Genomic organization of rat rDNA

Senescence of human fibroblasts after psoralen photoactivation is mediated by ATR kinase and persistent DNA damage foci at telomeres

Cellular senescence is a phenotype that is likely linked with aging. Recent concepts view different forms of senescence as permanently maintained DNA damage responses partially characterized by the presence of senescence-associated DNA damage foci at dysfunctional telomeres. Irradiation of primary human dermal fibroblasts with the photosensitizer 8-methoxypsoralen and ultraviolet A radiation (PUVA) induces senescence. In the present study, we demonstrate that senescence after PUVA depends on DNA interstrand cross-link (ICL) formation that activates ATR kinase. ATR is necessary for the manifestation and maintenance of the senescent phenotype, because depletion of ATR expression before PUVA prevents induction of senescence, and reduction of ATR expression in PUVA-senesced fibroblasts releases cells from growth arrest. We find an ATR-dependent phosphorylation of the histone H2AX (gamma-H2AX). After PUVA, ATR and gamma-H2AX colocalize in multiple nuclear foci. After several days, only few predominantly telomere-localized foci persist and telomeric DNA can be coimmunoprecipitated with ATR from PUVA-senesced fibroblasts. We thus identify ATR as a novel mediator of telomere-dependent senescence in response to ICL induced by photoactivated psoralens.

Senescence of human fibroblasts after psoralen photoactivation is mediated by ATR kinase and persistent DNA damage foci at telomeres

Cellular senescence is a phenotype that is likely linked with aging. Recent concepts view different forms of senescence as permanently maintained DNA damage responses partially characterized by the presence of senescence-associated DNA damage foci at dysfunctional telomeres. Irradiation of primary human dermal fibroblasts with the photosensitizer 8-methoxypsoralen and ultraviolet A radiation (PUVA) induces senescence. In the present study, we demonstrate that senescence after PUVA depends on DNA interstrand cross-link (ICL) formation that activates ATR kinase. ATR is necessary for the manifestation and maintenance of the senescent phenotype, because depletion of ATR expression before PUVA prevents induction of senescence, and reduction of ATR expression in PUVA-senesced fibroblasts releases cells from growth arrest. We find an ATR-dependent phosphorylation of the histone H2AX (gamma-H2AX). After PUVA, ATR and gamma-H2AX colocalize in multiple nuclear foci. After several days, only few predominantly telomere-localized foci persist and telomeric DNA can be coimmunoprecipitated with ATR from PUVA-senesced fibroblasts. We thus identify ATR as a novel mediator of telomere-dependent senescence in response to ICL induced by photoactivated psoralens.

Aging results in hypermethylation of ribosomal DNA in sperm and liver of male rats

There is a concern that increased paternal age may be associated with altered fertility and an increased incidence of birth defects in man. In previous studies of aged male rats, we have found abnormalities in the fertility and in the embryos sired by older males. Aging in mammals is associated with alterations in the content and patterns of DNA methylation in somatic cells; however, little is known in regard to germ cells. A systematic search for global and gene-specific alterations of DNA methylation in germ cells and liver of male rats was done. Restriction landmark genomic scanning, a method used to determine specific methylation patterns of CpG island sequences, has revealed a region of the ribosomal DNA locus that is preferentially hypermethylated with age in both spermatozoa and liver. In contrast, all single copy CpG island sequences in spermatozoa and in liver remain unaltered with age. We further demonstrate that a large proportion of rat ribosomal DNA is normally methylated and that regional and site-specific differences exist in the patterns of methylation between spermatozoa and liver. We conclude that patterns of ribosomal DNA methylation in spermatozoa are vulnerable to the same age-dependent alterations that we observe in normal aging liver. Failure to maintain normal DNA methylation patterns in male germ cells could be one of the mechanisms underlying age-related abnormalities in fertility and progeny outcome.

Inhibition of 3beta-hydroxysteroid dehydrogenase-isomerase in mouse adrenal cells: a direct effect of testosterone

Gonadal steroids modulate adrenal gland size and function in a variety of species, and our previous studies demonstrate that circulating androgens suppress 3beta-hydroxysteroid dehydrogenase-isomerase (3betaHSD) activity in the adrenal cortex of male mice. The present study tests the hypothesis that androgens have a direct, receptor-mediated inhibitory effect on adrenal 3betaHSD. Treatment of cultured adrenal cells from C57BL/6J and C3H/HeJ mice with 0.02-2.0 microM testosterone for 7 days significantly reduces 3betaHSD activity in cells from both strains. However, treatment for 3 days reduces 3betaHSD activity in the adrenal cells from C3H/HeJ, but not C57BL/6J mice. The decreases in 3betaHSD activity in response to testosterone treatment is reflected in decreases in the amount of 3betaHSD immunoreactive protein, such that extended treatment decreases 3betaHSD immunoreactive protein in adrenal cells from both strains, but short-term treatment only decreases 3betaHSD immunoreactive protein in adrenal cells from C3H/HeJ mice. Thus, there appears to be a temporal difference between strains in the effect of the testosterone on 3betaHSD activity and immunoreactive protein. Treatment of the adrenal cells with androgen agonists and an antagonist indicate that the effect of testosterone is androgen receptor mediated. The effect of testosterone appears to be specific for 3betaHSD, since none of the treatments alter P450(scc) in cells from either strain. Testosterone treatment also causes a decrease in the amount of 3betaHSD mRNA. However, in contrast to the effect on activity and immunoreactive protein, there is no strain-related temporal difference because testosterone decreases 3betaHSD mRNA within 24h in adrenal cells from both strains. These results indicate that testosterone can act directly on the adrenal gland to decrease 3betaHSD activity, immunoreactive protein, and mRNA content in mouse adrenal glands, and thus contribute to the sex difference in adrenal function observed in many species.

Accelerated methylation of ribosomal RNA genes during the cellular senescence of Werner syndrome fibroblasts

Ribosomal DNA (rDNA) metabolism has been implicated in cellular and organismal aging. The role of rDNA in premature and normal human aging was investigated by measuring rDNA gene copy number, the level of rDNA methylation, and rRNA expression during the in vitro senescence of primary fibroblasts from normal (young and old) donors and from Werner syndrome (WS) patients. In comparison to their normal counterparts, WS fibroblasts grew slowly and reached senescence after fewer doublings. The rDNA copy number did not change significantly throughout the life span of both normal and WS fibroblasts. However, in senescent WS and normal old fibroblasts, we detected rDNA species with unusually slow electrophoretic mobility. Cellular aging in Saccharomyces cerevisiae is accompanied by the formation and accumulation of rDNA circles. Our analysis revealed that the rDNA species observed in this study were longer, linear rDNA molecules attributable to the inhibition of ECO:RI cleavage by methylation. Furthermore, isoschizomeric restriction analysis confirmed that in vitro senescence of fibroblasts is accompanied by significant increases in cytosine methylation within rDNA genes. This increased methylation is maximal during the abbreviated life span of WS fibroblasts. Despite increased methylation of rDNA in senescent cells, the steady-state levels of 28S rRNA remained constant over the life span of both normal and WS fibroblasts.

Homogenous repair of singlet oxygen-induced DNA damage in differentially transcribed regions and strands of human mitochondrial DNA

Photoactivated methylene blue was used to damage purified DNA and the mitochondrial DNA (mtDNA) of human fibroblasts in culture. The primary product of this reaction is the DNA lesion 7-hydro-8-oxo-deoxyguanosine (8-oxo-dG). The DNA damage was quantitated using Escherichia coli formamidopyrimidine DNA glycosylase (Fpg) in a gene-specific damage and repair assay. Assay conditions were refined to give incision at all enzyme-sensitive sites with minimal non-specific cutting. Cultured fibroblasts were exposed to photoactivated methylene blue under conditions that would produce an average of three oxidative lesions per double-stranded mitochondrial genome. Within 9 h, 47% of this damage had been removed by the cells. This removal was due to repair rather than to replication, cell loss or degradation of damaged genomes. The rate of repair was measured in both DNA strands of the frequently transcribed ribosomal region of the mitochondrial genome and in both strands of the non-ribosomal region. Fpg-sensitive alkali-resistant oxidative base damage was efficiently removed from human mtDNA with no differences in the rate of repair between strands or between two different regions of the genome that differ substantially with regard to transcriptional activity.

Chromatin structure and methylation of rat rRNA genes studied by formaldehyde fixation and psoralen cross-linking

By using formaldehyde cross-linking of histones to DNA and gel retardation assays we show that formaldehyde fixation, similar to previously established psoralen photocross-linking, discriminates between nucleosome- packed (inactive) and nucleosome-free (active) fractions of ribosomal RNA genes. By both cross-linking techniques we were able to purify fragments from agarose gels, corresponding to coding, enhancer and promoter sequences of rRNA genes, which were further investigated with respect to DNA methylation. This approach allows us to analyse independently and in detail methylation patterns of active and inactive rRNA gene copies by the combination of Hpa II and Msp I restriction enzymes. We found CpG methylation mainly present in enhancer and promoter regions of inactive rRNA gene copies. The methylation of one single Hpa II site, located in the promoter region, showed particularly strong correlation with the transcriptional activity.

Prostaglandin A2 specifically represses insulin-like growth factor-I gene expression in C6 rat glioma cells

The cyclopentenone PGs (PGA and PGJ series) inhibit tumor cell proliferation in vitro and tumorigenesis in vivo via mechanisms that are at present poorly understood. The C6 rat glioma cell line synthesizes and secretes insulin-like growth factor-I (IGF-I), which is believed to act as an autocrine factor for these cells. PGA2 inhibits the proliferation of the C6 cells and causes an increase in the fraction of cells in the G1 phase of the cell cycle. The inhibition of cell proliferation by PGA2 is accompanied by a decrease in the abundance of IGF-I messenger RNA (mRNA). This regulation of IGF-I gene expression is specific, as the abundance of hypoxanthine-guanine phosphoribosyl transferase (HPRT) and ubiquitin mRNA is not significantly affected by PGA2. The repression of IGF-I gene expression is observed at PGA2 concentrations as low as 10 microM and is evident within 4 h after treatment of the C6 cells with PGA2. In addition to specifically regulating the expression of the IGF-I gene, PGA2 also decreases the abundance of cyclin D1 mRNA and increases the abundance of Waf1 mRNA. The inhibition of cell proliferation by PGA2 is partially reversed by coaddition of IGF-I, indicating partial dominance of IGF-I action over PGA2 action. To investigate the molecular basis for the regulation of IGF-I gene expression by PGA2, we developed a sensitive RT-PCR assay for IGF-I nuclear transcripts. A similar assay was developed for quantifying HPRT transcripts, which were used as a control. Treatment of the C6 cells with 20 microM PGA2 resulted in approximately a 6-fold decrease in IGF-I mRNA and IGF-I nuclear transcripts. In contrast, HPRT mRNA and nuclear transcript levels were not significantly affected by PGA2. These results indicate that the decrease in IGF-I mRNA abundance that occurs in response to PGA2 is caused largely by a decrease in IGF-I nuclear transcript levels. To identify the cis-acting element that mediates the effect of PGA2 on IGF-I transcription, C6 cells were transiently transfected with IGF-I/luciferase expression constructs in which luciferase transcription is driven by IGF-I P1 promoter fragments extending from -1711 to -328 or from -1114 to +328 relative to the beginning of exon 1. Treatment of cells with PGA2 in these transient transfection assays did not decrease luciferase activity. These results suggest that the cis-acting regulatory element required for the response to PGA2 is located outside the -1711 to +328 promoter interval.

Estrogen-induced changes in rRNA accumulation and RNA polymerase I activity in the rat pituitary: correlation with pituitary tumor susceptibility

Chronic treatment with the synthetic estrogen diethylstilbestrol induces pituitary tumors in rats and the susceptibility to such tumors is highly strain dependent. The Fischer 344 (F344) strain, which is particularly susceptible, develops pituitary tumors after 30-55 days of estrogen treatment. In contrast, the Sprague-Dawley (SD) strain is relatively resistant to such tumors. DES implants (5 mg) were placed in 21-day-old male rats over a 10-day period and changes in their testes and pituitaries were monitored. Both F344 and SD strains responded similarly by exhibiting a measurable decrease in testes weight to one-third that of controls on day 10. In F344 rats, DNA synthesis in the pituitary increased to 228% as compared with controls after 3 days of DES treatment and remained high on days 7 and 10. In SD rats, DNA synthesis increased to only 150% of that exhibited by controls on day 3 and started to decline on day 7. Surprisingly, total RNA accumulation also responded to DES differentially between these two strains. In F344 rats, the RNA level was 250% as compared with that of controls after 3 days of DES treatment and continued to increase gradually on days 7 and 10. The RNA level in the SD strain increased only slightly from the same DES treatment. A nuclear run-on assay showed elevated pituitary transcription of ribosomal DNA in the F344 rats after 3 days of estrogen administration. The enzymatic activity of pituitary RNA polymerase I, the enzyme responsible for initiating rRNA synthesis, increased twofold in F344 rats when measured after 3 days of estrogen treatment whereas no increase was observed in the SD rats. These results suggest that estrogen-induced changes in the accumulation of rRNA occur at a very early stage in tumorigenesis, prior to any visible tumor growth in the rat pituitary.

Alteration of the adrenal antioxidant defense system during aging in rats

The goal of this study was to determine to what extent aging affects the antioxidant defense system of the rat adrenal and to evaluate the impact of any change in this system on the recognized age-related decline in steroidogenic capacity of adrenocortical cells. The studies were conducted on young (2-5 mo) and aging (12-27 mo) Sprague-Dawley rats and involved procedures measuring steroidogenesis; oxidative damage to tissue; non enzymatic antioxidants such as vitamin C, E, and glutathione; and tissue antioxidant enzyme (Mn and CuZn superoxide dismutases, catalase, and glutathione peroxidase) activity and expression (mRNA, protein mass, and location). Some measurements were made also on rats maintained on vitamin E-deficient diets. The data show that adrenals from young animals are especially well protected against oxidative events; i.e., these adrenals show the least endogenous lipid peroxidation and the highest level of resistance to prooxidant-induced damage (of various tissues measured) and show exceedingly high levels of tissue antioxidants. Aging, on the other hand, results in oxidative changes in adrenal tissue that are generally linked in time to a reduction in efficiency of the normally protective antioxidant defense system and to the decline in corticosterone production. We speculate that these events are causally related, i.e., that the age-related reduction in oxidative mechanisms in adrenal tissues leads to oxidative damage of membrane or cytosolic factors important to cholesterol transport, and, as a consequence of this damage, cholesterol cannot reach appropriate mitochondrial cholesterol side chain cleavage sites, and corticosterone production fails.

Structure and regulation of the mouse GRP78 (BiP) promoter by glucose and calcium ionophore

Dietary calorie restriction, also termed energy restriction, increases mean and maximum life span, reduces the incidence of tumors and increases the mean age of onset of diseases and tumors in every animal tested. Because life-span is genetically determined, we are studying the mechanisms by which energy restriction regulates the expression of genes. We found that energy restriction reduces hepatic glucose-regulated protein-78 (GRP78) and protein-94 mRNA levels by 2-3-fold in mice [Spindler et al., J. Nutr. 20 (1990) 1412-1417]. To investigate this down-regulation, we have cloned the mouse GRP78 promoter (pGRP78) and studied its regulation by glucose. The mouse pGRP78 and the previously cloned rat promoter mediate responsiveness to glucose deprivation, as well as to the calcium ionophore A23187. These studies are the first demonstration that cis-elements in the pGRP78 mediate responsiveness to glucose deprivation.

Transcriptional and post-transcriptional mechanisms regulating neurofilament and tubulin gene expression during normal development of the rat brain

The transcription of the beta II-, beta IV- and alpha 1-tubulin genes as well as that of the three neurofilament genes, NF-L, NF-M and NF-H, was examined during the course of postnatal brain development. Changes in the transcriptional activity of these genes were studied using run-off transcription assays with nuclei isolated from the rat cerebral cortex at postnatal days P2, P5, P10 and adult stages. Northern blotting of total RNA isolated from the cerebral cortex was used to compare changes in steady-state mRNA levels with transcriptional changes that occurred in the cerebral cortex during the postnatal interval. Nuclear run-off assays showed that beta II- and alpha 1-tubulin gene transcription rates were maximal from P2-P5 and declined at later times. Changes in the steady-state mRNA levels for these two genes followed the same general pattern as transcription, but in the case of beta II-tubulin mRNA, were more dramatic. beta IV-tubulin gene transcription dropped between P2 and P5 and then increased progressively to the adult stage, coordinate with an increase in beta IV-tubulin steady-state mRNA levels. NF-L and NF-H genes showed similar patterns of transcriptional change during the postnatal interval, with maximal rates of transcription at P5 followed by a decline at later times. The steady-state levels of NF-L and NF-H mRNAs changed in a manner opposite to that of transcription and increased progressively during the postnatal interval. This suggests that mRNA stabilization is the main factor regulating the steady-state levels of NF-L and NF-H mRNAs in postnatal brain. For the NF-M gene, the developmental transcription pattern was also dissociated from steady-state mRNA level changes, but differed from the transcription patterns of the NF-L and NF-H genes. This suggests the importance of post-transcriptional mechanisms in regulating NF-M mRNA levels in brain and also indicates that some differences exist in the regulatory mechanisms which control NF-M compared to NF-L and NF-H mRNA levels.

Tissue plasminogen activator expression in the embryonic nervous system

Tissue plasminogen activator (tPA) expression during embryogenesis was determined by in situ hybridization of whole mouse embryos from E10.5 through E17.5. The strongest expression occurs in the basal midbrain and hindbrain, and continues posteriorly into the neural canal. This expression coincides with extensive cell migration and proliferation, and tissue remodelling of this region. tPA mRNA is also associated with cells that appear to be invading the cerebellar anlage. Presumptive proliferating and migrating cells in the olfactory neuroepithelium also express tPA. These results indicate that tPA is expressed by a number of different cell types in the developing nervous system and suggest a role for tPA in cell migration and tissue remodelling of the developing CNS.

Luteinizing hormone-releasing hormone receptor messenger ribonucleic acid expression in the rat pituitary during lactation and the estrous cycle

To study mechanisms underlying the modulation of luteinizing hormone-releasing hormone receptor (LHRH-R) during lactation and the estrous cycle, we used a reverse transcriptase-polymerase chain reaction (RT-PCR) procedure to generate a probe for rat LHRH-R messenger RNA (mRNA). Using primers based on the mouse sequence, we amplified an approximately 300 bp fragment from rat pituitary complementary DNA. This PCR product was shown to be part of LHRH-R cDNA by direct sequencing and by comparing to the rat LHRH-R cDNA reported recently. Then, this PCR fragment was used as a probe for northern blotting analysis. The level of LHRH-R mRNA in the pituitary was significantly decreased during lactation, by approximately 80%, compared to that of ovariectomized and intact (diestrous and metestrous cycling) rats while no statistical difference in glyceraldehyde-3-phosphate-dehydrogenase (GAPDH) mRNA level was observed between groups. During the estrous cycle, the level of LHRH-R mRNA in the pituitary was about two-fold higher on diestrous day 2 and the morning of proestrus than that on diestrous day 1 and quickly returned toward control level by noon of proestrus. In addition, we found that GAPDH mRNA levels from a so-called housekeeping gene often thought to be unchanged under different conditions, were significantly higher on proestrus while levels of 18S rRNA were not significantly changed. The large decrease in LHRH-R mRNA during lactation could account for the changes in LHRH binding previously reported.

Repeated swim-stress reduces GABAA receptor alpha subunit mRNAs in the mouse hippocampus

The effects of brief repeated swim stress on the expression of GABAA receptor alpha 1 subunit mRNAs was investigated in the mouse. Adult male mice were exposed to repeated brief (10 min) swim-stress once daily for 7 or 14 days and the levels of GABAA receptor alpha subunit mRNAs were quantified in the hippocampus 24 h after the last session by Northern analysis. Repeated swim stress for 14 days resulted in a 47.3% +/- 6.5 and 39.8% +/- 7.6 decrease in the levels of the 4.8 kb and 4.4 kb GABAA receptor alpha 1 subunit mRNAs, respectively. While there was a trend toward a reduction in the level of GABAA receptor alpha 1 subunit mRNAs following 7 days of repeated swim stress, the latter did not reach statistical significance. In contrast, no significant alterations in the levels of glutamic acid decarboxylase or beta-actin mRNAs were observed at either time point. The reduction in GABAA receptor alpha 1 subunit mRNAs following repeated swim stress may underlie similar alteration(s) in hippocampal GABAA receptor density previously observed following repeated swim stress.

Effect of dexamethasone on mRNA levels for 5-aminolevulinate synthase in different rat tissues

5-Aminolevulinate synthase mRNA levels from different tissues were quantitated by Northern blot hybridization analysis utilizing the rat liver 5-aminolevulinate synthase cDNA clone as probe. A 5-aminolevulinate synthase mRNA species of size 2.3 kb was seen in all the tissues examined. Densitometric scanning of the autoradiographs demonstrated that the adrenal gland contained the largest amount of 5-aminolevulinate synthase mRNA. Levels corresponding to approximately 50% of this amount were found in the small intestine, lung, heart, muscle and testes. In the liver and kidney the level was approximately 25% of that found in the adrenal gland. These results demonstrate the housekeeping role of this gene. Dexamethasone treatment for 1 day or 5 days dramatically induced 5-aminolevulinate synthase mRNA levels in the liver and small intestine, and to a lesser extent in lung, heart, kidney and muscle. Nuclear run-off experiments suggest that a post-transcriptional mechanism predominantly contributes to the dexamethasone-induced increase in 5-aminolevulinate synthase mRNA levels observed in the liver. Interestingly, in the steroidogenic tissues of the adrenal gland and testes, there was a substantial decrease in 5-aminolevulinate synthase mRNA levels after dexamethasone administration but the mechanism of this control remains to be investigated.

Corticospinal neurons exhibit a novel pattern of cytoskeletal gene expression after injury

We examined changes in the expression of major cytoskeletal protein mRNAs in adult hamster corticospinal neurons after axotomy. While a number of studies had determined that peripheral neurons exhibit major alterations in cytoskeletal gene expression after axotomy, no previous studies had addressed the question of whether or not intrinsic mammalian CNS neurons, which do not have the ability to successfully regenerate axons after injury, alter their expression of tubulin and neurofilament genes after injury. In the present study we used in situ hybridization methods to examine this issue. 35S-labeled cDNA probes for the low molecular weight neurofilament protein (NF-L) mRNA and an alpha-tubulin mRNA species (M alpha 1) were used for in situ hybridizations of sections of the sensorimotor cortex obtained 2, 7, and 14 days after unilateral axotomy of the corticospinal tract in the caudal medulla. Film as well as emulsion autoradiography showed dramatic decreases in both alpha-tubulin and NF-L mRNA levels within axotomized neurons in layer Vb of the sensorimotor cortex. Tubulin mRNA levels were decreased as early as 2 days after injury whereas NF-L mRNA levels were not decreased until later times. Ribosomal RNA (rRNA) levels in axotomized corticospinal neurons were also examined using in situ hybridization with a 35S-labeled rDNA probe. These studies showed only a slight decrease in rRNA levels in corticospinal neurons at 14 days after axotomy. Immunoblotting experiments of total protein from corticospinal axons in the medulla were performed to assess whether the axonal composition immediately proximal to the injury site reflected changes in cell body gene expression. Both alpha-tubulin and NF-L levels were found to decrease in corticospinal axons by 28 days after injury. These findings, to our knowledge, are the first to demonstrate that a class of mammalian CNS neurons have an intrinsically different cytoskeletal response to axonal injury than do PNS neurons. The failure to upregulate tubulin gene expression following injury may contribute to the ineffective regenerative response of these long-tract CNS neurons.

Structure and organization of ribosomal DNA

Three trends are seen in the organization of ribosomal DNA genes during evolution: 1) gradual separation and separability of the regulation of transcription of 5S and larger subunit rRNAs; 2) retention of a transcription unit containing both large and small rRNAs; and 3) clustering of genes for both 5S and 18S-28S rDNAs, with the possible association of other 'non-rDNA' in the clusters of 18S-28S rDNA genes by the time mammals evolve.

Differential regulation of peripherin and neurofilament gene expression in regenerating rat DRG neurons

Quantitative in situ hybridization and RNA blotting methods were used to define the time course and magnitude of changes in expression of mRNAs encoding peripherin and the neurofilament (NF) triplet proteins in rat dorsal root ganglion (DRG) neurons during axonal regeneration. mRNA levels in adult rat L4 and L5 DRGs were examined in autoradiograms after in situ hybridization with specific 35S-labeled cDNA probes 1-56 days following unilateral crush lesions of the sciatic nerve. The results of quantitative analyses indicated that peripherin mRNA levels were significantly increased in large-sized (greater than 1000 microns 2) DRG neurons at 7, 14, and 28 days after axotomy while the mRNA levels for each of the NF triplet proteins were significantly decreased at these same time points. The mRNA levels of the low (NF-L) and middle (NF-M) sized NF subunits were significantly decreased as early as 1 day postaxotomy but the mRNA level of the large NF subunit (NF-H) did not change until 7 days after axotomy. The maximal reduction in NF mRNA levels was observed at 14 days postaxotomy when NF-L mRNA levels were only 35% of those in large-sized, normal control neurons. Recovery toward normal levels of both NF and peripherin mRNAs was observed at 8 weeks postaxotomy. RNA blot analyses with total RNA obtained from DRGs at different postaxotomy times confirmed that NF-L mRNA levels were reduced in the DRG during the first 4 weeks after axotomy but, interestingly, failed to detect an increase in peripherin mRNA levels. This difference concerning peripherin mRNA levels in axotomized preparations obtained by RNA blotting vs. in situ hybridization was attributed to the fact that RNA blots utilized total DRG RNA which includes mRNAs from both small and large-sized DRG neurons. A recent in situ hybridization study showed that the small-sized DRG neurons which contain the majority of the peripherin mRNA in the DRG do not increase their peripherin mRNA levels 14 days after axotomy (Oblinger et al., 1989b). This may mask any change in the large neuron response when total RNA is examined. Overall, the results of this study demonstrate (1) that type III (peripherin) and type IV (NF) intermediate filament genes are regulated differently during axonal regeneration, and (2) that the three NF genes are down-regulated in a fairly coordinate manner during regeneration. These data suggest that an important component of the regeneration program is the alteration of the composition of the IF component of the cytoskeleton.(ABSTRACT TRUNCATED AT 400 WORDS)

Parallel increases in striatal glutamic acid decarboxylase activity and mRNA levels in rats with lesions of the nigrostriatal pathway

Adult male rats were lesioned with 6-hydroxydopamine in order to destroy the nigrostriatal dopaminergic projections. In rats with such a lesion, we found a parallel increase in glutamic acid decarboxylase (GAD) activity and GAD mRNA in the striatum ipsilateral to the lesion at 4 weeks and 4 months after the lesion. These observations support the proposal that nigral dopaminergic neurons exert a tonic inhibitory control over the striatal GABAergic neurons. Our observations also suggest that the dopaminergic neurons can inhibit gene expression in striatal GABAergic neurons and that the enhanced striatal GAD activity following lesions of the dopaminergic projections is due to 'de novo' synthesis of the enzyme.

Enhancers for RNA polymerase I in mouse ribosomal DNA

The intergenic spacer of the mouse ribosomal genes contains repetitive 140-base-pair (bp) elements which we show are enhancers for RNA polymerase I transcription analogous to the 60/81-bp repetitive enhancers (enhancers containing a 60-bp and an 81-bp element) previously characterized from Xenopus laevis. In rodent cell transfection assays, the 140-bp repeats stimulated an adjacent mouse polymerase I promoter when located in cis and competed with it when located in trans. Remarkably, in frog oocyte injection assays, the 140-bp repeats enhanced a frog ribosomal gene promoter as strongly as did the homologous 60/81-bp repeats. Mouse 140-bp repeats also competed against frog promoters in trans. The 140-bp repeats bound UBF, a DNA-binding protein we have purified from mouse extracts that is the mouse homolog of polymerase I transcription factors previously isolated from frogs and humans. The DNA-binding properties of UBF are conserved from the mouse to the frog. The same regulatory elements (terminators, gene and spacer promoters, and enhancers) have now been identified in both a mammalian and an amphibian spacer, and they are found in the same relative order. Therefore, this arrangement of elements probably is widespread in nature and has important functional consequences.

Functional difference between the sites of ribosomal 40S precursor 3' end formation in Xenopus laevis and Xenopus borealis

In the ribosomal genes of X. laevis, the sequence GACTTGCNC is found about 60bp upstream of the gene promoter (T3) and is necessary and sufficient to cause termination of RNA polymerase I transcription. At the 3' end of the 40S precursor coding region (T2) a sequence differing by one nucleotide, GACTTGCNG, directs RNA 3' end formation but allows polymerase to transcribe on into the intergenic spacer (Labhart and Reeder, 1989, Genes and Dev. 4: 269-276). Sites corresponding to T2 and T3 are also found in a related species, X. borealis. Inspection of the T2 sequence in X. borealis reveals that it contains two copies of the terminator sequence, GACTTGCNC, located 15 and 96 bp downstream of the 3' end of the 40S precursor coding region. Here we present functional tests of those two T2 elements that show that, as predicted from the sequence, they both show termination activity and are functionally indistinguishable from the T3 site in X. laevis. These results suggest that X. laevis T2 is an example of a naturally occurring point mutation, and the inability to terminate transcription at T2 is an exception to the general pattern of ribosomal gene transcription in higher eukaryotes.

Enhancers for RNA polymerase I in mouse ribosomal DNA

The intergenic spacer of the mouse ribosomal genes contains repetitive 140-base-pair (bp) elements which we show are enhancers for RNA polymerase I transcription analogous to the 60/81-bp repetitive enhancers (enhancers containing a 60-bp and an 81-bp element) previously characterized from Xenopus laevis. In rodent cell transfection assays, the 140-bp repeats stimulated an adjacent mouse polymerase I promoter when located in cis and competed with it when located in trans. Remarkably, in frog oocyte injection assays, the 140-bp repeats enhanced a frog ribosomal gene promoter as strongly as did the homologous 60/81-bp repeats. Mouse 140-bp repeats also competed against frog promoters in trans. The 140-bp repeats bound UBF, a DNA-binding protein we have purified from mouse extracts that is the mouse homolog of polymerase I transcription factors previously isolated from frogs and humans. The DNA-binding properties of UBF are conserved from the mouse to the frog. The same regulatory elements (terminators, gene and spacer promoters, and enhancers) have now been identified in both a mammalian and an amphibian spacer, and they are found in the same relative order. Therefore, this arrangement of elements probably is widespread in nature and has important functional consequences.

Sex-related differences and thyroid hormone regulation of vasoactive intestinal peptide gene expression in the rat brain and pituitary

To determine the effects of hypothyroidism and sexual dimorphism on the gene expression of vasoactive intestinal peptide (VIP) in the rat brain, VIP mRNA levels were measured in the cerebral cortex, hypothalamus and anterior pituitary of control and hypothyroid (thionamide-treated) rats. A tissue-specific increase in VIP mRNA level was observed in the hypothyroid pituitary. In addition, higher levels of VIP mRNA were found in the pituitaries of male rats suggesting a sex-related difference in VIP gene expression. Similar differences were not observed in the cortex or hypothalamus.

Age-related down regulation of hepatic cytochrome P1-450, P3-450, catalase and CuZn-superoxide dismutase RNA

The influence of age on liver gene expression was investigated in two strains of H-2 congenic mice. In B10.RIII mice (H-2r), basal P1- and P3-450 RNA levels progressively decreased 65 and 95%, respectively, between 4 and 28 months of age (P less than or equal to 0.05). Polyaromatic hydrocarbon (PAH) induced P1- and P3-450 RNA levels decreased about 50% during this time (P less than or equal to 0.05). In contrast, in C57BL/10 mice (H-2b) little or no change was detected in basal or induced P1- or P3-450 RNA levels. CuZn-superoxide dismutase RNA decreased 80 to 90% between 4 and 9 months of age in B10.RIII mice, while a quantitatively smaller decrease of 50 to 65% was found in C57BL/10 mice (P less than or equal to 0.05). Catalase RNA decreased approximately 80% between 4 and 9 months of age in B10.RIII mice, and a similar decrease was found in C57BL/10 mice. Down regulation of these genes may explain the reduced activities of the cognate hepatic enzymes, and reduced xenobiotic metabolism found in older animals.

Day-night variation in prepro vasoactive intestinal peptide/peptide histidine isoleucine mRNA within the rat suprachiasmatic nucleus

Neurons within the suprachiasmatic nuclei of the hypothalamus (SCN) appear to function as a circadian clock that controls the timing of many physiological systems. The SCN contain several chemically distinct neuronal subpopulations, including a large group of interneurons within the ventrolateral SCN that exhibit co-localizable immunoreactivity for both vasoactive intestinal peptide (VIP) and peptide histidine isoleucine (PHI). The purpose of the present study was to determine whether VIP/PHI neurons within the rat SCN exhibit rhythmicity in the cellular levels of the messenger RNA encoding the precursor from which both VIP and PHI are derived. Using both quantitative in situ and solution hybridization prepro-VIP/PHI mRNA levels early in the dark phase were demonstrated to be significantly higher than those 5 h after the onset of the daily light period. Since no statistically reliable (P greater than 0.05) day-night variation was observed in the levels of prepro-VIP/PHI mRNA within cortex, these data suggest that the rhythmicity in prepro-VIP/PHI mRNA is an intrinsic property of VIP/PHI-containing SCN neurons, or rhythmically driven by local synaptic events within the SCN.

Induction of heat shock protein 70 mRNA in adult hamster facial nuclear groups following axotomy of the facial nerve

In this study, the effects of axotomy on heat shock protein 70 (hsp70) mRNA levels were analyzed by northern blot hybridization with a mouse-inducible hsp70 cDNA probe. The right facial nerve of adult golden hamsters was axotomized external to the skull, with the left nerve serving as sham-operated and internal control. Postoperative survival times were 0.5, 2, 6, 12, and 24 hr, with three to six animals per time point. Total RNA in the axotomized and control facial nuclear groups, dissected from the brain stem, was isolated by guanidinium-thiocyanate extraction and analyzed by northern hybridization and scanning densitometry. For normalization, the blots were rehybridized with a genomic cDNA probe complementary to the 28 S rRNA. At 0.5 hr postoperative, there was a 68% induction of hsp70 mRNA levels as compared to control. This increase peaked at 2 hr postoperative with a 280% induction and declined subsequently to 160% at 6 hr, 33% at 12 hr, and -56% at 24 hr, relative to control levels. As a positive control, hyperthermia-induced hsp70 expression was established in hamster whole brain using northern blot hybridization and the mouse-inducible hsp70 cDNA probe. There was a 126% increase in hsp70 mRNA levels relative to control at 1.5 hr following hyperthermia. By 6.5 hr after the 1.5-hr hyperthermic period, there was a 40% decrease in hsp70 mRNA levels below control. The results provide the first evidence that peripheral axotomy acts as a cell stressor to induce the expression of hsp70 mRNA.(ABSTRACT TRUNCATED AT 250 WORDS)

New tandem repeat region in the non-transcribed spacer of human ribosomal RNA gene

A new repetitive DNA region was identified in the non-transcribed spacer of human rDNA, namely a long (4.6 kb) sequence motif (Xbal element) was present in two copies. The repeating unit composed of two parts. One of them consisted of unique nucleotide sequences, interrupted by some simple sequences. The other, about 3.1 kb long one assembled only from highly repeated simple sequences. The unique sequence region contained two, inverted copies of the human AluI type repetitive DNA family. The authors suggest that the XbaI elements may flank the tandem arrays of human rRNA genes as terminal repeats and they might function both as the origin of rDNA replication and/or site of homologous recombination.

Organization of the ribosomal RNA genes of Schizophyllum commune

The 18, 5.8, 25 and 5S ribosomal RNA (rRNA) cistrons have been mapped on the ribosomal DNA (rDNA) unit repeat of Schizophyllum commune strain 4-40. These genes are spatially ordered in the sequence given. The presence of a large primary precursor rRNA which is processed to form the mature 18, 5.8 and 25S rRNAs has been demonstrated. We have mapped the site of transcriptional initiation for this rRNA primary precursor. The sequence surrounding this site has been determined and shown to be highly conserved, with considerable identity to those in Neurospora crassa and Dictyostelium discoideum. The direction of transcription of the rRNA genes has been determined. The 5S rRNA cistron is transcribed in the same direction as the other rRNAs, however it is not transcribed as a part of the large primary precursor. The previously identified rDNA strain-specific length polymorphisms (Specht et al. 1984) are shown to be located within the transcribed region of the rDNA unit repeat.

In situ hybridization analysis of osmotic stimulus-induced changes in ribosomal RNA in rat supraoptic nucleus

A quantitative in situ hybridization analysis was used to investigate changes in levels of ribosomal RNA (rRNA) in neurons of the supraoptic nucleus (SON) of rats stimulated osmotically by giving 2% NaCl as drinking solution for 0 (control rats), 1, 4, and 14 days. The quantitation was autoradiographically accomplished by in situ hybridization with a nick-translated tritiated ribosomal DNA probe and with the use of computer-based image analysis system. The mean number of grains per neuron in the ventral SON was significantly increased: 1.8-fold for 1 day, 2.9-fold for 4 days, and 1.7-fold for 14 days of salt loading, whereas the mean number of grains per neuron in the dorsal SON was increased 1.3-fold for 1 day, 2.5-fold for 4 days, and 1.7-fold for 14 days. Kolmogorov-Smirnov analysis of frequency histograms of grains per neuron indicated that the amount of rRNA in neurons in the ventral and dorsal SON was significantly increased by osmotic stimulation. These increases were accompanied by increases in cell size. The subcellular location of hybridizable rRNA in magnocellular neurons was altered by osmotic stimulation. Following 1-14 days of salt-drinking, rRNAs appeared to be more unevenly distributed throughout the cytoplasm. These findings are consistent with the notion that hyperosmotic stimulation has a substantial effect on the expression of rRNA genes in neurons of both the ventral and dorsal SON.

Independent regulation of transcription of the two strands of the c-myc gene

Previously we demonstrated the existence of transcripts from the noncoding strand of a rearranged, truncated c-myc gene in murine plasmacytomas in which this oncogene is translocated to an immunoglobulin constant-region gene element (M. Dean, R. B. Kent, and G. E. Sonenshein, Nature [London] 305:443-446, 1983). Here we report on the transcription of the two strands of a normal, unrearranged c-myc gene. We examined the effects of gene rearrangements, growth state transitions, and differentiation on the relative levels of usage of the two strands. Transcription from intron 1 to exon 3 of the murine c-myc gene was studied in in vitro nuclear runoff assays. The level of transcription of the noncoding strand across this region of a germ line c-myc gene in a murine B-cell lymphoma line was comparable to the level observed in plasmacytomas with translocated c-myc genes. Rapid changes in transcription of the coding strand of the c-myc gene could be seen during growth arrest of WEHI 231 cells and during activation of splenic T lymphocytes. Transcription of the noncoding strand was constitutive during these growth state transitions and during activation of primary cultures of quiescent calf aortic smooth muscle cells as well. In contrast, differentiation of murine erythroleukemia cells was accompanied by an early drop in transcription of the two strands of this gene. The ramifications of these findings with respect to measurements of c-myc gene transcription and to the regulation of this gene are discussed.

ARS activity along the yeast mitochondrial apocytochrome b region: correlation with the location of petite genomes and consensus sequences

Seven MboI fragments spanning the mitochondrial apocytochrome b gene in Saccharomyces cerevisiae strain D273-10B were cloned in the BamHI site of the integrative yeast vector YIp5 and the capacity for autonomous replication was subsequently assayed in yeast. The positive correlation found between the ars-like activity in four fragments and the presence of regions common to multiple ethidium bromide-induced petite (rho-) genomes suggests that the mitochondrial sequences possibly active as origins of replication in low-complexity neutral or weakly suppressive rho- mutants could be functionally related to the yeast nuclear replicator 11 nucleotide motif defined by Broach et al. (1983).

Ribosomal DNA sequences attached to the nuclear matrix

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

Increases in ribosomal RNA within the denervated neuropil of the dentate gyrus during reinnervation: evaluation by in situ hybridization using DNA probes complementary to ribosomal RNA

Previous studies have revealed that there are increases in the incorporation of [3H]amino acids into protein in the denervated neuropil of the dentate gyrus during periods of reactive synaptogenesis. The present study evaluates whether the increase in incorporation reflects an increase in protein synthetic machinery (ribosomes) in the denervated zone. We evaluated the distribution of ribosomal RNA (rRNA) in the denervated dentate gyrus 2-14 days after unilateral destruction of the entorhinal cortex using DNA probes complementary to rRNA for in situ hybridization. Animals with comparable lesions were injected with [3H]leucine 30 min prior to sacrifice and prepared for autoradiography in order to define the extent of protein synthesis within the denervated neuropil. Quantitative analyses revealed that the increases in [3H]leucine incorporation were accompanied by increases in labeling with the rRNA probe. In both cases, the increases were first apparent at 2 days postlesion, reached a peak on day 6, and then declined between 8 and 14 days postlesion. Plots of grain density across the neuropil revealed that the increases in rRNA, like the increases in amino acid incorporation, occurred selectively within the denervated portion of the neuropil. We propose that increased incorporation of protein precursor is the result of an increase in protein synthetic machinery within the denervated neuropil. These increases may reflect in part the increases that we have previously noted in polyribosomes under dendritic spines.

Independent regulation of transcription of the two strands of the c-myc gene

Previously we demonstrated the existence of transcripts from the noncoding strand of a rearranged, truncated c-myc gene in murine plasmacytomas in which this oncogene is translocated to an immunoglobulin constant-region gene element (M. Dean, R. B. Kent, and G. E. Sonenshein, Nature [London] 305:443-446, 1983). Here we report on the transcription of the two strands of a normal, unrearranged c-myc gene. We examined the effects of gene rearrangements, growth state transitions, and differentiation on the relative levels of usage of the two strands. Transcription from intron 1 to exon 3 of the murine c-myc gene was studied in in vitro nuclear runoff assays. The level of transcription of the noncoding strand across this region of a germ line c-myc gene in a murine B-cell lymphoma line was comparable to the level observed in plasmacytomas with translocated c-myc genes. Rapid changes in transcription of the coding strand of the c-myc gene could be seen during growth arrest of WEHI 231 cells and during activation of splenic T lymphocytes. Transcription of the noncoding strand was constitutive during these growth state transitions and during activation of primary cultures of quiescent calf aortic smooth muscle cells as well. In contrast, differentiation of murine erythroleukemia cells was accompanied by an early drop in transcription of the two strands of this gene. The ramifications of these findings with respect to measurements of c-myc gene transcription and to the regulation of this gene are discussed.

Evolution of the ribosomal DNA spacers of Drosophila melanogaster: different patterns of variation on X and Y chromosomes

Length variation of the ribosomal gene spacers of Drosophila melanogaster was studied. Analysis of 47 X chromosomal and 47 Y chromosomal linked rDNA arrays collected from five continents indicates that the arrays on the two chromosomes differ qualitatively. The Y-linked arrays from around the world share little or no similarity for either their overall length or the organization of their spacers. Most of the X-linked arrays do, however, share a major length spacer of 5.1 kb. In addition, those X-linked arrays that have a major 5.1-kb band have similar spacer organization as demonstrated by genomic DNA digestions with several restriction enzymes. These data strongly support the hypothesis that spacer length patterns on only X-linked genes are maintained primarily by natural selection.

Transcription of spacer sequences flanking the rat 45S ribosomal DNA gene

The transcriptional activity of spacer sequences flanking the rat 45S ribosomal DNA (rDNA) gene were studied. Nascent RNA labeled in in vitro nuclear run-on reactions hybridized with both 5' and 3' spacer regions. The highest level of hybridization was seen with an rDNA fragment containing tandem repeats of a 130-base-pair sequence upstream of the 45S rRNA initiation site. Synthesis of RNA transcripts homologous to this internally repetitious spacer region was insensitive to high levels of alpha-amanitin, suggesting that it is mediated by RNA polymerase I. Analysis of steady-state RNA showed that these transcripts were present at extremely low levels in vivo relative to precursor rRNA transcripts. In contrast, precursor and spacer run-on RNAs were synthesized at similar levels. This suggests that spacer transcripts are highly unstable in vivo; therefore, it may be the process of transcription rather than the presence of spacer transcripts that is functionally important. Transcription in this upstream rDNA region may be involved in regulation of 45S rRNA synthesis in rodents, as has been suggested previously for frog rRNA. In addition, the presence of transcriptional activity in other regions of the spacer suggests that some polymerase I molecules may transcribe through the spacer from one 45S gene to the next on rodent rDNA.

Transcription of spacer sequences flanking the rat 45S ribosomal DNA gene

The transcriptional activity of spacer sequences flanking the rat 45S ribosomal DNA (rDNA) gene were studied. Nascent RNA labeled in in vitro nuclear run-on reactions hybridized with both 5' and 3' spacer regions. The highest level of hybridization was seen with an rDNA fragment containing tandem repeats of a 130-base-pair sequence upstream of the 45S rRNA initiation site. Synthesis of RNA transcripts homologous to this internally repetitious spacer region was insensitive to high levels of alpha-amanitin, suggesting that it is mediated by RNA polymerase I. Analysis of steady-state RNA showed that these transcripts were present at extremely low levels in vivo relative to precursor rRNA transcripts. In contrast, precursor and spacer run-on RNAs were synthesized at similar levels. This suggests that spacer transcripts are highly unstable in vivo; therefore, it may be the process of transcription rather than the presence of spacer transcripts that is functionally important. Transcription in this upstream rDNA region may be involved in regulation of 45S rRNA synthesis in rodents, as has been suggested previously for frog rRNA. In addition, the presence of transcriptional activity in other regions of the spacer suggests that some polymerase I molecules may transcribe through the spacer from one 45S gene to the next on rodent rDNA.

In situ hybridization detection of estradiol-induced changes in ribosomal RNA levels in rat brain

In this study, quantitative assessment of estradiol (E2)-induced changes in levels of ribosomal RNA within brain regions concentrating the hormone was accomplished by in situ hybridization with nick-translated tritiated ribosomal DNA probes and use of a computer-based image analysis system. Ovariectomized rats were either implanted with estradiol capsules for 6 h, 24 h, or 15 days, or sham-implanted under the same time course to serve as controls. The mean number of grains, somal area, and grain density of neurons within three E2-concentrating brain regions, the ventrolateral portion of the ventromedial and the arcuate nuclei of the hypothalamus (VL-VMN and ARC, respectively) and the corticomedial nucleus of the amygdala (AMY) were determined. In the VL-VMN and ARC, levels of rRNA were significantly increased after 6 h of E2 treatment (70% and 30%, respectively) and after 24 h of E2 treatment (60% and 62%, respectively). However, these effects on rRNA levels in VL-VMN and ARC were not observed after prolonged exposure of 15 days to the hormone. Neuronal hypertrophy was present only after 24 h of E2 treatment in the VL-VMN and ARC (32% and 14%, respectively). No changes were found in the AMY. As an additional internal control, measurements were also collected from the dorsomedial portion of the VMN (DM-VMN), a region with few E2-concentrating neurons. No changes in any of the parameters were found in DM-VMN at any time after exposure to the hormone. By extending the in situ hybridization technique to the quantitative level, these findings demonstrate differential estrogenic regulation of a known gene product, rRNA, in rat brain that is temporally and regionally specific.

Variation in the ribosomal RNA genes among individuals of Vicia faba

Length heterogeneity in the ribosomal repeat of Vicia faba is due to the presence of variable numbers of a 325 bp subrepetitive element within the nontranscribed spacer region. The distribution of size classes among 88 individuals within a population was investigated by blot-hybridization. We find that individual plants can exhibit more than 20 size classes and that hybridization patterns are highly diverse from individual to individual, more so than for any species so far investigated. In contrast, no such differences are observed in patterns for different tissues from a single plant or from parental to F1 generation. Some changes were observed in the F2 generation. We conclude that unequal recombination can give rise to the diversity that we observe for the V. faba rDNA repeats.

Supercoil induced S1 hypersensitive sites in the rat and human ribosomal RNA genes

Rat and human ribosomal RNA gene fragments in supercoiled plasmids were examined for S1 nuclease hypersensitivity. In the transcribed portion of genes the number and distribution of S1 sites were found to be species specific. No S1 sites were detected in the promoter regions. In the nontranscribed spacer (NTS), downstream of the 3' end of 28S RNA gene, S1 sites appear to be conserved in rat and human rDNAs. A rat NTS fragment (2987 nucleotides long), containing three S1 sites was sequenced and the S1 sites in this region were localized in polypyrimidine . polypurine simple repeat sequences. Other types of simple sequences, two type 2 Alu repeats and an ID sequence were also found in the sequenced region. The possible role of simple sequences and S1 sites in transcription and in recombination events of rDNA is discussed.

Nucleotide sequence analysis of the spacer regions flanking the rat rRNA transcription unit and identification of repetitive elements

We investigated the organization of the rat rDNA non-transcribed spacer (NTS) by determining the sequence of large NTS segments located upstream (2501 bp) and downstream (4025 bp) from the rRNA transcription unit. We identified four B2-like and two ID mobile elements. They may be grouped in three pairs with the members of each pair located in the upstream and downstream NTS. The ID sequences are identical to the consensus sequence, while the pairs of B2-like elements show 85% and 50/65% homology to the consensus B2 sequence. The proximal part of the downstream NTS contains a region of widely diverged SalI tandem repeats. A considerable part of the analyzed upstream and downstream NTS sequences is constituted by different types of simple sequences and long poly(purine) X poly(pyrimidine) tracts. These data show that the rat rDNA NTS regions flanking the rRNA transcription unit are characterized by a combination of short interspersed (B2-superfamily) and various simple sequences.

Characterization of the region around the start point of transcription of ribosomal RNA in the Chinese hamster

The initiation site for ribosomal RNA transcription in the Chinese hamster was identified and the sequence around and upstream determined. The start point region shows considerable homology with comparable regions in the mouse and rat. In the Chinese hamster, the region between bp -700 and -200 consists of imperfect repeats approximately 120-130 bp in length which are flanked by T-rich regions. The region within each repeat which is homologous with an adjacent repeat decreases in length as the start point is approached. The final promoter-proximal repeat preserves only an 11-bp region of the promoter-distal repeats. This short sequence, termed the repeat core, appears with a periodicity of about 120-130 bp in the Chinese hamster, and is conserved in both mouse and rat. In humans, a short repeated sequence occupies similar positions, suggesting that while complete 120-130-bp repeats are not a feature of all mammalian RNA polymerase I promoter-proximal r X DNA spacers, a short sequence repeating with approximate 120-130-bp periodicity may be such a feature.

The ribosomal RNA genes of three salmonid species

The ribosomal RNA cistrons of three species of trout: Salvelinus namaycush (lake trout), Salvelinus fontinalis (brook trout), and Salmo gairdneri (rainbow trout) were examined by Southern blot analysis of genomic DNA. The repeat length of the cistron of S. namaycush is 26 kb. A repeat-length polymorphism was observed in some of the individual fish examined. These individuals showed 24-kb repeats. In some individuals both forms were present. The restriction maps of the transcribed regions of all three species were similar and showed a site homology with other vertebrate ribosomal RNA genes. Interspecific comparison showed restriction-site differences within the spacer regions examined. A restriction-site polymorphism within the 28 S gene was observed in S. fontinalis. The rDNA of S. namaycush liver showed a high degree of methylation as determined by digestion with the restriction endonucleases MspI and HpaII.

Sister chromatid exchange and the evolution of rDNA spacer length

The structures of rDNA spacers from several species have been characterized and virtually all have internally repeated sequences. Different numbers of these internal repeats are responsible for most spacer length variation. Because unequal recombination between these internal repeats will cause new length variation, while unequal exchange between rDNA copies will homogenize the variants, we modeled the interaction of these two processes. Two models were used to simulate both types of unequal exchange at the sister chromatid level. Both models indicate that a narrow range of relative recombination frequencies is required to produce levels of variability comparable to those published. One model puts a lower limit on the number of internal repeats, and the other puts both a lower and upper limit on the number of repeats. The model with both maximum and minimum constraints produces a distribution closer to actual spacer distributions. These results imply that small changes in recombination rates can generate the differences in numbers of length variants observed in different species.