Zinc modulation of a transient potassium current and histochemical localization of the metal in neurons of the suprachiasmatic nucleus

The effect of Zn2+ on a voltage-dependent, transient potassium current (IA) in acutely dissociated neurons from the suprachiasmatic nucleus was studied with the whole-cell patch-clamp technique. At micromolar concentrations, Zn2+ markedly potentiated IA activated from a holding potential of -60 mV, which is the resting potential of these neurons. This potentiation occurred at a Zn2+ concentration as low as 2 microM and increased with higher Zn2+ concentrations. The Zn2+ action appears to arise from a shift in the steady-state inactivation of IA to more positive voltages. At 30 microM, Zn2+ shifted the half-inactivation voltage by +20 mV (from -80 mV to -60 mV), and 200 microM Zn2+ shifted this voltage by +45 mV (from -80 mV to -35 mV). Histochemically, we have also observed Zn2+ staining throughout the suprachiasmatic nucleus; the staining is particularly intense in the ventrolateral region of the nucleus, which receives the major fiber inputs. Our findings suggest that Zn2+, presumably synaptically released, may modulate the electrical activity of suprachiasmatic nucleus neurons through IA. Because vesicular Zn2+ is fairly widespread in the central nervous system, it is conceivable that this kind of Zn2+ modulation on IA, and possibly on other voltage-activated currents, exists elsewhere in the brain.

cAMP-activated Na+ current of molluscan neurons is resistant to kinase inhibitors and is gated by cAMP in the isolated patch

The cAMP-dependent Na+ current (INa,cAMP) modulates excitability in many molluscan neurons. Rapid activation of INa,cAMP by cyclic nucleotide, its ion dependence, and its blockade by divalent cations resemble cyclic nucleotide-activated cation currents in vertebrate photoreceptors and olfactory receptors, where activation has been found to be independent of kinase activity. We tested the phosphorylation dependence of INa,cAMP in neurons of the feeding and locomotory networks of the predatory marine snail Pleurobranchaea. Identified neurons of pedal and buccal ganglia were axotomized for recording the INa,cAMP response to iontophoretic injection of cAMP under two-electrode voltage clamp. Intracellular injections of specific peptide inhibitor of protein kinase A had no blocking effects on activation of INa,cAMP by iontophoretic injection of cAMP. Inward single-channel currents were activated in excised inside-out patches during exposure to cAMP in salines without added ATP. Sodium was the major current carrying ion. Two distinct types of INa,cAMP channel activity were observed, where opening probability and open times differed, but conductance was similar, 36.7 pS. These observations suggest that INa,cAMP activation occurs by direct binding of cAMP to a regulatory site at the channel, rather than by phosphorylation.

Expression and structural analysis of a teleost homolog of a mammalian zona pellucida gene

Gene expression in oviparous vertebrates during vitellogenesis is hormonally regulated. Our laboratory has characterized a unique gene (wf female), which is seasonally expressed in the liver of the female winter flounder Pseudopleuronectes americanus. The wf female mRNA is coexpressed with vitellogenin mRNA and reaches a high level during vitellogenesis. The wf female gene is 2554 base pairs in length and encodes a putative protein of 509 amino acids. The gene consists of eight exons separated by seven introns of different sizes. Within exon 1, there are six PQQ-rich repeats. Four of them encode a putative (PQQ)1PKY polypeptide, similar to the repeats found in the extracellular domains of other proteins. Exons 2-7 share homology with the zona pellucida protein genes rc55 of rabbit and zp-2 of mouse, and the positions of intron boundaries are conserved in the wf female and mouse zp-2 genes. In addition, the transcriptional regulatory cis elements (estrogen response element, CCAAT and TATAAA boxes), as found in vertebrate genes, are also conserved for the wf female promoter and mapped upstream from the initiation site of the wf female primary transcript.

Sodium and calcium currents in acutely dissociated neurons from rat suprachiasmatic nucleus

1. Neurons were acutely dissociated from the suprachiasmatic nucleus (SCN) of adult rats and studied with whole-cell and perforated-patch recordings at room temperature. 2. Acutely dissociated SCN neurons had spherical cell bodies of 12 microns in average diameter. The recorded cells were randomly selected and had either no process (38%), one (41%), two (19%), or three processes (2%). They had a resting potential of about -60 mV, an input resistance of approximately 5 G omega, and a cell capacitance of approximately 7 pF. 3. The dissociated neurons had variable spontaneous firing rates, typically (76%) < 1 Hz. 4. Under current clamp, continuous current injection elicited repetitive action potentials. 1 microM tetrodotoxin (TTX) reduced the amplitudes of the action potentials as well as the firing rate, whereas 200 microM Cd2+ stopped repetitive firing altogether. Action potentials were completely eliminated with Cd2+ and TTX present. These results suggest that both Na+ and Ca2+ contribute to the action potential in these cells. 5. With 200 microM Cd2+ present to block calcium currents, a train of brief depolarizing pulses could still elicit repetitive sodium action potentials, but these became attenuated at stimulating frequencies as low as 1 Hz. 6. Under voltage clamp, the sodium current was activated at about -40 mV and peaked at about -10 mV. It inactivated with a time constant of approximately 0.5 ms at 0 mV, and in steady state the current was half-inactivated at about -60 mV. Recovery of the current from inactivation showed two very different phases with time constants of approximately 30 and 600 ms at -60 mV. The slow phase was probably responsible for the very low firing rate of the sodium action responsible for the very low firing rate of the sodium action potential. 7. In the absence of external sodium, depolarization-activated calcium action potentials were preferentially blocked by 20 microM Cd2+, whereas a posthyperpolarizing depolarizing (or anode break) was preferentially reduced by 100 microM Ni2+. These differential effects hinted at the presence of both low-threshold and high-threshold calcium currents in these cells. 8. Voltage-clamp experiments confirmed the presence of a low-threshold, transient calcium current that was activated by depolarizations above -70 mV. It inactivated with a time constant of approximately 25 ms between -50 and -30 mV. Steady-state inactivation was half-complete at about -90 mV and complete at about -70 mV.(ABSTRACT TRUNCATED AT 400 WORDS)

Upper excited state photochemistry of DNA

The quantum yields for cyclobutylpyrimidine dimers, alkali-labile sites, and frank strand breaks in double-stranded DNA have been measured using low-intensity radiation at 199.8, 217.8, and 239.5 nm from a Raman-shifted frequency quadrupled Nd:YAG laser. The quantum yield for cyclobutylpyrimidine dimers was also measured using 254 nm radiation from a low-pressure mercury lamp. The quantum yield for cyclobutylpyrimidine dimers is constant within a factor of two between 254 and 199.8 nm except for 239.5 nm, indicating that upper excited singlet states of bases convert efficiently to the lowest singlet state. The quantum yields for alkali-labile sites and frank strand breaks both increase as the wavelength decreases but follow different patterns. These results indicate that alkali-labile sites from a higher excited state of the base, whereas frank strand breaks form by excitation of the sugar-phosphate backbone.

Co-regulation of cAMP-activated Na+ current by Ca2+ in neurones of the mollusc Pleurobranchaea

1. The cAMP-gated Na+ current (INa, cAMP) was studied in axotomized neurons of the pedal ganglion of the sea slug Pleurobranchaea. INa, cAMP responses were elicited by iontophoretic injection of cAMP and recorded in voltage clamp. 2. The current-voltage relation for INa, cAMP was flat between -90 and -50 mV, but declined steeply with depolarization from -50 to -30 mV. Depolarizing pulses also suppressed the INa, cAMP response, which recovered slowly over tens of seconds. 3. The inactivating effects of depolarization on the current were abolished both by blockade of Ca2+ current and intracellular injection of Ca2+ chelator. Thus, Ca2+ influx through voltage-dependent Ca2+ channels probably mediates inactivation of INa, cAMP within its normal physiological range of action. 4. Increasing intracellular cAMP levels antagonized the effects of Ca2+ influx on INa, cAMP. The mutual antagonism of the ions suggests that cAMP and Ca2+ act competitively in regulation of the INa, cAMP channel. 5. Measures of fractional inactivation of INa, cAMP provided evidence for the existence of an appreciable basal level of current, and hence cAMP, in the unstimulated neuron. Since INa, cAMP is a direct function of cAMP activity, measures of fractional inactivation permit quantification of cAMP levels in the living neuron. 6. Calcium inactivation of INa, cAMP completes a negative feedback loop that can contribute to endogenous burst activity. Over the burst cycle, depolarization and action potential activity driven by INa, cAMP would lead to Ca2+ influx, consequent inactivation of the inward current, and hyperpolarization. This mechanism of endogenous bursting resembles other in which the burst cycle has been found to be regulated by kinetics of Ca2+ influx and removal. However, INa, cAMP may vary in its Ca2+ sensitivity in different neurons and these variations may affect the functional expression of endogenous oscillatory activity.

The mouse intracisternal A particle-promoted placental gene retrotransposition is mouse-strain-specific

Insertion of a single long terminal repeat (LTR) of an intracisternal A particle (IAP) gene into a placenta-expressed cellular gene (mouse IAP-promoted placental gene, MIPP) has recently been found for the mouse strains Swiss and CF-1. To test whether such a retrotransposition event has also taken place in other strains of mouse, genomic DNA and total RNAs were analyzed from the outbred CF-1 strain and five inbred strains of mouse, AKR/J, C57BL/6J, DBA/2J, C3H/HeJ, and BALB/c. Specific DNA fragments flanking the LTR region were isolated from MIPP cDNA and genomic clones and used as hybridization probes. Three transcripts [two minor, 4.4 kilobases (kb) and 2.2 kb; one major, 1.2 kb] were detected. The 4.4-kb and 2.2-kb species were found in all strains of mouse studied. The 1.2-kb transcript (promoted by IAP LTR) is present only in placentas of C3H/HeJ and BALB/c mice. Both of these strains contain an IAP LTR in the MIPP gene. In contrast, there is no IAP LTR in this cellular gene in strains DBA/2J, C57BL/6J, and AKR/J. Thus, the IAP MIPP retrotransposition is strain-specific. The parents of the outbred CF-1 mice used for the present studies were both heterozygous at the MIPP locus. Restriction fragment length polymorphism studies using inbred strains and recombinant inbred mice have further established the linkage between the MIPP gene (D4Jhu8) and several loci on distal mouse chromosome 4. The symbol Ipp is being used for this gene in all major mouse data bases and in the comparative section of the human genome data base.

Nuclear protein binding to the 5' enhancer region of the intracisternal A particle long terminal repeat

The interactions of nuclear proteins from embryonal carcinoma cells (PCC3) with the long terminal repeats (LTRs) of murine intracisternal A particle (IAP) genes were studied. Two protein-DNA complexes were detected between PCC3 nuclear extract and IAP LTRs in a gel mobility shift assay. An additional complex was observed when enriched fractions from a heparin-agarose column were used as the source of proteins. Two regions within the LTR of IAP 81 were identified as the sites of protein interaction by DNase I protection. One region encompasses 43 nucleotides within the U3 region at the 5' end of LTR 81. The other covers a 78 base pair region lying within 100 nucleotides upstream from the transcription initiation site. Studies using constructs containing intact or deleted versions of the LTR fused to the bacterial chloramphenicol acetyltransferase gene indicated that the absence of the 5' 47 base pairs reduced the level of chloramphenicol acetyltransferase transcription to 20% of that driven by the entire LTR. Southwestern analysis of PCC3 nuclear extracts and column fractions revealed that a 28,000- and a 46,000-dalton protein were the major species that interact with the 5' end of IAP LTR 81.

Kinetic analysis of cAMP-activated Na+ current in the molluscan neuron. A diffusion-reaction model

cAMP-activated Na+ current (INa,cAMP) was studied in voltage-clamped neurons of the seaslug Pleurobranchaea californica. The current response to injected cAMP varied in both time course and amplitude as the tip of an intracellular injection electrode was moved from the periphery to the center of the neuron soma. The latency from injection to peak response was dependent on the amount of cAMP injected unless the electrode was centered within the cell. Decay of the INa,cAMP response was slowed by phosphodiesterase inhibition. These observations suggest that the kinetics of the INa,cAMP response are governed by cAMP diffusion and degradation. Phosphodiesterase inhibition induced a persistent inward current. At lower concentrations of inhibitor, INa,cAMP response amplitude increased as expected for decreased hydrolysis rate of injected cAMP. Higher inhibitor concentrations decreased INa,cAMP response amplitude, suggesting that inhibitor-induced increase in native cAMP increased basal INa,cAMP and thus caused partial saturation of the current. The Hill coefficient estimated from the plot of injected cAMP to INa,cAMP response amplitude was close to 1.0. An equation modeling INa,cAMP incorporated terms for diffusion and degradation. In it, the first-order rate constant of phosphodiesterase activity was taken as the rate constant of the exponential decay of the INa,cAMP response. The stoichiometry of INa,cAMP activation was inferred from the Hill coefficient as 1 cAMP/channel. The equation closely fitted the INa,cAMP response and simulated changes in the waveform of the response induced by phosphodiesterase inhibition. With modifications to accommodate asymmetric INa,cAMP activation, the equation also simulated effects of eccentric electrode position. The simple reaction-diffusion model of the kinetics of INa,cAMP may provide a useful conceptual framework within which to investigate the modulation of INa,cAMP by neuromodulators, intracellular regulatory factors, and pharmacological agents.

Identification of a novel murine IAP-promoted placenta-expressed gene

We have cloned and characterized a novel cellular gene that is promoted by an intracisternal A-particle (IAP) LTR and expressed in the mouse placenta (mouse IAP promoted placental gene, MIPP). A 1067bp cDNA clone containing an IAP LTR U5 region duplicated in its 5' terminus and an ORF coding for a potential 202 amino acids protein was isolated from an 8.5 day old mouse embryo cDNA library. Sequence analysis of the 5' region of a genomic clone revealed the presence of a solo IAP LTR with the same U5 duplication, and primer extension analysis confirmed that transcription of the MIPP gene is under the control of the IAP LTR. Expression of the MIPP gene parallels that of IAP genes in normal mouse tissues with abundant transcripts present in the placenta and also in the myeloma MOPC-315. The MIPP-encoded protein is composed of four 48-amino acid repeat units and shares homology with a vaccinia virus gene product. MIPP-related sequences were also detected in higher eukaryotic genomes including human.

Cell lineage-specific expression of the MIPP gene

The expression of the mouse IAP promoted placental (MIPP) gene was examined in the tissues of the 13.5 day mouse conceptus by Northern hybridization analysis. MIPP transcripts were found in total cellular RNA isolated from the placenta, parietal yolk sac, and visceral yolk sac, but not the embryo or amnion. Expression in the visceral yolk sac was confined to the visceral endoderm cell layer suggesting that the MIPP gene is specifically expressed in tissues derived from the trophectoderm and primitive endoderm cell lineages. The expression of IAP genes paralleled that of MIPP in all tissues studied except for the presence of IAP transcripts in the amnion.

Seasonal cycle and regulation by temperature of antifreeze protein mRNA in a Long Island population of winter flounder

The seasonal cycle and regulation by temperature of antifreeze protein mRNA (AF mRNA) were investigated in a Long Island population of winter flounder (Pseudopleuronectes americanus) by Northern blot hybridization and by in vitro translation of liver RNA. AF mRNA was expressed at high levels in the fall and winter (Nov.-Feb.) and at low or undetectable levels in the summer. The time of accumulation of AF mRNA coincides with the time during which water temperature and photoperiod decrease to 4°C and 9 h of light per day, respectively. A temperature and photoperiod decrease in the laboratory during this time also resulted in high levels of AF mRNA. The levels of other mRNAs, as assayed by in vitro translation, were relatively constant during both seasonal acclimation and laboratory acclimation. The seasonal cycle of AF mRNA in Long Island winter flounder is similar to that of a more northern, Newfoundland population of winter flounder and different from that of an intermediate, New Brunswick population. These similarities and dissimilarities are discussed in light of potentially different exogenous and endogenous regulatory cues in the different populations.

A self-inducing runaway-replication plasmid expression system utilizing the Rop protein

A highly efficient prokaryotic expression system has been developed that produces proteins at levels exceeding 150 micrograms/ml of culture medium. The system consists of a temperature-sensitive-copy-number plasmid that carries the rop gene and promoter downstream from the trp promoter. Any sequence cloned into the PvuII site of the rop gene alters Rop protein activity and causes lethal runaway plasmid DNA replication. This plasmid replication can be suppressed in trans by complementation with a similar wild-type plasmid. Cells harboring both plasmids are quite stable, and induction of plasmid DNA synthesis occurs only after cells are grown for several generations under conditions that lead to the loss of the trans-acting repressor. Large amounts of Rop fusion proteins accumulate in the cell as the trp operon is gradually induced via repressor titration. All chimeric proteins accumulate as insoluble aggregates, and are therefore easily purified. They can be solubilized using relatively mild conditions, and the partially purified proteins are highly amenable to cleavage by chemical methods. Using this system we have made Rop fusions with the HIV Tat protein, the herpes simplex virus type-2 38K protein, and Chinese hamster metallothionin.

Functional analysis of the long terminal repeats of intracisternal A-particle genes: sequences within the U3 region determine both the efficiency and direction of promoter activity

The transcriptional activity of five intracisternal A-particle (IAP) long terminal repeats (LTRs) in mouse embryonal carcinoma PCC3-A/1 cells and in Ltk- cells was determined. We tested the promoter activity of the LTRs by coupling them to the reporter gene chloramphenicol acetyltransferase (CAT) or guanosine-xanthine phosphoribosyltransferase (gpt). Each LTR was tested for promoter function in both the sense (5' to 3') and antisense (3' to 5') orientation preceding the reporter gene. The transcriptional activity of individual IAP gene LTRs varied considerably, and the LTR from IAP81 possessed promoter activity in both directions. The bidirectional activity of the IAP81 LTR confirmed by monitoring Ecogpt expression in stably transfected Ltk- cells, with the initiation sites for sense and antisense transcription being localized to within the IAP81 LTR by S1 nuclease mapping. Deletions of LTR81 show that for normal 5'-to-3' gene transcription (sense direction), the 3'U3/R region determines the basal level of transcription, whereas sequences within the 5'U3 region enhance transcription four- to fivefold. Deletion mapping for antisense transcription indicates that a 64-base-pair region (nucleotides 47 to 110) within the U3 region is essential for activity. These data indicate that the U3 region contains all the regulatory elements for bidirectional transcription in IAP LTRs.

Murine A type retroviruses promote high levels of gene expression in embryonal carcinoma cells

The expression of Intracisternal A Particle (IAP) genes in the mouse embryonal carcinoma cell line PCC3 was investigated by cDNA cloning and transient gene expression assays. A group of 26 IAP cDNA clones, products of transcriptionally active IAP proviruses, were selected from a cDNA library made from undifferentiated PCC3 cell RNA. Several of these clones were characterized by restriction enzyme mapping and DNA sequence analysis. The DNA sequence in both the promoter and structural regions of two cDNAs closely resembles those of IAP genomic clones. Three new sequence elements were identified within the U3 region, an Sp1 transcription-factor-binding site, an adenovirus E1a enhancer sequence and a region of homology to a promoter element of adenovirus E4 gene. Hybrid constructs were made that place the U3/R region of the IAP cDNAs immediately 5′ to the chloramphenicol acetyl transferase (CAT) gene. IAP-CAT constructs were transfected into PCC3 cells, and cell extracts prepared and analysed for CAT enzyme activity and CAT RNA levels. IAP-CAT transfected cells were shown to contain substantial levels of CAT enzyme activity and to accumulate much greater levels of CAT RNA than two standard promoters, pRSVcat and pSV2cat. The ability of these A type retroviral promoters to function in PCC3 cells is in direct contrast to the near total restriction of normal C type retroviral expression in EC cells.

Post-transcriptional regulation and DNA undermethylation of intracisternal A particle genes in embryonal carcinoma cell lines

Northern blot analysis and in vitro nuclear transcription assays were performed in order to clarify conflicting reports on the expression of intracisternal A particle (IAP) genes in embryonal carcinoma (EC) cell lines. Results demonstrate that post-transcriptional mechanisms control the final steady-state levels of IAP RNA in EC cells. IAP genes were further found to be undermethylated in IAP-expressing EC cell lines.

Structure and in vitro transcription of a mouse B1 cluster containing a unique B1 dimer

A highly repetitive DNA element located 950 bp upstream from a mouse U2 small nuclear RNA gene has been cloned and characterized. The repetitive element is composed of a simple sequence repeat and a cluster of three B1 sequences. Two of these B1 elements are arranged head-to-tail and are joined by an oligo(dA)-rich linker. This unique B1 dimer, comprised of 339 bp, resembles the dimeric structure of primate Alu-family sequences, particularly that of a prototypic human Alu element. The other B1 element within the mouse cluster is a typical monomeric unit. Transcription studies performed in HeLa cell extracts with deletion mutants of the B1 cluster reveal that the single B1 unit is expressed at least 50 times more efficiently than the B1 dimer region. Furthermore, the B1 dimer which contains mutations in the first polymerase III promoter region is not transcribed end-to-end. We conclude that this B1 dimer is unlikely to give rise to a new dimeric retroposon family in the mouse genome.

mRNA from human colon tumor and mucosa related to the pol gene of an endogenous A-type retrovirus

The expression of endogenous retroviral genes in mammals may be etiologically related to genetic diseases including cancer. Recently, A-type human endogenous retroviral genomes have been cloned using the reverse transcriptase (pol) genes of rodent intracisternal A-particles (IAP). In this report, RNA from human colon adenocarcinoma and surrounding mucosa was hybridized to mouse IAP pol and gag genes to examine the expression of human endogenous A-type retroviruses. Abundant, heterogeneous size, polyadenylated transcripts homologous to the mouse IAP pol gene were detected in both tissues. Transcripts homologous to the mouse IAP gag region were not found.

Decreased methylation of the major mouse long interspersed repeated DNA during aging and in myeloma cells

Sequences of DNA that hybridize on Southern blots with cloned EcoR1 1.3 kb (ER1) of long interspersed repeated sequence (L1Md) of mouse have been examined in genomic DNA of neonatal mice, livers and brains of adult mice (3, 10, 27, and 30 mo old), and the solid myeloma tumor MOPC-315. The isoschizomers Hpa II (CCGG or mCCGG) and Msp I (CCGG or CmCGG) were used to assess methylation. We found that the L1Md sequence is fully methylated in young animals but demethylated in myeloma. Demethylation of L1Md sequence also occurred in aged animals. By scanning the autoradiogram, we found that approximately 8% of the 10(4)-10(5) copies have been demethylated in 27-mo-old liver.

Complete nucleotide sequence of an EcoRI-1.35-kb repeated element of mouse: homology with the cellular flanking region between two intracisternal A-particle genes

The complete DNA sequence (1369 bp) of an EcoRI-1.35-kb repeated element (ER-1) of the mouse BamHI family has been determined. Analysis of this sequence revealed that a portion of the 3' end (positions 1277-1369) of ER-1 was found to share 91% homology with the flanking cellular sequence between two adjacent intracisternal A-particle (IAP) genes, IAP-19A and IAP-19B.

Genetic relatedness between intracisternal A particles and other major oncovirus genera

Intracisternal A particles represent a major oncovirus genus. By reciprocal hybridization between molecularly cloned A particles and representatives of other oncovirus genera, we established pol gene homology with type B, type D and avian type C viruses. The most extensive homology was with mammalian type D viruses. The transcriptional orientation of the IAP genome was determined, as well as evidence indicating that its pol gene, which is apparently defective, contains coding regions for both reverse transcriptase and endonuclease proteins.

Nucleotide sequences of murine intracisternal A-particle gene LTRs have extensive variability within the R region

Nucleotide sequences of the long terminal repeats (LTRs) of four murine intracisternal A-particle (IAP) genes IAP62, 19, 81 and 14 were determined. Each IAP LTR contains three sequence domains, 5'-U3-R-U5-3', and each is bound by 4 bp imperfect inverted repeats. The transcriptional regulatory sequences, CAAT and TATA, as well as the enhancer core sequence GTGGTAA are conserved and precisely positioned within the U3 region. In the R region, the sequence AATAAA is located twenty base pairs preceding the dinucleotide CA, the polyadenylation site. In IAP19 and IAP81, the 5' and 3' LTRs are flanked by a six nucleotide direct repeat of cellular sequences representing the possible integration sites for these IAP proviruses. Both the size and sequences of different IAP LTRs vary considerably, with the majority of the variation localized within the R regions. The size of R varies from 66 bp in IAP14 to 222 bp in IAP62; in contrast, the U3 and U5 regions are all similar in size. These extra sequences within the R region of large LTRs consist of several unusual directly repeating sequences which account for this variability.

Winter flounder antifreeze proteins: a multigene family

The nucleotide sequence of a cDNA clone of winter flounder antifreeze protein was determined by the dideoxynucleotide method. The sequence would predict a protein of 91 amino acids composed of a prepropeptide of 38 amino acids and a mature protein of 53 amino acids, which includes four complete 11-amino acid repeats. This predicted sequence corresponds to an antifreeze protein of intermediate size which is one 11-amino acid repeat longer than the smallest antifreeze proteins found in the serum of winter flounder during the cold season. Southern blot hybridization analysis of winter flounder genomic DNA with radioactive cDNA probes reveals a multigene family of potential antifreeze protein genes. This conclusion is supported by amino acid sequence analysis of several serum antifreeze proteins.

Correlation of undermethylation of intracisternal A-particle genes with expression in murine plasmacytomas but not in NIH/3T3 embryo fibroblasts

We report here comparative studies of DNA methylation and expression of intracisternal A-particle (IAP) genes in murine plasmacytomas, TEPC-15 and MOPC-315, in NIH/3T3 embryo fibroblasts, and in normal liver from young adult BALB/c mice. In Southern blot analysis using methylation-sensitive restriction enzymes, we observed hypomethylation of 4.7- and 5.3-kilobase pair IAP proviruses, and partial undermethylation of other IAP DNA fragments in TEPC-15, MOPC-315, and 3T3 cells, while most of these DNA fragments were hypermethylated in liver. The extent of undermethylation at 12 different sites including the long terminal repeat sequence region and 5'-flanking sequence within one specific IAP gene was found to be similar between 3T3 cells and plasmacytomas. Little or no undermethylation of these sites was found in liver. Hypomethylation of IAP genes, however, is not correlated with their expression in 3T3 cells (as it is found for plasmacytomas), since 3T3 cells, like liver cells, have no detectable transcripts. We also observed hypomethylation of the kappa-light chain gene in 3T3 cells, suggesting that undermethylation may be a generalized phenomenon in these cells. The relationships between gene undermethylation and the control of gene expression in 3T3 cells is discussed.

Transcription of intracisternal A-particle genes in mouse myeloma and Ltk- cells

In vivo- and in vitro-synthesized RNA from the murine plasmacytoma MOPC-315 was found to hybridize to all regions of a 7.2-kilobase-pair intracisternal A-particle (IAP) gene. IAP-specific transcripts were also detected in mouse Ltk- cells, but not in cells derived from normal tissues (kidney, liver, spleen) of 6-week-old BALB/c mice. Three RNA species of 7.2, 5.3, and 3.8 kilobases were identified by Northern blot analysis of MOPC-315 polyadenylated RNA. The 7.2- and 5.3-kilobase transcripts were found in greater levels in nuclear as compared with whole cell RNA, suggesting the involvement of one or more of the following mechanisms: RNA processing, preferential nuclear transport, or differential RNA stability. We show that the primary IAP transcript is initiated within the long terminal repeat by hybridization analysis with restriction digests of cloned IAP DNA and [gamma-S]pppApNp ... RNA synthesized in nuclei with [gamma-S]ATP as the RNA initiating probe. Low concentrations of alpha-amanitin (2 micrograms/ml) inhibited IAP RNA synthesis by greater than 90%, suggesting that RNA polymerase II is responsible for IAP transcription.

The nucleotide sequence of a new human repetitive DNA consists of eight tandem repeats of 66 base pairs

Three cloned human DNA fragments obtained from a fibroblast genomic DNA were sequenced and identified as containing members of the well-known 300-bp Alu family of interspersed, middle-repetitive DNA sequences. One of these cloned DNA fragments, p16, also contains members of a new repetitive DNA family, which repeats several thousand times in the human genome. Each member of the new 528-bp family consists of eight tandem repeats of a 66-bp sequence. An AluI recognition site is present at the same location in each repeat, and a 25-bp sequence occurs twice (as a tandem repeat) in each of the eight repeats. There is no sequence homology between the new 528-bp family and the 300-bp Alu family, and the new family lacks the flanking 7- to 20-bp direct repeats as well as the dAMP-rich sequences characteristic of the 300-bp Alu family. Construction of a putative evolutionary tree indicates that six duplication events are needed to give rise to the eight tandemly repeated 66-bp units in the new 528-bp family.

Methylation and rearrangement of mouse intracisternal a particle genes in development, aging, and myeloma

Sequences of DNA that hybridize on Southern blots with cloned intracisternal A-particle (IAP) sequences have been examined in genomic DNAs of neonatal mice, livers of adult mice (3, 6, 12, 18, 24, and 26 months old), and the solid myeloma tumor MOPC-315. The isoschizomers HpaII (CCGG or mCCGG) and MspI (CCGG or CmCGG) were used to assess methylation. All the DNAs produced a major 0.5-kilobase MspI fragment that hybridizes with IAP probe. Only the myeloma DNA, and to a much lesser degree DNA from senescent mouse liver, produced this fragment in HpaII digest; the other DNAs all had IAP sequences resistant to HpaII digestion. These sequences thus become fully methylated to CmCGG early and remain so in adult life, except in the myeloma cells that are expressing the IAP genes. An increase in MspI-sensitive sites in IAP gene-containing DNA was observed in aging mice. The probe used to assess methylation, a 0.8-kilobase fragment produced by BamHI-HindIII double digestion, is common to several cloned IAP genes and is part of a region of DNA which is conserved in genomes of all mouse tissues. The probe hybridized to 1.5- and 1.4-kilobase doublet bands produced by BamHI, HindIII, and EcoRI triple digestions of neonatal DNA. These two bands were found in neonatal livers of Swiss Webster, BALB/c, and C57BL/6J mouse strains, showed less in adult liver, and were barely detectable in senescent livers from C57BL/6J mice.

Synthesis and affinity purification of beta-32P-labeled [gamma-S]GTP

A method for the synthesis and purification of guanosine 5'-[gamma-S]triphosphate labeled with 32P in the beta-position is described. The first step in the synthesis involves the quantitative transfer of 32Pi from [gamma-32P]dATP to 5'-GMP catalyzed by GMP kinase. Further incubation of the beta-32P]GDP product with [gamma-S]GTP and nucleoside diphosphate kinase results in the synthesis of [beta-32P][gamma-S]GTP with a yield of 10 to 18%. The 32P-labeled [gamma-S]nucleotide is purified by binding to mercury-agarose and eluting with buffer containing beta-mercaptoethanol. Specific incorporation of 32P into the beta-position was demonstrated by treating [beta-32P][gamma-S]GTP with 7% formic acid to remove the gamma-thiophosphate and digesting the remaining [beta-32P]GDP with nucleotide pyro-phosphatase. Although 5'-GMP was released after pyrophosphatase digestion, the only 32P radioactivity detected was as inorganic phosphate.

Mouse EcoRI satellite DNA contains a sequence homologous to the long terminal repeat of the intracisternal A particle gene

EcoRI restriction endonuclease fragments from the mouse 1,350-base-pair EcoRI satellite sequence were cloned in pBR322 plasmid. One of these fragments, SAT-1, was hybridized to various restriction fragments from cloned mouse intracisternal type A particle (IAP) genes and to mouse total genomic DNA. Hybridization occurred between the SAT-1 sequence and each of the IAP clones. The common region of hybridization in each of the clones was the long terminal repeat region of the IAP genes.

Guanosine 5'-O-(3-thiotriphosphate) inhibits capping of reovirus mRNA

RNA synthesized by reovirus cores was not capped or methylated when GTP was replaced by guanosine 5'-O-(3-thiotriphosphate) [gamma-S]GTP as a reaction substrate. Full length transcripts were synthesized in the presence of [gamma-S]GTP which indicated that capping could be dissociated from the process of transcription. Exogenous [gamma-S]GTP was not cleaved by the virion-associated phosphohydrolase and the majority of transcripts contained triphosphorylated 5'-termini. [gamma-S]GTP did, however, act as a donor for the capping of RNA chains initiated with GTP. Chromatography on mercury-agarose of products initiated with [gamma-S]GTP resulted in the binding of only the small (14 S) size class of RNA, although transcripts not bound to the affinity column were also thiophosphorylated.

Intracisternal A-particle genes: structure of adjacent genes and mapping of the boundaries of the transcriptional unit

Adjacent intracisternal A-particle (IAP) genes were identified in two different recombinant DNA clones, gamma 81 and gamma 19. In clone gamma 81, the most common form of IAP gene was separated by 5.3 kilobases from another IAP gene that had two apparent internal deletions. The two genes were in a head-to-tail configuration. In clone gamma 19, two different types of IAP genes were separated by less than 0.5 kilobase. Blot hybridization analysis of mouse DNA demonstrated that the DNA sequence found in clone gamma 81 is identical to the in vivo configuration. Using isolated DNA fragments from clone gamma 19, we mapped the boundaries of the IAP RNA by S1 digestion of RNA-DNA hybrids and by cDNA extension. With these techniques, both the 5' end and the 3' end of the IAP RNA in two different plasmacytomas (MOPC 315 and TEPC 15) were shown to fall within the long terminal direct repeat of the IAP gene. The fragment sizes generated by S1 digestion of IAP RNAs isolated from the two tumor lines were found to differ, indicating that different IAP genes may be transcribed in these two plasmacytomas.

Terminally redundant sequences in cellular intracisternal A-particle genes

The sequences coding for intracisternal A-particle RNA form a family of related but not identical genetic elements which are present in 650 to 1,000 copies within the mouse genome. We showed that different intracisternal A-particle genes had a terminally redundant sequence of about 400 base pairs, one-half of which arose from the 3' end of the intracisternal A-particle RNA. A second portion of the redundant region did not contain 3-related sequences and was probably derived from the 5' end of intracisternal A-particle RNA. Thus, there were endogenous intracisternal A-particle genes in the cellular DNA-3'-5'--3'-5'-cellular DNA configuration identified for type B and C retroviruses. This indicated that the initial integration of intracisternal A-particle genes into the Mus musculus genome occurred by the same mechanism as the integration of other retroviruses. Two types of heterogeneity were identified among the 5' sequences of the two genes.

Sequence organization of cloned intracisternal A particle genes

Seven recombinant DNA clones containing mouse intracisternal A particle genes were isolated and analyzed by restriction enzyme digestion, Southern blot analysis and heteroduplex mapping. The sequence organization of the individual genes was found to differ, with one end of the gene region being most variable, while a central segment of 1.8 kb was missing from two of the clones. A third region, common to all the clones and containing the 3' end of the gene, is present in about 1800 copies per haploid genome, but the central portion is found in only 650 copies. The same reiteration frequency is found in both myeloma tumor and mouse liver DNA. The most abundant intracisternal A particle RNA in two different myeloma lines was found to be 3.5 kb, and RNA/DNA hybrids show that the RNA is homologous to all but a small internal segment of one of the clones.

Analysis of RNA initiated in isolated mouse myeloma nuclei using purine nucleoside 5'[gamma-S]triphosphates as affinity probes

The purine ribonucleoside triphosphate analogues adenosine 5'[gamma-S]triphosphate and guanosine 5'[gamma-T]triphosphate were used as affinity probes for studying RNA chain initiation in isolated nuclei from the mouse myeloma 66.2 cell line. Transcripts initiated with either nucleotide analogue were isolated by affinity chromatography on a mercury-agarose affinity column. The binding was specific and dependent upon the inclusion of the sulfur nucleotide analogues in the in vitro synthetic reaction. Several lines of evidence indicate that the affinity-labeled RNA is initiated in vitro. First, the sulfur nucleotide is recovered in high yield as a single nucleoside 5'[gamma-S]triphosphate 2',3'-monophosphate product following alkaline hydrolysis of RNA bound to the affinity column. Second, authentic ribosomal 5S RNA is known to initiate with GTP; in vitro 5S RNA is bound to mercury-agarose only if [gamma-S]GTP is used as the affinity label in the synthesis, and not if [gamma-S]ATP is used. Under the conditions studied, nuclei incorporated 1.2--2.4 pmole of UMP per 10(6) nuclei per min, and the rate of synthesis was unaffected by substitution of the nucleotide analogues for the normal nucleotides. The percentage of the total RNA synthesized that was incorporated into sequences initiated in vitro was 7.8 +/- 1.5% with [gamma-S]ATP and 9.6 +/- 6.4% with [gamma-S]GTP. The size of the total RNA synthesized, determined by sedimentation on sucrose density gradients containing dimethylsulfoxide, ranged from less than 5S to 45S, and the size of the affinity-labeled sequences ranged from less than 5S to 28S. Approximately half of the incorporation into RNA initiated in vitro was sensitive to a concentration of alpha-amanitin which selectively inhibits polymerase II activity. Most of the remaining incorporation into initiated sequences can be abolished by concentrations of alpha-amanitin that are inhibitory for polymerase III activity. Over 70% of the total incorporation into ribosomal 5S RNA transcripts was into sequences initiated in vitro. This initiation was catalyzed by polymerase III and was specific for GTP as the initiating nucleotide. The RNAase T1 fingerprint of the newly initiated 5S RNA indicates that this gene is accurately initiated and faithfully elongated in vitro. The use of these affinity label probes provides much greater sensitivity for studying the initiation of RNA in vitro.

Incorporation of purine nucleoside 5'-[gamma-S]triphosphates as affinity probes for initiation of RNA synthesis in vitro

Synthetic DNA templates were transcribed by Escherichia coli RNA polymerase using nucleoside 5'-[gamma-S]triphosphates as one of the nucleotide substrates. Substitution of the thiol analogues for the normal nucleotides had no effect on the rate of RNA synthesis. RNA synthesized with either adenosine 5'-[gamma-S]triphosphate or guanosine 5'-[gamma-S]triphosphate was isolated with high efficiency on mercury-agarose columns prepared by activation with low concentrations of cyanogen bromide. Sulfur was shown to be incorporated at the 5' end of RNA by identification of the tetraphosphate HSpppA32p liberated after alkaline hydrolysis of HS(A-32pU)n (alternating copolymer synthesized by the action of E. coli RNA polymerase on d(A-T)n-d(A-T)n with adenosine 5'-[gamma-S]triphosphate and uridine 5'-[alpha-32P]triphosphate as substrates). Transcripts elongated but not initiated with these thiol analogues did not bind to the affinity column. This technique provides an extremely sensitive assay for RNA synthesis initiation in vitro, since initiated transcripts containing radiolabel throught the entire transcript can be isolated.

Comparative study of hen yolk phosvitin and plasma vitellogenin

Vitellogenin, the only phosphoprotein detectable in the plasma of laying hens, is present at an approximate concentration of 1 mg/mL and can be isolated by chromatography on diethylaminoethylcellulose. Vitellogenin has a molecular weight of 235 000--240 000 and contains approximately 3% phosphorus by weight. Evidence that this protein is the precursor of phosvitins includes its ability to act as an acceptor for phosphate with a phosvitin specific kinase, the generation of a peptide similar to phosvitin by trypsinization, and the presence of distinctive peptides of multiple clustered phosphoserine upon partial acid hydrolysis. This partial sequence similarity between phosvitins and vitellogenin has not been previously reported. The phosphorus content and amino acid composition of vitellogenin are consistent with a model which contains two phosvitins and one lipovitellin. The total molecular weights of these proteins (28 000 + 34 000 + 170 000 = 232 000) are close to that of vitellogenin.

Initiation and translation in vitro of mRNA for MOPC 315 immunoglobulin heavy chain and characterization of translation product

An initiation study of mineral oil-induced plasmacytoma (MOPC) 315 heavy chain immunoglobulin (H315) in vitro has been conducted using formyl-[35S]methionyl-tRNAfMet and a highly purified 18 S message from MOPC 315 solid tumor in a crude rabbit reticulocyte lysate system. The product was specifically precipitated by antibodies directed against MOPC 315 immunoglobulin and H315. The in vitro H315 products terminally labeled with formyl-[35S]methionine or internally labeled with [3H]leucine were electrophoretically identical with in vivo H315 on sodium dodecyl sulfate-polyacrylamide gels. All of the [35S]-methionine was incorporated at the NH2 terminus, not internally, since there is a near complete recovery of [35S]methionine following one cycle of Edman degradation. The NH2-terminal cyanogen bromide peptide, CN2, of in vivo and in vitro H315 co-migrated exactly on gel electrophoresis under conditions which completely resolved two proteins differing in size by only 14 amino acids. These data strongly suggest that there is no NH2-terminal precursor of H315 in this system. Cyanogen bromide peptide profiles of in vivo and in vitro H315 were chromatographically indistinguishable. Three peptides, CN1, CN2, and CN4, which represent approximately 85% of the total amino acids of H315 were isolated and further characterized by electrophoresis and paper chromatography. All were very similar to the corresponding peptides of authentic H315. We conclude that the fidelity of H315 translation is preserved in vitro.

Transcription in vitro of immunoglobulin kappa light chain genes in isolated mouse myeloma nuclei and chromatin

Messenger RNA sequences for immunoglobulin kappa light chain were synthesized in vitro in isolated mouse myeloma nuclei using bound endogenous RNA polymerase (RNA nucleotidyltransferase; nucleoside triphosphate:RNA nucleotidyltransferase; EC 2.7.7.6) and from isolated myeloma chromatin using exogenous Escherichia coli RNA polymerase. The in vitro RNA was transcribed using 5-mercuriuridine triphosphate and separated from in vivo RNA by chromatography on an agarose sulfhydryl affinity column. Template restriction is retained in vitro since synthesis of kappa chain messenger RNA, As determined by hybridization with complementary DNA, was much more efficient in nuclei and chromatin isolated from myeloma 66.2 tissue culture cells, a kappa-chain-producing cell line, than from MOPC 315 tissue culture cells, a lambda-chain-producing cell line. Transcription of kappa chain messenger RNA was 25 times more efficient in myeloma 66.2 nuclei than in myeloma 66.2 chromatin.

Low molecular weight RNA species from chromatin

Several methods of preparing low molecular weight RNA from chick embryo chromatin have been examined. Traditional methods for dissociating chromatin utilizing high concentrations of salt (greater than 2 M) followed by high-speed centrifugation resulted in very low yields of RNA. Increased yields of RNA were obtained by treating chromatin at lower salt concentration (0.2-0.5 M). By using low salt extraction and sodium dodecyl sulfate-phenol deproteinization, six to eight low molecular weight homogeneous RNA species were isolated from chick embryo chromatin and mouse myeloma chromatin. In the myeloma system, all these RNAs are metabolically stable. Each component is homogeneous as examined by gel electrophoresis and hybridizes with mouse DNA at a rate consistent with a single species. There are multiple gene copies for these RNA species in the mouse genome, varying from 100 to 2000 copies for the different species. One of these RNAs is identical with 5S rRNA. In addition, the redundancy of genes for 18S, 28S, and 5S rRNA and tRNA was determined. Approximately 300 copies for 18 and 28S rTRNA and 500 copies for 5S rRNA were found. tRNAs were on an average 110-fold redundant with about 55 different species measured.

The conformation of proteins in chromatin. A circular dichroism study below 250 nm

This paper is an investigation of the circular dichroism (CD) spectra of DNA and protein in chromatin. The circular dichroism (CD) of chromatin below 250 nm is due to DNA and protein peptide chromophores. The spectrum in this region is resolved into contributions from salt-extractable proteins (histone and non-histone proteins extractable with sodium chloride), residual non-histone proteins (not extractable with 3 M sodium chloride), and DNA. Below 250 nm, DNA in chromatin has the same CD spectrum as DNA free in solution, in contrast to the CD of DNA above 250 nm (Hjelm, R. and Huang, R. C., (1974), Biochemistry 13, 5275). Histones and salt-extractable non-histone proteins in chromatin are seen to have an average CD like those observed for globular proteins. The average CD of the residual non-histone proteins is consistent with a population of proteins with more extended conformation. The CD of each of these components is found to be the same in chromatins isolated from tissues having different nuclear synthetic activities: chick embryo brain, pig cerebellum, myeloma K41, calf thymus, and chicken erythrocyte.

The contribution of RNA and non-histone proteins to the circular dichroism spectrum of chromatin

This paper is an investigation of the contribution of low salt extractable RNA and non-histone proteins to the circular dichroism of chromatin. Circular dichroism (CD) of chromatin above 250 nm is due mainly to DNA and is different from that of DNA free in solution. In addition, to a smaller extent, we find that low salt extractable RNA and/or non-histone protein side chain chromophores contribute significantly to the spectra in this region and account for the major differences observed among the CD spectra of chromatins isolated from the five tissues studied; pig cerebellum, myeloma, calf thymus, chick embryo brain, and chick erythrocytes.

Chromatin directed transcription of 5S and tRNA genes

Chromatin prepared by gentle methods from mouse myeloma cells retained its ability to synthesize RNA using bound endogenous RNA polymerase (RNA nucleotidyltransferase; nucleosidetriphosphate:RNA nucleotidyltransferase, EC 2.7.7.6). The transcription resembles that observed in vivo in several respects. The low-molecular-weight RNA species 5S RNA and the 4.5S precursor to 4S RNA, are transcribed accurately and transcription is reinitiated continually in vitro. Their synthesis was not inhibited by alpha-amanitin (1 mug/ml) as was found previously for these species in isolated nuclei.