormone silencer.

In vivo observation of the puff-specific protein no-on transient A (NONA) in nuclei of Drosophila embryos

The spatial distribution of no-on transient A (NONA), a protein associated with specific puffs on polytene chromosomes, was followed in nuclei of living Drosophila embryos by microinjection of fluorescently labeled monoclonal antibody to NONA. The injected antibodies remained active until the larval stage, revealing the distribution of the NONA protein throughout embryogenesis. Most injected animals completed embryonic development and hatched as normal larvae. NONA was restricted to the cytoplasm until the end of cycle 11. We document an active uptake of the NONA-antibody complex into early interphase nuclei from nuclear cycle 14 onwards, following each mitosis. Significant differences in the distribution of the protein between fixed and living embryos were apparent, particularly at high resolution. The NONA protein was localized in the nuclei of living embryos at discrete sites, most of which lay at the periphery and some of which were tightly clustered. The constellation of sites changed with time; in some nuclei these changes were fast whereas in other nuclei the pattern was quite stable. These data suggest that specific protein complexes associated with active interphase chromatin, and possibly chromatin in general, are mobile in the living organism.

Expression of the rat growth-hormone gene is under the influence of a cell-type-specific silencer element

We have previously shown that a cell-type-specific negative-regulatory element, or silencer, acts to specifically restrict rat-growth-hormone(rGH)-promoter activity to pituitary cells. Here we report a detailed characterization of this element. The activity of the silencer is dependent on its position relative to the promoter. The negative regulatory effect can be diminished by cotransfection with a high-copy-number, silencer-containing competitor plasmid, suggesting that the function of the element is mediated by specific binding of a trans-acting negative-regulatory factor. The minimal region required for silencer function is contained between positions -309 and -266 relative to the start of the rGH mRNA. The specific interaction of a nuclear protein from non-pituitary cells with this rGH DNA segment was shown by DNaseI as well as dimethylsulfate methylation-interference footprinting. A detailed examination of the DNA-binding site for that protein clearly suggest that it belongs to the NF1 family of transcription factors.

Tissue-specific expression of the rat growth hormone gene is due to the interaction of multiple promoter, not enhancer, elements

Expression of the rat growth hormone (rGH) gene is highly tissue-specific, being limited to a subset of cells in the anterior pituitary. DNA sequences within 237 bp of the transcription start site of the rGH gene play a major role in directing the expression of this gene in the pituitary. Transfection studies in cultured rat pituitary (GC) cells demonstrate that optimal expression of rGH requires the binding of at least two non-tissue-specific factors whose contribution to rGH expression is dependent on the binding of the pituitary-specific factor, Pit-1. Although the segment of DNA containing the elements to which these factors bind can direct pituitary-specific expression of a gene lacking upstream promoter elements, it cannot confer stimulation to either a heterologous or homologous promoter when placed downstream from the coding sequences. These results suggest that expression of the rGH gene exclusively in the pituitary is due to the activity of a tissue-specific promoter element, not an enhancer.

Characterisation of tissue-specific trans-acting factor binding to a proximal element in the rat growth hormone gene promoter

Using an exonuclease III protection assay, tissue-specific binding of rat pituitary tumour cell (GH3 cell) nuclear factors to a proximal region (-68 to -138) of the rat growth hormone gene promoter has been detected. The binding is particularly strong between the borders -68 to -102. The binding is eliminated in the presence of excess unlabelled rat growth hormone gene promoter sequences but also by proximal (-423 to +38) or distal (-1960 to -1260) rat prolactin gene promoter sequences and simian virus 40 enhancer/promoter sequences. Extracts of rat pituitaries showed identical binding characteristics. Methylation interference analysis indicated that the contact points between the pituitary-specific factor and the proximal rat growth hormone gene promoter-binding element (-65 to -95) are over a conserved sequence which occurs twice in the rat growth hormone gene promoter and at least eight times in the rat prolactin gene 5'-flanking sequences. This sequence has previously been proposed to constitute the binding site for the somatotroph/lactotroph tissue-specific transcription factor. Gel-retardation and exonuclease III competition analysis showed that three of the rat prolactin gene promoter elements (-46 to -71, -156 to -180 and -174 to -204) share the ability to bind the pituitary-specific factor. The binding to the most proximal rat prolactin gene promoter element (-46 to -71) was clearly more avid than to the rat growth hormone gene promoter (-65 to -95) proximal element. However, both these elements displayed the formation of two gel-retarded complexes while the more distal rat prolactin gene binding elements (-156 to -180 and -174 to -204) formed only the smaller of the two complexes. Finally, we demonstrated by co-transfection competition analysis that plasmids containing the most proximal rat prolactin gene promoter binding element completely inhibited transcription from the rat growth hormone gene promoter while rat growth hormone gene promoter sequences only partially inhibited transcription from the rat prolactin gene promoter. This suggests that the higher affinity for factor binding displayed by the proximal rat prolactin gene promoter binding site in vitro is reflected in factor binding activity in vivo.

Low-abundance 32-kilodalton nuclear protein specifically enriched in the central nervous system

Recently, a low-abundance nuclear protein, p32/6.3, has been identified in brain tissue (Egle and Shelton: Journal of Biological Chemistry 261:2294-2298, 1986). Using a Western blot procedure, we describe its distribution in the nervous system, determine its relative enrichment in brain versus liver, kidney, and certain other tissues, and describe an isolation procedure from brain. Selective enrichment occurs in basal ganglia, diencephalon, hippocampus, cerebellum, brainstem, spinal cord, and cerebral cortex but not in retina, dorsal root ganglia, and sympathetic ganglia. Thus, enrichment is limited to areas of the central nervous system. p32/6.3 appears to be preferentially enriched in neurons, because in bulk-isolated fractions from rat grey matter it is more abundant in neuron-enriched fractions than in astrocyte-enriched fractions. p32/6.3 is approximately 20-fold more concentrated in an insoluble nuclear protein or matrix fraction from forebrain than from kidney, liver, adrenal gland, or retina. This degree of enrichment is an ancient trait, detectable in the chicken as well as mammals.

Regulation of cell-type-specific transcription and differentiation of the pituitary

The transcription of rat prolactin and growth hormone genes in vitro requires a pituitary transcription factor, specific to certain cell types in the pituitary, which currently appears to be the PUF-I/Pit-1/GHF-1 protein. This factor binds to cis-regulatory elements in the 5' region of both genes and exerts a positive influence on transcription initiation presumably by interacting with general transcription factors. The PUF-I/Pit-1/GHF-1 transcriptional regulatory protein probably has an important role in not only the differentiation of the pituitary lactotroph/somatotroph cell lineage; it is also expressed in the early development of the nervous system but its function there is less well documented. It appears to be one member of a family of trans-activator proteins involved in differential gene expression in several cell types.

The nucleoskeleton and the topology of transcription

Transcription is conventionally believed to occur by passage of a mobile polymerase along a fixed template. Evidence for this model is derived almost entirely from material prepared using hypotonic salt concentrations. Studies on subnuclear structures isolated using hypertonic conditions, and more recently using conditions closer to the physiological, suggest an alternative. Transcription occurs as the template moves past a polymerase attached to a nucleoskeleton; this skeleton is the active site of transcription. Evidence for the two models is summarised. Much of it is consistent with the polymerase being attached and not freely diffusible. Some consequences of such a model are discussed.

Reversion in thymidine kinase deficient variants of mouse lymphoma P388

The ability of 5 independently isolated thymidine kinase-deficient clones of mouse lymphoma P388 to revert has been examined. We were unable to detect spontaneous revertants in any of the 5 clones. Treatment with the hypomethylating agent 5-azacytidine induced reversion in 4 of the clones, but the frequency of revertants was very low (less than 10(-6). The response was not dose-dependent. The mutagen EMS was capable of inducing reversion in 3 of the clones with a variable level of response. The activity of thymidine kinase in 16 revertants was determined. In half of these the level of enzyme activity was considerably greater than the original P388 cell line. The high frequency loss of thymidine kinase that occurs in these cells may represent a stable inactivation of gene activity rather than an alteration in the DNA base sequence.

Thyroid hormone action and the erbA oncogene family

In this review, we discuss the biological action and biochemical function of the v-erbA oncogene product, and the role of c-erbA proto-oncogene products as thyroid hormone receptors, as related to the molecular structure and function of the nuclear hormone receptors at large.

A proposal for a possible role of nucleosome positioning in the evolutionary adjustment of introns

1. Prokaryotes and yeast have mostly intronless genes, whereas the presence of a large number of extended introns are characteristic of the genes of of multicellular eukaryotic organisms which, however, as an exception also have a few intronless genes. 2. According to the current view, the lack of introns in prokaryotic organisms and yeast is due to the selective pressure of a short cell division time. On the other hand, the presence of introns in multicellular eukaryotic organisms is explained by the lack of selective forces against them. 3. In the present hypothesis it is proposed that introns were used as tools in the course of evolution for the organization of eukaryotic genes within the repeating units of nucleosomes, since the distinct DNA conformations of the nucleosome core particle and of the linker region, respectively, represent a constraint for the positioning of genes. 4. Recently it was shown that initiation of transcription is inhibited when the promoter sequence is within a nucleosome. 5. Since the nucleosomal organization of DNA leads to a severely deformed DNA helix and recognition of sequences by regulatory proteins is likely to depend on the conformation of the double helix, it is postulated that for the different sizes of eukaryotic genes which have to be organized within repeating units of nucleosomes, introns provided the flexibility of adjustment for the positioning of regulatory sequences, by drifting in length, sequence and position.

A domain model for eukaryotic DNA organization: a molecular basis for cell differentiation and chromosome evolution

A model for eukaryotic chromatin organization is presented in which the basic structural and functional unit is the DNA domain. This simple model predicts that both chromosome replication and cell type-specific control of gene expression depend on a combination of stable and dynamic DNA-nuclear matrix interactions. The model suggests that in eukaryotes, DNA regulatory processes are controlled mainly by the intranuclear compartmentalization of the specific DNA sequences, and that control of gene expression involves multiple steps of specific DNA-nuclear matrix interactions. Predictions of the model are tested using available biochemical, molecular and cell biological data. In addition, the domain model is discussed as a simple molecular mechanism to explain cell differentiation in multi-cellular organisms and to explain the evolution of eukaryotic genomes consisting mainly of repetitive sequences and "junk" DNA.

Generation of high specificity of effect through low-specificity binding of proteins to DNA

It is proposed that proteins can bind with relatively low-affinity and specificity to multiple sites, defined as sequence motifs, on polynucleotide chains, and that such binding can collectively be turned into high-affinity, high-specificity binding through cooperative effects, especially when the sequence motifs recur periodically. The selection of individual nucleotides has in general been thought to be the condition of the existence and conservation of function in most of the noncoding sequences. This condition seems unnecessary. Calculations are presented as a step in the direction of giving credibility to a model of stable gene repression.

Role of replication time in the control of tissue-specific gene expression

Late-replicating chromatin in vertebrates is repressed. Housekeeping (constitutively active) genes always replicate early and are in the early-replicating R-bands. Tissue-specific genes are usually in the late-replicating G-bands and therein almost always replicate late. Within the G-bands, however, a tissue-specific gene does replicate early in those cell types that express that particular gene. While the condition of late replication may simply be coincident with gene repression, we review evidence suggesting that late replication may actively determine repression. As mammals utilize a developmental program to Lyonize (facultatively heterochromatinize) whole X chromosomes to a late-replicating and somatically heritable repressed state, similarly another program seems to Lyonize individual replicons. In frogs, all genes begin embryogenesis by replicating during a very short interval. As the developmental potency of embryonic cells becomes restricted, late-replicating DNA gradually appears. This addition to the repertoire of gene control--i.e., repression via Lyonization of individual replicons--seems to have evolved in vertebrates with G-bands being a manifestation of the mechanism.

Regulation of growth hormone messenger RNA synthesis by dexamethasone and triiodothyronine. Transcriptional rate and mRNA stability changes in pituitary tumor cells

We have characterized the process by which the growth hormone (GH) gene is stimulated in rat pituitary tumor cells (GC or GH3) by the steroid hormone dexamethasone (Dex) and the thyroid hormone, L-triiodothyronine (T3). A primary transcriptional response is detected within 60 minutes of addition of T3 or Dex + T3 to GH-producing cells (GC or GH3). A fivefold transcriptional stimulation of GH nuclear RNA occurs in cells cultured with serum substitute medium and induced with Dex + T3, while T3 alone induces a modest two- to threefold stimulation. The absence of fetal calf serum from the cell culture medium does not decrease the level of transcriptional activity of the GH gene during hormone stimulation. Twenty-four hours after addition of Dex + T3 the cytoplasmic GH mRNA shows a 50-fold increase, as measured by S1 nuclease analysis. This large accumulation of cytoplasmic GH mRNA in contrast to the relatively small changes in GH gene activity is inconsistent with solely a transcriptional mechanism of hormone induction. We suggest that a change in specific GH mRNA stability also takes place in response to Dex + T3. In contrast to other reports, transcriptional stimulation of the GH gene by Dex is insignificant except in the presence of T3.

High-level expression of the bovine growth hormone gene in heterologous mammalian cells

The gene coding for bovine growth hormone (bGH) was isolated from a lambda-phage library constructed using bovine pituitary DNA partially digested with MboI. Expression of this gene transfected into mouse and monkey cells was studied. CV-1 monkey cells transfected with simian virus 40 (SV40) vectors containing the intact bGH gene, including the putative promoter region, did not express bGH. However, replacement of the bGH promoter with the mouse metallothionein-I (MT) promoter resulted in high-level synthesis and secretion of bGH. These results show that the bGH promoter functions poorly in CV-1 cells but CV-1 cells process and translate the bGH mRNA accurately. The MT-bGH chimeric gene was used to establish permanent bGH-secreting mouse C127 cell lines using the 69% transforming fragment of bovine papilloma virus (BPV) as the vector. One such cell line produced high levels of bGH and secreted it into the medium efficiently. Secreted bGH is processed accurately and is bioactive as judged by its ability to bind to rabbit liver membrane preparations.

Histone-H1-dependent chromatin superstructures and the suppression of gene activity

I have identified a chromatin particle containing DNA as large as 20-40 kb that migrates as a discrete entity on agarose gels. With increasing nuclease digestion, the particle becomes cleaved in the linker regions between nucleosomes, but remains intact, probably held together by the outer histones, H1 and H5. By hybridization analysis, inactive genes are found in these particles. Active genes (and their flanking sequences) are also found in particles containing H1 and H5, but in contrast to inactive supranucleosome particles, active polynucleosome particles are not held together after cleavage of linker DNA. This suggests that H1 cross-links adjacent nucleosomes in inactive regions and that H1 is bound differently in expressed regions. The results raise the possibility that the marked degree of suppression of repressed, tissue-specific genes may be determined, in part, by their assembly into these inactive supranucleosome structures.