Genetic mapping and exome sequencing identify variants associated with five novel diseases

The Clinic for Special Children (CSC) has integrated biochemical and molecular methods into a rural pediatric practice serving Old Order Amish and Mennonite (Plain) children. Among the Plain people, we have used single nucleotide polymorphism (SNP) microarrays to genetically map recessive disorders to large autozygous haplotype blocks (mean = 4.4 Mb) that contain many genes (mean = 79). For some, uninformative mapping or large gene lists preclude disease-gene identification by Sanger sequencing. Seven such conditions were selected for exome sequencing at the Broad Institute; all had been previously mapped at the CSC using low density SNP microarrays coupled with autozygosity and linkage analyses. Using between 1 and 5 patient samples per disorder, we identified sequence variants in the known disease-causing genes SLC6A3 and FLVCR1, and present evidence to strongly support the pathogenicity of variants identified in TUBGCP6, BRAT1, SNIP1, CRADD, and HARS. Our results reveal the power of coupling new genotyping technologies to population-specific genetic knowledge and robust clinical data.

Differential mechanisms of transmission at three types of mossy fiber synapse

The axons of the dentate gyrus granule cells, the so-called mossy fibers, innervate their inhibitory interneuron and pyramidal neuron targets via both anatomically and functionally specialized synapses. Mossy fiber synapses onto inhibitory interneurons were comprised of either calcium-permeable (CP) or calcium-impermeable (CI) AMPA receptors, whereas only calcium-impermeable AMPA receptors existed at CA3 principal neuron synapses. In response to brief trains of high-frequency stimuli (20 Hz), pyramidal neuron synapses invariably demonstrated short-term facilitation, whereas interneuron EPSCs demonstrated either short-term facilitation or depression. Facilitation at all CI AMPA synapses was voltage independent, whereas EPSCs at CP AMPA synapses showed greater facilitation at -20 than at -80 mV, consistent with a role for the postsynaptic unblock of polyamines. At pyramidal cell synapses, mossy fiber EPSCs possessed marked frequency-dependent facilitation (commencing at stimulation frequencies >0.1 Hz), whereas EPSCs at either type of interneuron synapse showed only moderate frequency-dependent facilitation or underwent depression. Presynaptic metabotropic glutamate receptors (mGluRs) decreased transmission at all three synapse types in a frequency-dependent manner. However, after block of presynaptic mGluRs, transmission at interneuron synapses still did not match the dynamic range of EPSCs at pyramidal neuron synapses. High-frequency stimulation of mossy fibers induced long-term potentiation (LTP), long-term depression (LTD), or no change at pyramidal neuron synapses, interneuron CP AMPA synapses, and CI AMPA synapses, respectively. Induction of LTP or LTD altered the short-term plasticity of transmission onto both pyramidal cells and interneuron CP AMPA synapses by a mechanism consistent with changes in release probability. These data reveal differential mechanisms of transmission at three classes of mossy fiber synapse made onto distinct targets.

Long-term specification of AMPA receptor properties after synapse formation

AMPA receptors expressed at auditory nerve synapses in the mammalian and avian cochlear nuclei display exceptionally rapid channel gating, an adaptation well suited for acoustic processing. We examined whether cellular interactions during development might determine the subunit composition of these receptors. After synapse formation in the avian nucleus magnocellularis (nMag) in vivo, the rate of receptor desensitization increased threefold, sensitivity to channel block by polyamines increased, and sensitivity to cyclothiazide, an inhibitor of desensitization, increased, indicating a reduction in glutamate receptor subunit 2 and of flip splice variants. This phenotypic switch was prevented, but not reversed, by isolating nMag neurons in a cell-culture environment. We propose that the switch in receptor kinetics is an outcome of cellular interactions during a critical period that result in the long-term determination of receptor phenotype.

One- and two-dimensional histone separations in acidic gels: usefulness of methylene blue-driven photopolymerization

We tested the recently introduced methylene blue-toluene sulfinate-diphenyl-iodonium polymerization system in order to prepare acetic acid-urea-Triton X-100 gels for histone separations. When compared to standard persulfate-based initiators, this system exhibited several advantages. First, the polymerization proceeds at a much faster rate but is easily controlled since it is light-dependent. Second, no prerunning of the gel was required, since there is no oxidizing molecule able to introduce artifacts. Moreover, this procedure produces gels presenting cleaner backgrounds with silver staining. The ability of the procedure to carry out high resolution two-dimensional electrophoresis of histones was also examined. High resolution two-dimensional gels, using photopolymerized acidic gels as the first or second dimension were obtained.

Early events in erythroid differentiation: accumulation of the acidic peroxidoxin (PRP/TSA/NKEF-B)

The acidic peroxidoxin [also named thiol-specific antioxidant protein (TSA) or protector protein (PRP)], which plays a role in the response against oxidative stress, is one of the major proteins of red blood cells. In this work, we show that this protein is induced at early stages of erythroid differentiation prior to haemoglobin accumulation, which suggests that it may play a role at the erythroblast stage, where haemoglobinized, nucleated and genetically active cells are submitted to a maximally dangerous oxidative stress. The early accumulation of this protein has been demonstrated both on transformed cell systems and on normal differentiating human erythroid cells. This suggests that this protein may play an important role in the differentiation of the erythroid cells.

Induction of stathmin expression during erythropoietic differentiation

Stathmin is a M(r) 19,000 cytosolic protein proposed to act as a relay for signal-activating pathways regulating cell proliferation and differentiation. In a study of erythropoietic differentiation, stathmin was detected as a protein that is induced during the early stages of differentiation in several cellular model systems. The unphosphorylated form of stathmin was most prominently induced, which suggests that this form does not only play a role in pathways oriented toward cell proliferation, as is the case for lymphocytic systems, but may also play a role in various differentiation pathways.

Developmentally regulated chromatin acetylation and histone H1(0) accumulation

There exists a close relationship between core histone acetylation and the induced expression of the histone H1(0) gene. We took advantage of this fact to evaluate the influence of chromatin hyperacetylation on the developmentally regulated expression of this specific gene. In this study, the in situ immunodetection approach has been used to analyze both the acetylated histone H4 isoforms and histone H1(0) accumulation during early Xenopus laevis development. We have chosen two stages of development, gastrula stage, when H1(0) is not expressed and not inducible by butyrate treatment, and stage 27 when H1(0) is not expressed but is inducible by butyrate. At stage 27 of development, the early induced accumulation of histone H1(0) under butyrate treatment, occurs mainly in tissues that express the protein normally during later development. These experiments suggest that histone acetylation may be part of a pathway which, in a specific set of cells, keeps H1(0) and probably a series of specific genes, competent for transcription, but cell-specific factors are involved in the induced expression of these genes.

Accumulation of histone H1(0) during early Xenopus laevis development

It is known that a transition in the linker-histone variants takes place within chromatin during early development of Xenopus laevis; a cleavage-type H1 is replaced by the somatic type. Based on cytofluorimetric analysis of the distribution of the embryo cells in the cell cycle, we showed that this previously described transition occurs when significant modifications of the proliferative capacities of the cells occur. Moreover, this analysis allowed us to show that cell proliferation decreases gradually after the gastrula stage of development. This period terminates with the arrest of more than 90% of cells in the G0/G1 phase of the cell cycle at stage 45. We showed that the major accumulation of the differentiation-specific H1 subtype, histone H1(0), occurs at this time. H1(0), first detected in a restricted set of tissues, is then widely expressed during the later development at stage 45. Moreover, the double staining of nuclei isolated from embryo cells, for H1(0) and DNA, allowed us to show that this accumulation of H1(0) is not restricted to arrested cells. The example of the Xenopus early development shows that there may be an adaptation of the type of H1 expressed to the proliferative abilities of cells. This observation may provide insight into the significance of the expression of different H1 subtypes during development.

Variation of H1(0) content throughout the cell cycle in regenerating rat liver

Histone H1(0), a differentiation-specific member of the histone H1 family, accumulates in cells during the terminal phase of cell differentiation, in tissues composed of arrested cells or cells exhibiting little proliferation. Moreover, the induction of cell proliferation in vivo, i.e., after partial hepatectomy, is accompanied by a decrease in H1(0) content. These observations suggest that H1(0) may be involved in the arrest of cell proliferation in vivo. In order to investigate this possibility, we took advantage of the fact that after partial hepatectomy the initiation of cell division is not synchronous. The strategy was to know, at the level of a single cell, whether H1(0) decreases prior to the initiation of the S phase or whether a cell can initiate DNA replication having a significant amount of H1(0) in the nucleus. We defined new protocols to analyze H1(0) content and cell proliferation at the level of a single cell, both in situ and by flow cytometry. The simultaneous determination of the relative amount of H1(0) and the position of cells in the cell cycle showed that no significant difference in H1(0) content was detected in cells actively replicating their DNA compared to nondividing cells. These observations have been confirmed by the successive immunodetections of H1(0) and BrdU in situ on the same cells. Therefore, we show here that in vivo, cells can initiate DNA replication with significant amounts of H1(0) and that the decrease of H1(0) is not a prerequisite of cell division. We propose that the accumulation of H1(0) is not related to the arrest of cell proliferation, but is controlled in such a manner that the protein accumulates in slowly dividing cells and decreases in rapidly growing cells.

Pharmacological characterization of heterodimeric NMDA receptors composed of NR 1a and 2B subunits: differences with receptors formed from NR 1a and 2A

Pharmacological and molecular biological evidence indicates the existence of multiple types of NMDA receptors within the CNS. We have characterized pharmacological properties of receptors assembled from the combination of NR 1a and NR 2B subunits (NR 1a/2B) expressed in transfected cells using both 125I-MK-801 binding assays and electrophysiological measures. Binding of 125I-MK-801 to cells transfected with NR 1a/2B is saturable with a KD of 440 pM. The binding is potently inhibited by ketamine, dextromethorphan, phencyclidine, and MK-801 and is stimulated by low concentrations of magnesium. These properties resemble those of native receptors and receptors produced by NR 1a/2A. However, 125I-MK-801 binding to membranes from cells transfected with NR 1a/2B is inhibited with high affinity by ifenprodil and is stimulated by spermidine, unlike receptors assembled from NR 1a/2A. NMDA-induced currents measured in cells transfected with either NR 1a/2A or NR 1a/2B have pharmacological properties that correlate well with the binding studies. Currents in cells transfected with NR 1a/2B are potentiated by spermidine and blocked with high affinity by ifenprodil, whereas currents in cells transfected with NR 1a/2A are not enhanced by spermidine and are weakly inhibited by ifenprodil. These data suggest that pharmacological heterogeneity in native NMDA receptors may be explained by combinations of different subunits.

Sample application by in-gel rehydration improves the resolution of two-dimensional electrophoresis with immobilized pH gradients in the first dimension

We describe a modification in the sample application mode for isoelectric focusing with immobilized pH gradients. Instead of being applied at the surface of the gel in a sample cup, the sample is introduced into the gel during the immobilized pH gradient strip rehydration step. This modification implies the use of low percentage gels (below 3.5% T) and specially designed, but simple, rehydration chambers. The main advantages are a uniform resolution without side effects and the possibility of handling large sample volumes (500 microL for a standard 3 x 160 x 0.5 mm strip), allowing micropreparative work (milligram samples) with a simple experimental design.

Relationship between core histone acetylation and histone H1(0) gene activity

In this study we show a striking correlation between histone H1(0) gene expression and histone acetylation. Trichostatin A, a highly specific inhibitor of histone deacetylase, efficiently induces H1(0) gene expression. Moreover, using a cell line sensitive to trichostatin A (FM3A) and a derived cell line selected for its resistance to this inhibitor (TR303), it is shown that the level of H1(0) gene expression is related to the extent of chromatin acetylation. After showing the S-phase-dependent activation of H1(0) gene expression, we demonstrate that hyperacetylation has a dominant effect on H1(0) gene expression, since it enhances the expression of the gene independent of the position of cells in the cell cycle. This response to deacetylase inhibitors is specific to H1(0), since it is not shared by other cell-cycle-dependent histone genes (H1 and H4). Finally, by transfection of trichostatin-A-resistant and trichostatin-A-sensitive cells with a plasmid containing a H1(0) promoter, we show that the exogenous H1(0) promoter is also highly sensitive to trichostatin A treatment and that activation of transcription follows exactly the same pattern as activation of the endogenous gene. These data show that histone acetylation may be used to modulate H1(0) gene activity and offers insight into a possible mechanism in which the developmentally regulated chromatin acetylation acts to potentiate H1(0) gene expression.

Molecular basis of the activation of basal histone H1(0) gene expression

Histone H1(0) is encoded by a gene that is expressed only in cells committed to differentiation. We have previously cloned the Xenopus laevis H1(0) gene and studied elements involved in the regulation of its expression in transfected Xenopus laevis A6 cells, and in microinjected embryos. In this work, in order to understand the basis of the action of these elements, we used an A6 cell nuclear extract and showed that the H1(0) promoter is able to direct efficient in vitro transcription, which is highly dependent on a functional TATA box. However, in contrast to what we observed in vivo, in transfected A6 cells, the in vitro transcription was independent of major regulatory elements, defined in vivo. We then used this in vitro system to reconstitute H1(0) gene regulation. The creation of a repressive environment by the addition of purified histone H1 to the in vitro transcription system allowed us to obtain transcription dependent on the integrity of the regulatory elements. Investigating the basis of this regulation we found that protein-DNA interaction on the proximal promoter region was dependent on the integrity of proximal elements, and moreover the distal regulatory element, the UCE, was able to modulate this interaction. We conclude that the role of these regulatory elements is to maintain the basal TATA-dependent transcription of H1(0) under repressive condition: i.e., H1-mediated repression of transcription, or chromatin assembly in general.

Characterization of baculovirus recombinant wild-type p53. Dimerization of p53 is required for high-affinity DNA binding and cysteine oxidation inhibits p53 DNA binding

A high-yield, rapid and non-denaturing purification protocol for baculovirus recombinant wild-type p53 is described. Gel-filtration chromatography and chemical cross-linking experiments indicated that purified p53 assembles into multimeric forms ranging from tetramer to higher oligomers. A gel-mobility-shift assay and protein-DNA cross-linking studies demonstrated that purified baculovirus recombinant p53 binds to consensus DNA target as a dimer but that additional p53 molecules may then associate with the preformed p53-dimer-DNA complexes to form larger p53 DNA complexes. These observations suggest that the p53 tetramers and higher oligomers that form the minimal p53 association in solution dissociate upon DNA binding to form p53 dimer-DNA complexes. Binding of the mAB PAb 421 to the oligomerization-promoting domain on p53 stimulated sequentially formation of both p53-dimer-DNA and larger p53-DNA complexes. This observation suggests that factors may exist in vivo that could participate in the formation and the stabilization of the various p53-DNA complexes. Further characterization of the purified p53 revealed that the protein possesses highly reactive cysteine residues. We show that intrachain disulfide bonds form within the purified p53 molecules during storage in the absence of reducing agent. Zn2+ binding to p53 protect sulfhydryl groups from oxidation. Cysteine oxidation by intramolecular disulfide-bond formation did not modify the wild-type immunoreactive phenotype of the p53 protein but totally inhibited its DNA-binding activities. The oxidation of the p53 cysteine residues was also observed for nuclear p53 in baculovirus-infected insect cells. The redox status of the nuclear p53 regulates its DNA-binding activity in vitro confirming the essential role of the reduced state of cysteine residues in p53 for detectable DNA-binding activity.

Two mRNA species encoding the differentiation-associated histone H1(0) are produced by alternative polyadenylation in mouse

Histone H1(0) is a differentiation-specific member of the histone H1 family. The accumulation of the protein is associated with the terminal stage of cell differentiation and is regulated at various levels. In mouse, the analysis of the expression of the single copy gene encoding H1(0) has shown that another H1(0)-related mRNA species (0.9 kb) is present in addition to the usual 2.1-kb mRNA. In this study, we have cloned and sequenced the smaller H1(0)-related mRNA. This mRNA seems to be produced by the use of an additional polyadenylation signal present in the 3' untranslated region (UTR) of the initial transcript. This smaller H1(0)-encoding mRNA is expressed only in mouse and is transferred into polysomes as efficiently as the larger version upon the induction of cell differentiation. The use of the described polyadenylation site removes over 1 kb of the 3' UTR of H1(0) mRNA and seems to be involved in the regulation of H1(0) mRNA stability.

Silver-staining of proteins in polyacrylamide gels: a general overview

On the basis of the physico-chemical principles underlying silver-staining of proteins, which are recalled in this paper, several methods of silver-staining of proteins after SDS electrophoresis in polyacrylamide gels or isoelectric focusing were tested. The most valuable protocols are presented in this report, including standard methods for unsupported gels and new methods devised for thin (0.5 mm) supported gels for SDS electrophoresis or isoelectric focusing and for staining of small peptides. Generally speaking, the most rapid methods were found to be less sensitive and less reproducible than more time-consuming ones. Among the long methods, those using silver-diammine complex gave the most uniform sensitivity. They require however special home-made gels and cannot be applied to several electrophoretic systems (e.g. systems using tricine or bicine as the trailing ion, or isoelectric focusing in immobilized pH gradients). For these reasons, protocols based on silver nitrate are of a more general use and might be favored. Future trends for silver-staining will also be discussed.

Flow and image cytometry for DNA analysis in bladder washings: improved concordance by using internal reference for flow

Using flow or image cytometry, we compared the DNA distribution of cells from bladder washings from 52 patients with bladder cancer. For image cytometry, urothelial nuclei (recognized visually) were analyzed for DNA content using polymorphonuclear nuclei as internal diploid reference. For flow cytometry, two methods can be used: either all cells can be analyzed, as commonly performed, or urothelial cells can be analyzed alone, after specific detection. In this flow cytometry study, cells were doubly stained for panurothelial antigens T16 and for DNA. All the cells were first analyzed using peripheral lymphocytes as an external reference; 79% of the results were similar with results obtained from image analysis. For discordant results, flow-cytometric data were reprocessed to identify immunologically stained urothelial cells; one additional case became concordant with image cytometry when only urothelial cells were analyzed, with lymphocytes as diploid reference; a better concordance (94%) was found when the nonurothelial cells of the samples served as a diploid reference instead of peripheral lymphocytes. This suggests that we achieved an improvement of the flow-cytometric evaluations for ploidy assessment, and we conclude that, on these conditions, flow or image analysis can be considered as equivalent methods for DNA content studies of tumors.

Selective cytotoxicity of L-glutamic acid gamma-monohydroxamate (GAH) for melanoma tumor cells

We have previously shown that L-glutamic acid gamma-monohydroxamate (GAH) exhibits an antitumor activity, both in vitro and in vivo. In this report we explore the selective cytotoxicity of GAH in vitro by comparing the survival of tumor and normal cells. GAH exerts an irreversible delayed effect with tumoral cells and a reversible effect with normal cells: after a short incubation time of 6 hrs in the presence of 1.2 mM GAH and after removal of the drug, the survival of N Ter Dau and MRC5 cells was identical reaching about 85% after 24 hrs of culture. But, after another 48 hrs of culture, MRC5 cells recovered 100% cell survival while with N Ter Dau cells the survival decreased to 65%. A longer exposure time to GAH (18 hrs) and an additional 54 hrs of culture after removal of GAH led to 50 +/- 10% of cell survival with normal cells but only 25 +/- 10% with tumor cells. Using a long-term clonogenic assay, we showed that the 25% N Ter Dau cells surviving at 72 hrs after GAH treatment led mainly to abortive colonies (17% +/- 3%) with only 2.3 +/- 0.9% of surviving colonies. Such a difference does not exist for normal cells. Cell cycle analysis of tumor and normal cells treated with GAH (18 hrs, 1,2 mM) has shown that the drug prevents both cell type from cycling from G1 to S phase. However, the two cell types started to cycle again after removal of GAH but a delay of 24 hrs was observed for tumoral cells compared to normal cells.

Light and electron microscope immunocytochemical analyses of histone H1(0) distribution in the nucleus of Friend erythroleukemia cells

The localization of histone H1(0) in murine erythroleukemia cells which were induced to resume a differentiation program was studied in cells which have recovered their proliferative capacity after transient blockage in the G1 phase of the cell cycle. Previous studies have shown that histone H1(0) accumulation occurs at early times of induction and is probably related to the commitment itself. The distribution of the protein was determined by immunomicroscopy with monoclonal antibodies specific for histone H1(0). Our observations showed that the histone accumulates in nuclei. Immunoelectron microscopy further demonstrated the presence of histone H1(0) in condensed chromatin areas, including perinucleolar chromatin. Moreover, histone H1(0) also occurred in the perichromatin regions, previously described as preferential sites of pre-mRNA synthesis, suggesting that histone H1(0) is not fully excluded from active chromatin.

p53-mediated cell death: relationship to cell cycle control

M1 clone S6 myeloid leukemic cells do not express detectable p53 protein. When stably transfected with a temperature-sensitive mutant of p53, these cells undergo rapid cell death upon induction of wild-type (wt) p53 activity at the permissive temperature. This process has features of apoptosis. In a number of other cell systems, wt p53 activation has been shown to induce a growth arrest. Yet, wt 53 fails to induce a measurable growth arrest in M1 cells, and cell cycle progression proceeds while viability is being lost. There exists, however, a relationship between the cell cycle and p53-mediated death, and cells in G1 appear to be preferentially susceptible to the death-inducing activity of wt p53. In addition, p53-mediated M1 cell death can be inhibited by interleukin-6. The effect of the cytokine is specific to p53-mediated death, since apoptosis elicited by serum deprivation is refractory to interleukin-6. Our data imply that p53-mediated cell death is not dependent on the induction of a growth arrest but rather may result from mutually incompatible growth-regulatory signals.

Characterization of the tumor suppressor protein p53 as a protein kinase C substrate and a S100b-binding protein

We report here that the negative cell cycle regulator protein p53 is an in vivo and in vitro substrate for protein kinase C, a cellular receptor for the tumor-promoter phorbol esters. We also demonstrate that p53 interacts in a calcium-dependent manner with S100b, a member of the S100 protein family involved in cell cycle progression and cell differentiation, and that such an interaction inhibits in vitro p53 phosphorylation by protein kinase C. The interaction between p53 and S100b was utilized for the purification of cellular and recombinant murine p53 by affinity chromatography with S100b-Sepharose. Furthermore, and of particular interest, we have shown that purified p53 undergoes temperature-dependent oligomerization and that the interaction between S100b and p53 not only induces total inhibition of p53 oligomerization but also promotes disassembly of the p53 oligomers. We suggest that these effects result from the binding of S100b to the multifunctional basic C-terminal domain of p53 and propose that p53 may be a cellular target for the S100 protein family members involved in the control of the cell cycle at the G0-G1/S boundary.

Antisense RNA and p53 regulation in induced murine cell differentiation

p53 expression is strongly modulated during the process of induced differentiation, at the same time as both cell cycle and genetic expression become modulated, giving rise to a commitment to terminal differentiation. We took advantage of two murine cell lines inducible for differentiation, an erythroleukemia and a melanoma cell line, to outline common features of the regulation of p53 expression during the differentiation process. We found that p53 mRNA decreased early after induced differentiation and that regulation was controlled at a posttranscriptional level. Our data showed that this regulation affects p53 pre-mRNA maturation. Because, in both systems used, actinomycin D treatment abolished the inducer-mediated decrease of p53 mRNA, we looked for induced RNAs potentially involved in this process. Using different parts of the p53 gene and flanking regions as probes, we identified three RNA species whose expression is modulated during induced differentiation. A first species is made of high molecular weight RNAs that accumulate in the nuclear compartment and seem to represent antisense transcripts of the p53 gene. A second species, 1.3-kb long, was found to accumulate in the nucleus of induced MEL cells and was homologous to a restricted part of the first intron of the p53 gene due to the presence of a B1 repetitive element in an antisense orientation with respect to the p53 pre-messenger RNA. Finally, a family of B2-containing RNAs was observed in both cytoplasmic and nuclear compartments. The variation in the amounts of sense and antisense RNAs, respectively, suggested an interesting speculative model for the maturation of B2-containing pre-messenger RNAs.

Induction of H1(0)-gene expression in B16 murine melanoma cells

Histone H1(0) accumulation is associated with the terminal stage of differentiation. Unlike other H1 histones, it is able to accumulate in the absence of DNA synthesis, however the transcription of its gene is cell-cycle dependent. The regulation of H1(0)-gene expression has been studied during the induced differentiation of B16 cells and during reversion of the process, which may be achieved when induced cells are released into an inducing-agent-free medium. During the earlier period of induced differentiation, H1(0) mRNA showed over-expression when the cells were still proliferating. Then the amount of H1(0) mRNA decreased as the cells became arrested in G0-G1. H1(0) mRNA half-life measurements and run-on experiments demonstrated that such modulation of the amount of mRNA originated from a transcriptional control of H1(0)-gene expression. When induced cells reverted to a proliferative undifferentiated state, H1(0) mRNA decreased very rapidly, indicating that an active process was involved in this decay. This behavior differed from that observed in rat liver hepatocytes allowed to proliferate and de-differentiate after partial hepatectomy, or in murine erythroleukemia cells when the inducing agent was removed from the culture.

Seric factors influence cell cycle modifications during commitment of murine erythroleukemia cells to differentiation

Cell cycle modifications are among the early events which take place during the induced differentiation of murine erythroleukemia (MEL) cells; a transient accumulation of the cells in the G1 phase of the cell cycle, followed by a re-entry of the cells into a proliferation state, has been described. In order to characterize a putative role of serum in such variations, we have studied the modifications of the cell cycle parameters when cells were induced to differentiate in the presence or in the absence of seric factors. We show that, in the absence of exogenous factors brought by serum, the G1 accumulation was enhanced both in amplitude and in duration, but cells were still able to bypass the G1 block and re-enter into the S phase. These results indicate that the resumption of cell proliferation after the transient block is under synergistic control of seric and endogenous factors, but these later are sufficient to overcome the block. However, MEL cells were unable to differentiate in the absence of seric factors, as measured by the number of benzidine-positive cells during induction with hexamethylene-bisacetamide (HMBA) or butyric acid. This capacity to differentiate was recovered when serum was added back to the culture medium, and the efficiency of recovery was maximal when cells underwent a full round of DNA replication in the presence of serum after the G1 block. The analysis of two molecular markers of cell differentiation confirmed these results.

Cell cycle-related accumulation of H1(0) mRNA: induction in murine erythroleukemia cells

H1(0), a member of histone H1 family, is associated with cell differentiation in vivo and in vitro. Unlike other histones its synthesis is known to be constitutive during the cell cycle. The present paper provides evidence showing that, in murine erythroleukemia (MEL) cells, H1(0) mRNA accumulation is coupled to DNA replication, but this mRNA is stable enough to remain present all over the cell cycle. Moreover the experiments suggest that H1(0) mRNA accumulates in mid or late S phase rather than when cells initiate DNA replication as does H3 mRNA. H1(0) gene transcription is drastically induced by chemical inducers of differentiation in this cell line. In an attempt to better understand the mechanism of this process, we have studied the inducibility of this gene with respect to the position of the cells in the cell cycle. The experiments show that the most efficient accumulation of H1(0) is observed when cells are treated by the inducer during the S phase of the cell cycle. In the same conditions, H3 mRNA accumulation remains unaffected. These results show that H1(0) mRNA, like H3 mRNA, accumulates during DNA replication, although at a different stage in this phase. The two genes differ, however, in their response to the inducer, suggesting that different regulatory elements might be involved in such a response.

Multiple control level governing H10 mRNA and protein accumulation

We have studied the variation of histone H10 and of its coding mRNA during rat liver regeneration after partial hepatectomy. Our data showed that while H10 decreased when cell proliferation was initiated, H10 mRNA accumulated in a proliferation-dependent manner as did H3 mRNA. These results showed two interesting aspects of the regulation of H10 expression in vivo, confirming results we have obtained previously in vitro: first H10 mRNA accumulation is a proliferation-dependent event; second, H10 protein accumulation may be uncoupled from that of its coding mRNA.

Modulation of B2 containing small RNAs during induced differentiation of murine erythroleukemia cells

We identified a B2 repetitive element approximately 1.9kb down stream from mouse p53 coding gene. This element was then used as a probe to investigate the expression of B2 containing RNA during the induced differentiation of murine erythroleukemia (MEL) cells. This probe revealed two nuclear and one cytoplasmic RNA species. Nuclear small RNAs had a biphasic variation: a decrease followed by a reaccumulation. The cytoplasmic species was essentially non polysomal, and disappeared after the induced differentiation. The presented results suggest that the regulation of these RNAs is associated to cell proliferation and differentiation respectively.

Regulation of histone H1(0) accumulation during induced differentiation of murine erythroleukemia cells

Histone H1(0) is one of the potential candidates that may contribute to the onset and stabilization of a genetic program during induced differentiation of murine erythroleukemia cells. In an attempt to understand better the role of H1(0) in this process we have tried to determine at which level the regulation of its induced accumulation occurs. Protein H1(0) was found to increase by a factor of 3 while its mRNA increased by a factor of 14, due to activation of gene transcription. As shown by H1(0) half-life measurements, the difference between the actual amount of H1(0) and that expected from the amount of mRNA was not due to increased turnover of the protein. Fractionation of the translational apparatus at several times during induction, revealed that H1(0) mRNA was efficiently transferred to the high molecular weight polysomes. The rate of synthesis of H1(0) was also increased by a factor of 4. Taken together, these results suggest the existence of a strong control at the translational level, which regulates H1(0) accumulation.

Recovery of RNA from flow-sorted fixed cells

We describe a method for the preparation of RNA from ethanol-fixed cells, allowing analysis of the RNA from cells "frozen" in a given physiological state. This technique may have important applications in experiments which require prolonged cell manipulations before RNA preparation, such as investigations of cell-cycle-regulated gene expression, which require the preparation of cells for cell-cycle flow analysis, and even for long-term cell sorting. It eliminates all the inconveniences associated with the use of fresh cells, and allows cell-cycle biologists to couple flow cytometry methodology with the advancing techniques of molecular biology.

An antisense RNA involved in p53 mRNA maturation in murine erythroleukemia cells induced to differentiate

A post-transcriptional control of gene expression was found to be responsible for a down-regulation of p53 mRNA accompanying the induced differentiation of murine erythroleukemia (MEL) cells. Such a post-transcriptional control was governed by the induced synthesis of an RNA species (inRNA). In an attempt to find a potential candidate for such a function, we have localized the post-transcriptional regulation of p53 mRNA in the nuclear compartment of the cells; the various fragments of the p53 gene were used as probes for induced RNA(s) susceptible to interacting with p53 pre-mRNA. This experimental approach allowed for the identification of a nuclear RNA molecule, approximately 1.3 kb long, which was recognized specifically by a PstI-HindIII fragment located in the 5' part of the first intervening sequence of the p53 gene. This RNA accumulated when cell were treated by the inducer concomitantly with high mol.wt p53 mRNA precursors. However this RNA was not a maturation product of p53 pre-mRNA as evidenced by its antisense orientation with respect to this RNA. Moreover it was markedly enriched in the poly(A)+ fraction. The complementary part of inRNA in the p53 gene has been sequenced over approximately 1200 bp; no extensive homology was found in gene data banks but three restricted areas of the sequence were found homologous to a limited number of genes; they were themselves partially homologous to known repetitive sequences. Possible implication of such a sequence in the regulation of p53 gene expression is discussed.

Flow cytofluorimetric determination of protein distribution throughout the cell cycle

Quantitative treatment of multiparametric determination on cells using flow cytofluorometry was made possible by the development of a computer program that allows the relative quantification of a specific protein as a function of the position of cells during the cell cycle. This type of analysis provides interesting information about the distribution of a given protein throughout the cell cycle. Four examples showing the distribution of specific proteins illustrate such a quantification during the cell cycle in two different cell lines. The program also allows for the handling of a series of histograms obtained by the analysis of protein distribution as a function of DNA content in relation to a third parameter. To illustrate possible applications for this program, the evolution of the distribution of two proteins, the oncoprotein p53 and the histone H1(0), during the induced differentiation of murine erythroleukemia cells has been studied.

Histone H1(0) mapping using monoclonal antibodies

Monoclonal antibodies (mAb) to ox liver histone H1 degree were produced and characterized. Two sets of mice were immunized either with pure H1(0) or with an H1(0)-yeast tRNA complex. Eleven hybridomas of various clonal origin were selected. Typing of the antibodies indicated that all but three IgM belonged to the IgG1 class and contained kappa light chains. Immunoblotting experiments using peptides derived from H1(0) or H5 treated by various proteolytic agents (trypsin, N-bromosuccinimide, cyanogen bromide, acetic acid), revealed that nine of the mAb reacted with the globular part of H1(0). More advanced characterization of the antigenic determinants allowed us to determine distinct regions within this globular part which are involved in the antigenic recognition. The peptopes could be subdivided into two groups. Three mAb bound to residues 24-27 and were specific for H1(0). Six mAb bound to residues 27-30 and were specific for H1(0) except one of them which strongly cross-reacted with H5 and GH5. Two mAb reacted with the entire histone H1(0) but failed to react with any of the peptides, suggesting that the corresponding epitope is a conformational antigenic determinant. In order to confirm the localization of the two distinct regions which are involved in the antigenic recognition, a synthetic decapeptide corresponding to the beginning of human H1(0) globular part (from residue 19 to residue 28) was synthesized. Inhibition experiments of the reaction between H1(0) and the various IgG1 mAb by increasing amounts of peptide-bovine serum albumin conjugates were then performed.

Unusual radiographic manifestations of chondrodysplasia punctata

We present six cases of chondrodysplasia punctata with radiographic findings that are either very rare or previously unreported in this entity.

Early events in murine erythroleukemia cells induced to differentiate: variation of the cell cycle parameters in relation to p53 accumulation

Among the early events of induced differentiation of murine erythroleukemia cells that we studied was the variations of cell distribution in the cell cycle as a function of the time of induction. Flow-cytofluorimetry measurements of DNA content and BrdU incorporation allowed for a precise determination of the variations of the cell cycle parameters. Cells underwent a transient arrest in both G1 and G2 + M between 6 to 16 h of induction. The progression of the cells through S phase seems not to be affected during this period. After this time cells escaped from G1 and reentered the S phase. We described previously [S. Khochbin et al. (1988) J. Mol. Biol. 200, 55-64], that p53 decreased continuously during the induction of MELC and remained at a steady-state level after 18 to 20 h of induction. In order to look for a possible redistribution of the protein along the cell cycle during the induction process, we measured the accumulation of the protein along the cell cycle. In noninduced cells there were four steps in the accumulation of the protein throughout the cell cycle: the amount of p53 was constant during G1 and it increased as cells progressed through S phase, which is characterized by an increased accumulation at the G1/S transition and a more moderate accumulation during progression through the rest of the S phase. A constant level in G2/M, approximately twice that obtained in G1, was achieved. There was no change in this distribution that correlated with the various modifications of the cell cycle in induced cells. It seems then, that p53 is associated neither with the progression of the cells in the S phase nor with the resumption of the DNA synthesis after the G1 block.

Application of bromodeoxyuridine incorporation measurements to the determination of cell distribution within the S phase of the cell cycle

Flow cytofluorimetric measurement of incorporated bromodeoxyuridine, using a double-stained cell population, allows the determination of the distribution of cells along the cell cycle. We have developed a simple computer program for the direct treatment of 64 x 64 channel histograms. This analysis appears to provide interesting data about the distribution of cells in the various phases of the cell cycle, namely the S phase. Two examples have been chosen to illustrate possible fields for the application of such a program. Comparison of two cell lines such as friend murine erythroleukemia cells (MELC) and fibroblasts FR3T3 cells has shown that this analysis can be used for cell-cycle characterization of a given cell line. The program also allows the differential analysis of cell distribution along the cell cycle as a function of a given parameter. This possibility has been applied to study the variation of cell-cycle parameters as a function of the time of induced differentiation of MELC and reveals changes in the distribution of the cells along the various phases of the cell cycle, namely in the S phase.

Conformational effects of histones H1 on DNA structure. Comparative study between H1-1, H1(0), H5 and sperm holothuria phi 0

Interactions of mammalian histones, H1-1 and H1(0), phi 0 from holothuria sperm and H5 with poly(dA-dT), poly(dG-dC) and poly(dG-me5dC) were measured by a nitrocellulose filter binding assay and circular dichroism. All of the proteins bound to every one of the polymers, but differed in the extent of binding, which depended on the polynucleotide/protein ratios and ionic strength. The order of retention of all polymers was phi 0 greater than H1-1 greater than H1(0). The binding of H1(0) to poly(dG-me5dC) was remarkably sensitive to ionic strength. The proteins caused changes in the spectral features of the polynucleotides, but differed in the type and extent of the change. Complexes prepared with H1-1 and H1(0) with all polymers showed a strongly negative psi spectrum. Complexes of poly(dA-dT) and phi 0, at a protein/polynucleotide ratio of 0.4, displayed a distinctive spectrum, giving the appearance of a Z-like DNA spectrum, at low ionic strength. At higher ionic strength the complexes showed a psi spectrum. Complexes of poly(dG-me5dC) in the Z or B conformation with phi 0 showed spectral features characteristic of a mixture of a Z-like and a psi spectrum. In contrast, H5 reduced the Z-DNA spectral features in the presence of Mg, and produced an inversion of the B spectrum up to a polynucleotide/protein ratio of 0.24. These findings demonstrate the ability of different proteins to produce changes in the conformation of DNA. This may reflect the ability of chromatin to undergo differential condensation, depending on both the base composition of DNA and the type of H1 histone bound to it.

Cell cycle regulation of poly(ADP-ribose) synthetase in FR3T3 cells

The properties of poly(ADP-ribose) synthetase were studied throughout the cell cycle progression of non-synchronized rat FR3T3 fibroblasts using an immunological and biochemical approach. Cells in the various phases of the cell cycle were sorted from an asynchronously growing population by using flow cytofluorometry. G1, S and G2 + M fractions were used for enzymatic assays in the presence of saturating concentrations of DNAase I for the analysis of total poly(ADP-ribose) synthetase; maximal enzyme activity was found in the G2 + M phase. Purified IgG, specific for the FR3T3 poly(ADP-ribose) synthetase were used for the labelling of endogenous synthetase in order to quantify the enzyme immunologically. Localization of nuclear immunofluorescence was observed and analysis of poly(ADP-ribose) synthetase content throughout the cell cycle were carried out using double fluorescent staining and cytofluorometry. Poly(ADP-ribose) synthetase content as measured immunologically was found to increase from G1 to S and G2 + M phases. Quiescent cells showed a lower content as measured immunologically of poly(ADP-ribose) synthetase than cells in the G1 phase. In exponentially growing cells, the ratio between enzyme activity of poly(ADP-ribose) synthetase over the amount of enzyme measured immunologically was found to be higher in the G2 + M phase. These results show that a cell-cycle specific event activates poly(ADP-ribose) synthetase in the G2 + M phase.

Early events in murine erythroleukemia cells induced to differentiate. Accumulation and gene expression of the transformation-associated cellular protein p53

Oncogenes may play a crucial role in the genetic program of cellular differentiation; even, probably, at a very early stage in this program, which can be described as pre-commitment. We have investigated the variation in, and the control level of, the accumulation of the transformation-associated cellular protein p53 in murine erythroleukemia cells induced to differentiate by hexamethylene bisacetamide. Using flow cytofluorimetry after double staining of the cells, we have found that p53 decreased from two hours after the input of the inducer, to reach a basal level of about 30% of the starting value. The stability of the protein was found to be affected neither by the inducer nor by the position of the cells in the cell cycle. Looking for the regulation mechanism of the p53 decay, we found that the mRNA started to decrease as early as half an hour after the hexamethylene bisacetamide was put in the culture medium, and that the transcription rate of the gene itself could not account for the observed down-regulation of the mRNA, suggesting a post-transcriptional control for the mRNA accumulation. This control did not require the de-novo synthesis of a protein component, as shown by cycloheximide experiments, but seemed to be governed by the induced synthesis of an RNA molecule. Hypothetical models for such a regulation process are discussed in the light of recent reports on the metabolism of mRNA.

Flow cytometric sorting of human epidermal pure basal cell suspensions using a specific antikeratin monoclonal antibody

A method is described for flow cytometric sorting of epidermal basal cells, based on the cellular keratin content. KL1, a monoclonal antikeratin antibody specific for the 56.5 kD polypeptide present in suprabasal cells was used to distinguish suprabasal from basal cells. After the action of Triton X-100, epidermal cells were stained in suspensions with KL1 antibody, and KL1-positive cells were separated by flow cytometry from KL1-negative cells (basal cells). This makes it possible to sort and analyze pure fractions of human epidermal basal cells since no less than 99% of the KL1 sorted cells were bearing bullous pemphigoid antigen. Therefore, the use of specific antibodies to cytoplasmic antigens can be of help in sorting pure fractions of cells of a particular tissue for further studies.

Permanent expression of p53 in FR 3T3 rat cells but cell cycle-dependent association with large-T antigen in simian virus 40 transformants

The p53 oncogene is thought to play a role in the proliferation of normal and transformed cells and its expression was postulated to be cell cycle dependent. Using flow cytofluorimetry sorting of populations of exponentially growing cells, coupled to a radioimmune assay, we have investigated the accumulation of p53 along the cell cycle in normal FR 3T3 rat cells as well as in two types of SV40-transformed derivatives, one of which only expresses the large-T protein during the G2 phase of the cell cycle. p53 was accumulated at a constant level throughout the cell cycle in FR 3T3 cells. Its level and stability increased to different extents in the two types of transformants. However, the formation of complexes between p53 and large-T was modulated by the G2-restricted accumulation of large-T, thus leading to a differential increase in the levels of p53 both in exponentially growing cells and along the cell cycle. This increase in the levels of p53 appeared to be regulated at a post-transcriptional level.

Effects of butyric acid on cell cycle regulation and induction of histone H1(0) in mouse cells and tissue culture. Inducibility of H1 (0)in the late S-G2 phase of the cell cycle

We have examined the regulation of the synthesis of histone H1(0) in cultured mammalian cells treated with butyric acid. Treatment of cells with the inducer results in the arrest of synthesis of DNA and the other histones, while increasing the synthesis of H1(0) by a factor of 11. The induction of H1(0) by butyric acid occurs in a pulse with a peak at six hours, followed by a decrease to negligible levels. This pulse-like induction appears to be due to the fact that the cells are inducible for H1(0) only in the late S or G2 phases of the cell cycle. This, coupled with the fact that butyric acid blocks cells in G1, results in the burst of H1(0) synthesis after addition of the inducer. The G1 block provoked by butyric acid does not appear to result from the accumulation of H1(0). Removal of butyric acid from G1-blocked cells resulted in the resumption of cellular proliferation without prior loss of H1(0), demonstrating that the presence of this histone is not sufficient to prevent cellular proliferation.

The involvement of histone H1[0] in chromatin structure

Micrococcal nuclease digestion and light scattering are used to compare native chromatins with various histone H1[0] contents. The experimental data show that the higher the H1[0] content, the greater the ability to form compact structures with increasing ionic strength, and the lower the DNA accessibility to micrococcal nuclease. On the contrary, reconstituted samples from H1-depleted chromatin and pure individual H1 fractions behave in such a way that samples reconstituted with pure H1 degree give rise to a looser structure, more accessible to nuclease than samples reconstituted with H1-1. This contradiction suggests that the effect of H1o on chromatin structure must originate from the interaction of this histone with other components in native chromatin among which other histone H1 subfractions are good candidates.

Association of histone H1(0) with a gene repressed during liver development

Histone H1(0) has a number of unusual properties that set it apart from other H1 subtypes (for review see ref. 1). For example, H1(0) synthesis is not strictly coupled to DNA synthesis, it is absent from the embryonic liver of mice (but present shortly after birth) and its synthesis is hormone-dependent in some of the glands of adult rodents. All the H1 subtypes differ in their DNA binding properties, and H1(0) has been shown to be preferentially associated with nuclease-resistant chromatin. These features suggest that the H1(0) may have a role in developmental gene control. To investigate this further, we have fractionated the H1(0)-containing nucleosomes of chromatin from adult mouse liver. We report here that the gene for alpha-fetoprotein, which is expressed in embryonic tissue but repressed soon after birth, is preferentially associated with the H1(0)-containing nucleosomes. The related gene for albumin, which is expressed in both embryonic and adult tissues, is absent from the H1(0)-containing nucleosome fraction. These results support a role for histone H1(0) in the control of gene expression.

Association-dissociation of histone oligomers. A spin label study

The spin label method has been used to obtain information about conformational changes of histone oligomers taking advantage of the fact that at a low ionic strength and in the presence of other histones about 45% of cysteine residues of histone H3 react with the 3-maleimido-2,2,5,5-tetramethyl-1-pyrrolidinyloxyl spin label. For the labeled complexes H3-H4 and H nu the degree of immobilization of the spin label is a function of the ionic strength. This variation is identical for both complexes within a long range of ionic strengths, including the interval of 0.8-2 M NaCl, under which conditions interactions are known to exist between the tetramer (H3)2 (H4)2 and the dimer (H2A) (H2B). This finding suggests a negligible influence of the dimer for modifying the cysteine residue environment of histone H3 on octamer formation. GuHCl treatment at high ionic strength of the labeled complexes gives rise to a non-lineal increase in the degree of mobility of the spin label. This increase, at low GuHCl concentration (0-0.5 M GuHCl), is interpreted as showing a lowering in rigidity for the Cys residue environment, without affecting the general stability of the tetramer (H3)2 (H4)2. At higher GuHCl concentration (2-3 M GuHCl) the increase in the spin label mobility is related to a dissociation of the complexes in single histones. Our results are consistent with the view that the overall structure of the tetramer, as well as its conformational changes during complex structuration or denaturation, are not strongly affected by the presence of the dimer (H2A) (H2B).

Cell cycle-dependent expression of early viral genes in one group of simian virus 40-transformed rat cells

SV40-transformed FR 3T3 rat cells were previously shown to exhibit different patterns of accumulation of the virus-coded T-antigen. One group of transformants accumulates T-antigen throughout the cell cycle, whereas in another group, only the cells in the G2 phase of the cell cycle are stained by immunofluorescence with anti-T antigen antibodies. We investigated the mechanism involved by determining the amounts of early SV40 RNA during the cell cycle. Cells in the various phases of the cell cycle were sorted from an asynchronously growing population using a flow cytofluorimeter. Determination of the amounts of viral RNA in the different nuclear and cytoplasmic RNA fractions showed that in transformants with a G2-restricted accumulation of T-antigen, viral RNA was present in G2, to some extent in S, but could not be detected in cells in G1. In contrast, equivalent amounts of viral RNA were detected in all the phases of the cell cycle in the other group of transformants. Cell sorting, performed after pulse-labeling the cells for 2 h with [35S]methionine, confirmed that translation of the viral mRNAs occurred only in G2 in the first group of transformants, and throughout the cell cycle in the second group.

The role of the central globular domain of histone H5 in chromatin structure

Histone H5 contains three tyrosines in the central, apolar region of the molecule. All three tyrosines can be spin labeled at low ionic strength. When the central globular domain is folded at high ionic strength, only one tyrosine becomes accessible to the imidazole spin label. Spin labeling the buried tyrosines prevents the folding of the globular structure, which, in turn, affects the proper binding of the H5 molecule to stripped chromatin. Chromatin complexes reconstituted from such an extensively modified H5 molecule show a weaker protection of the 168 base pair chromatosome during nuclease digestion. However, when only the surface tyrosine of the H5 molecule is labeled, such a molecule can still bind correctly to stripped chromatin, yielding a complex very similar to that of native chromatin. Our data supports the idea that not just the presence of the linker histone H5, but the presence of an intact H5 molecule with a folded, globular central domain in essential in the recognition of its specific binding sites on the nucleosomes. Our data also show that during the chromatin condensation process, the tumbling environment of the spin label attached to the surface tyrosine in the H5 molecule is not greatly hindered but remains partially mobile. This suggests that either the labeled domain of the H5 molecule is not directly involved in the condensation process or the formation of the higher-order chromatin structure does not result is a more viscous or tighter environment around the spin label. The folded globular domain of H5 molecule serves in stabilizing the nucleosome structure, as well as the higher-order chromatin structure.

Electric birefringence of chromatin reconstituted with various histone H1 subfractions

Rat liver chromatin is stripped of H1 histone by exposure to 0.5 M NaCl and reassociated with individual purified subfractions of H1 by salt-step dialysis. The effectiveness of proteins H1-1 and H1 in the condensation of DNA is monitored by transient electric birefringence and circular dichroism. Steady-state birefringence and relaxation time measurements show that reconstitutions are not perfect although some features of native chromatin are restored when a ratio of 2 moles of H1 per nucleosome is used. The amplitude of the positive birefringence is better recovered with H1-1 than with H1 but the values of relaxation times and molar ellipticities indicate that reconstituted samples exhibit a more compact and rigid structure compared to that of native chromatin.