Gene expression in eukaryotes

Is RNA the working genome in eukaryotes ? The 60 year evolution of a conceptual challenge

About 80 years ago, in 1943, after a century of biochemical and genetic research, DNA was established as the carrier of genetic information. At the onset of Molecular Biology around 1960, the genome of living organisms embodied 3 basic, still unknown paradigms: its composition, organisation and expression. Between 1980 and 1990, its replication was understood, and ideas about its 3D-organisation were suggested and finally confirmed by 2010. The basic mechanisms of gene expression in higher organisms, the synthesis of precursor RNAs and their processing into functional RNAs, were also discovered about 60 years ago in 1961/62. However, some aspects were then, and are still now debated, although the latest results in post-genomic research have confirmed the basic principles. When my history-essay was published in 2003, describing the discovery of RNA processing 40 years earlier, the main facts were not yet generally confirmed or acknowledged. The processing of pre-rRNA to 28 S and 18 S rRNA was clearly demonstrated, confirmed by others and generally accepted as a fact. However, the "giant" size of pre-mRNA 10-100 kb-long and pervasive DNA transcription were still to be confirmed by post-genomic methods. It was found, surprisingly, that up to 90% of DNA is transcribed in the life cycle of eukaryotic organisms thus showing that pervasive transcription was the general rule. In this essay, we shall take a journey through the 60-year history of evolving paradigms of gene expression which followed the emergence of Molecular Biology, and we will also evoke some of the "folklore" in research throughout this period. Most important was the growing recognition that although the genome is encoded in DNA, the Working Genome in eukaryotic organisms is RNA.

The Nine RNA Methylation Regulatory Gene Signature Is Associated with the Pathogenesis of Atrial Fibrillation by Modulating the Immune Microenvironment in the Atrial Tissues

Background. Atrial fibrillation (AF) is the most common type of cardiac arrhythmias and a major cause of cardiovascular disease (CVD)-related deaths globally. RNA methylation is the most frequent posttranscriptional modification in the eukaryotic RNAs. Previous studies have demonstrated close associations between the status of RNA methylation and CVD. Methods. We comprehensively evaluated the relationship between RNA methylation and AF. Least absolute shrinkage and selection operator (LASSO) logistic regression analysis was used to establish a risk score model in AF. Biological functional analysis was used to explore the relationship between RNA methylation related signatures and immune microenvironment characteristics. Machine learning was used to recognize the outstanding RNA methylation regulators in AF. Results. There was a significant variant of the mRNA expression of RNA methylation regulators in AF. RNA methylation related risk score could predict the onset of AF and closely associated with immune microenvironment features. XG-Boost algorithm and SHAP recognized that NSUN3 and DCPS might play a key role in the development of AF. Meanwhile, NSUN3 and DCPS had potential diagnostic value in AF. Conclusion. RNA methylation regulatory genes are associated with the onset of AF by modulating the immune microenvironment. The nine AF risk-related RNA methylation regulatory gene signature is a potential diagnostic biomarker and therapeutic target for AF.

On the integration of LiDAR and field data for riparian biomass estimation

The role of vegetation in supporting life on Earth is widely known. Nevertheless, the relevance of riparian corridors has been overlooked for a long time, leading to a dramatic reduction of vegetated buffers alongside them. Vegetation monitoring systems, including those for biomass estimation, are required to manage riparian corridors properly. Field surveys may support monitoring, but their usefulness is reduced by numerous drawbacks, therefore needing coupling with other data sources. The present work shows how Light Detection And Ranging (LiDAR) datasets can integrate targeted field measurements to estimate above-ground biomass at temperate or boreal latitudes and generate accurate biomass maps over large areas. By referring to the case study of the Orco river (northwest Italy), we defined a technique to reconstruct the geometry of an individual shrub from LiDAR point clouds. We tested the technique by comparing field measurements with Terrestrial and Airborne Laser Scanner data (TLS and ALS, respectively), assessing the former's superiority but the broader range of applicability of the latter. After these preliminary tests, we coupled the presented technique with a literature algorithm for individual tree detection, providing a more generalized procedure for the overall mapping and budgeting of riparian biomass based on ALS data. We applied the procedure to a fluvial bar of the Orco river, achieving a quantitative assessment of the shrub and tree biomass budget for 2019 and 2021 and visualizing the changes that occurred in that period. These results allowed us to shed light on the prevailing natural and anthropogenic processes in the investigated area and provide insights into the strengths and weaknesses of the proposed procedure.

A healthy mind in a healthy body: Effects of arteriosclerosis and other risk factors on cognitive aging and dementia

In this review we start from the assumption that, to fully understand cognitive aging, it is important to embrace a holistic view, integrating changes in bodily, brain, and cognitive functions. This broad view can help explain individual differences in aging trajectories and could ultimately enable prevention and remediation strategies. As the title of this review suggests, we claim that there are not only indirect but also direct effects of various organ systems on the brain, creating cascades of phenomena that strongly contribute to age-related cognitive decline. Here we focus primarily on the cerebrovascular system, because of its direct effects on brain health and close connections with the development and progression of Alzheimer's Disease and other types of dementia. We start by reviewing the main cognitive changes that are often observed in normally aging older adults, as well as the brain systems that support them. Second, we provide a brief overview of the cerebrovascular system and its known effects on brain anatomy and function, with a focus on aging. Third, we review genetic and lifestyle risk factors that may affect the cerebrovascular system and ultimately contribute to cognitive decline. Lastly, we discuss this evidence, review limitations, and point out avenues for additional research and clinical intervention.

Rosa1, a Transposable Element-Like Insertion, Produces Red Petal Coloration in Rose Through Altering RcMYB114 Transcription

Rose (Rosa sp.) flowers have a rich diversity of colors resulting from the differential accumulation of anthocyanins, flavonols, and carotenoids. However, the genetic and molecular determinants of the red-petal trait in roses remains poorly understood. Here we report that a transposable element-like insertion (Rosa1) into RcMYB114, a R2R3-MYB transcription factor's promoter region causes its transcription, resulting in red petals. In red-petal varieties, RcMYB114 is expressed specifically in flower organs, but is absent from non-red varieties. Sequencing, yeast two-hybrid, transient transformation, and promoter activity assays of RcMYB114 independently confirmed the role of Rosa1 in altering RcMYB114's transcription and downstream effects on flower color. Genetic and molecular evidence confirmed that the Rosa1 transposable element-like insertion, which is a previously unknown DNA transposable element, is different from those in other plants and is a reliable molecular marker to screen red-petal roses.

New Biomass Estimates for Chaparral-Dominated Southern California Landscapes

Chaparral shrublands are the dominant wildland vegetation type in Southern California and the most extensive ecosystem in the state. Disturbance by wildfire and climate change have created a dynamic landscape in which biomass mapping is key in tracking the ability of chaparral shrublands to sequester carbon. Despite this importance, most national and regional scale estimates do not account for shrubland biomass. Employing plot data from several sources, we built a random forest model to predict aboveground live biomass in Southern California using remote sensing data (Landsat Normalized Difference Vegetation Index (NDVI)) and a suite of geophysical variables. By substituting the NDVI and precipitation predictors for any given year, we were able to apply the model to each year from 2000 to 2019. Using a total of 980 field plots, our model had a k-fold cross-validation R2 of 0.51 and an RMSE of 3.9. Validation by vegetation type ranged from R2 = 0.17 (RMSE = 9.7) for Sierran mixed-conifer to R2 = 0.91 (RMSE = 2.3) for sagebrush. Our estimates showed an improvement in accuracy over two other biomass estimates that included shrublands, with an R2 = 0.82 (RMSE = 4.7) compared to R2 = 0.068 (RMSE = 6.7) for a global biomass estimate and R2 = 0.29 (RMSE = 5.9) for a regional biomass estimate. Given the importance of accurate biomass estimates for resource managers, we calculated the mean year 2010 shrubland biomasses for the four national forests that ranged from 3.5 kg/m2 (Los Padres) to 2.3 kg/m2 (Angeles and Cleveland). Finally, we compared our estimates to field-measured biomasses from the literature summarized by shrubland vegetation type and age class. Our model provides a transparent and repeatable method to generate biomass measurements in any year, thereby providing data to track biomass recovery after management actions or disturbances such as fire.

A novel approach to fuel biomass sampling for 3D fuel characterization

Surface fuels are the critical link between structure and function in frequently burned pine ecosystems, which are found globally (Williamson and Black, 1981; Rebertus et al., 1989; Glitzenstein et al., 1995) [[1], [2], [3]]. We bring fuels to the forefront of fire ecology through the concept of the Ecology of Fuels (Hiers et al. 2009) [4]. This concept describes a cyclic process between fuels, fire behavior, and fire effects, which ultimately affect future fuel distribution (Mitchell et al. 2009) [5]. Low-intensity surface fires are driven by the variability in fine-scale (sub-m level) fuels (Loudermilk et al. 2012) [6]. Traditional fuel measurement approaches do not capture this variability because they are over-generalized, and do not consider the fine-scale architecture of interwoven fuel types. Here, we introduce a new approach, the "3D fuels sampling protocol" that measures fuel biomass at the scale and dimensions useful for characterizing heterogeneous fuels found in low-intensity surface fire regimes. •Traditional fuel measurements are oversimplified, prone to sampling bias, and unrealistic for relating to fire behavior (Van Wagner, 1968; Hardy et al., 2008) [7,8].•We developed a novel field sampling approach to measuring 3D fuels using an adjustable rectangular prism sampling frame. This voxel sampling protocol records fuel biomass, occupied volume, and fuel types at multiple scales.•This method is scalable and versatile across ecosystems, and reduces sampling bias by eliminating the need for ocular estimations.

Making the Message Clear: Concepts for mRNA Imaging

The transcriptome of each individual cell contains numerous RNA species, each of which can be controlled by multiple mechanisms during their lifetime. The standard transcriptome analysis focuses on the expression levels of the genes of interest. To gain additional insights into spatiotemporal RNA distribution and the underlying trafficking processes, RNA labeling and imaging are necessary-ideally in living cells. This perspective will summarize state-of-the-art RNA imaging methods including their strengths and weaknesses.

A multi-tissue analysis identifies HLA complex group 9 gene methylation differences in bipolar disorder

Epigenetic studies of DNA and histone modifications represent a new and important activity in molecular investigations of human disease. Our previous epigenome-wide scan identified numerous DNA methylation differences in post-mortem brain samples from individuals affected with major psychosis. In this article, we present the results of fine mapping DNA methylation differences at the human leukocyte antigen (HLA) complex group 9 gene (HCG9) in bipolar disorder (BPD). Sodium bisulfite conversion coupled with pyrosequencing was used to interrogate 28 CpGs spanning ∼700 bp region of HCG9 in 1402 DNA samples from post-mortem brains, peripheral blood cells and germline (sperm) of bipolar disease patients and controls. The analysis of nearly 40 000 CpGs revealed complex relationships between DNA methylation and age, medication as well as DNA sequence variation (rs1128306). Two brain tissue cohorts exhibited lower DNA methylation in bipolar disease patients compared with controls at an extended HCG9 region (P=0.026). Logistic regression modeling of BPD as a function of rs1128306 genotype, age and DNA methylation uncovered an independent effect of DNA methylation in white blood cells (odds ratio (OR)=1.08, P=0.0077) and the overall sample (OR=1.24, P=0.0011). Receiver operating characteristic curve A prime statistics estimated a 69-72% probability of correct BPD prediction from a case vs control pool. Finally, sperm DNA demonstrated a significant association (P=0.018) with BPD at one of the regions demonstrating epigenetic changes in the post-mortem brain and peripheral blood samples. The consistent multi-tissue epigenetic differences at HCG9 argue for a causal association with BPD.

From genetic to genomic regulation: iterativity in microRNA research

The discovery and ongoing investigation of microRNAs (miRNAs) suggest important conceptual and methodological lessons for philosophers and historians of biology. This paper provides an account of miRNA research and the shift from viewing these tiny regulatory entities as minor curiosities to seeing them as major players in the post-transcriptional regulation of genes. Conceptually, the study of miRNAs is part of a broader change in understandings of genetic regulation, in which simple switch-like mechanisms were reinterpreted as aspects of complex cellular and genome-wide processes. Among them are the activities of small RNAs, previously regarded as non-functional. Methodologically, the miRNA story suggests new ways of characterizing biological research that should prove helpful to philosophers of science who seek to develop more pluralistic, pragmatic models of scientific inquiry. miRNA research displays iterative movements between multiple modes of investigation that include not only the proposal and testing of hypotheses but also exploratory, technology-oriented and question-driven modes of research. As an exemplary story of scientific discovery and development, the miRNA case illustrates transitions from genetics to genomics and systems biology, and it shows how diverse configurations of research practice are related to major scientific advances.

Molecular biological mechanisms of speciation

Growing recognition that much of the evolutionary history of eukaryotic genomes reflects the operation of turnover processes involving repetitive DNA sequences has led to the recent formulation of models describing speciation as a consequence of such turnover. These models are of three general kinds: those attributing hybrid infertility to the process of transposition, those attributing hybrid infertility to mispairing between chromosomes of divergent repetitive DNA composition, and those assuming that change in repetitive DNA's can reset coordinated gene regulation. These models are discussed with respect to the kinds of evidence needed for their corroboration and to their significance for questions related to macroevolutionary punctuated equilibria and genetic revolutions.

mRNAs for the immobilization antigens of Paramecium

Immobilization antigens of stock 51 of Paramecium tetraurelia were subjected to electrophoresis in NaDodSO(4)/polyacrylamide gels. Type A is estimated to have a molecular size of 300,000 daltons; H is estimated to be 288,000, D to be 280,000, E to be 270,000, B to be 253,000, and C to be 250,000. Poly(A)(+)RNAs have been isolated from cells producing these antigens and subjected to electrophoresis in methylmercury gels. A major band is found to vary in mobility with antigenic type: Its position in preparations derived from paramecia synthesizing antigen A indicates a size of 8400 nucleotide residues; its position from paramecia synthesizing other antigens indicate H, 8200; D, 7900; E, 7500; B, 7600; and C, 7000. Because of the sizes and quantities of these RNAs, it is argued that they probably represent the mRNAs for the immobilization antigens. It is concluded that each immobilization antigen probably consists of a single polypeptide and that only one major serotype-determining mRNA is present in each antigenically different paramecium.

Extreme polyploidy in a large bacterium

Cells rely on diffusion to move metabolites and biomolecules. Diffusion is highly efficient but only over short distances. Although eukaryotic cells have broken free of diffusion-dictated constraints on cell size, most bacteria and archaea are forced to remain small. Exceptions to this rule are found among the bacterial symbionts of surgeonfish; Epulopiscium spp. are cigar-shaped cells that reach lengths in excess of 600 mum. A large Epulopiscium contains thousands of times more DNA than a bacterium such as Escherichia coli, but the composition of this DNA is not well understood. Here, we present evidence that Epulopiscium contains tens of thousands of copies of its genome. Using quantitative, single-cell PCR assays targeting single-copy genes, we have determined that copy number is positively correlated with Epulopiscium cell size. Although other bacteria are known to possess multiple genomes, polyploidy of the magnitude observed in Epulopiscium is unprecedented. The arrangement of genomes around the cell periphery may permit regional responses to local stimuli, thus allowing Epulopiscium to maintain its unusually large size. Surveys of the sequences of single-copy genes (dnaA, recA, and ftsZ) revealed genetic homogeneity within a cell consistent with only a small amount ( approximately 1%) of the parental DNA being transferred to the next generation. The results also suggest that the abundance of genome copies in Epulopiscium may allow for an unstable genetic feature, a long mononucleotide tract, in an essential gene. With the evolution of extreme polyploidy and large cell size, Epulopiscium has acquired some of the advantages of eukaryotic cells.

Establishment of order in the flow of genetic information in cells

The activities related to the flow of genetic information encoded in DNA in a cell are very orderly. This order, in a living cell, is achieved through specific, but noncovalent, interactions of varieties of structurally dynamic macromolecules under constantly changing physiological conditions. Hence, it is expected that there should be some force that can stabilize the multicomponent reaction processes and establish (or maintain) order in genetic regulatory functions under far-from-equilibrium conditions. The genetic regulatory functions in a cell, however, are believed to be energetically coupled. Expression of genes in a cell is often modulated under changing environmental conditions, raising the possibility of a state controlled nature of the genetic regulatory functions. Adenosine triphosphate (ATP) is the major free-energy contributor for these energy-consuming cellular activities. Enzymatic transfer of high-energy phosphate group from ATP to other reactive components is considered to be the chief mode of energy-transduction in a cell for various biosynthetic processes, as well as other activities related to the flow of information. In an effort to find a solution of the paradox, we assessed the contribution of physiological state of a cell in the process of maintaining order in genetic regulatory functions. As an approach, we systematically perturbed the normal energy flow of a cellular system (bovine aortic endothelial [BAE] cell) by a protein kinase inhibitor (staurosporine), and then followed the expression patterns of several constitutively-expressed protein-encoding genes to measure the effects. Staurosporine, as a function of its concentration, disintegrated the membrane structure of these cells, and eventually caused their death. These secondary consequences of staurosporine treatment offered two additional grossly altered physiological states of the cell to study. Under all of these dramatically altered energy states of the system, an extreme degree of functional coherence prevailed at every level of genetic regulatory function. Integrity at the level of gene transcription remained unaffected. Degradation rate of specific mRNA remained unaltered. Translational activities involving varieties of mRNA species continued in an well-ordered manner. Other state changes, resulting from nutrient and metabolic starvation, or inhibition of oxidative phosphorylation, in addition to the staurosporine treatments, also failed to disintegrate these ordered activities. The steady-state levels of specific mRNA underwent certain changes in these conditions, however, without maintaining any proportional relationships with the staurosporine concentrations applied or the ATP levels in the cell. These results thus led us to propose that the internal energy or a certain intrinsic property of the participating components, rather than the physiological state of the cell, acts as the dominant force in maintaining order and stability of genetic regulatory functions in a cell. Kinetic analyses under different energy states of the cell also supported the hypothesis, and further demonstrated the autoregulatory nature of the genetic order establishment. All of these results suggest a process of molecular self-organization as the fundamental principle for genetic regulation in a cellular system.

A possible role for the 60-kD Ro autoantigen in a discard pathway for defective 5S rRNA precursors

The Ro autoantigen is a 60-kD protein that is usually found in small cytoplasmic RNA-protein complexes known as Ro RNPs. Although the Ro RNPs are abundant and conserved components of a variety of vertebrate and invertebrate cells, their function is unknown. We have discovered that the Ro protein is also found complexed with certain variant 5S rRNAs in Xenopus oocytes. These RNAs contain one or more point mutations compared with the major oocyte 5S rRNA sequence as well as additional nucleotides at the 3' end. We demonstrate that the Ro protein binds specifically mutant 5S rRNAs containing 3' terminal extensions. These mutant RNAs are processed inefficiently to mature 5S rRNA and most eventually are degraded. The observation that the Ro autoantigen specifically associates with defective 5S rRNA precursors suggests that this protein may function as part of a novel quality control or discard pathway for 5S rRNA production.

Regulation of rodent myelin proteolipid protein gene expression

The regulation of rodent proteolipid protein (PLP) gene expression was studied during rat development and in cultured cells. Nuclear run-on assays demonstrate a strong transcriptional component associated with the developmental regulation of the PLP mRNA. Transcription rates of the PLP and MBP genes parallel their respective steady-state mRNA levels throughout rat brain development. In addition, a moderate 25-h half-life was measured for PLP mRNA in 37-day-old cultured oligodendrocytes, suggesting that regulation of PLP expression occurs predominantly at the transcriptional level. Finally, 5400 and 1400 bp of mouse PLP 5'-flanking sequence demonstrate transcriptional activity 13-fold and 5-fold above background, respectively, in hamster glial cells. Far upstream elements are clearly involved in transcription of the PLP gene. The 5400 bp sequence demonstrates no more activity than the 1400 bp in a mouse hepatoma cell line suggesting that elements involved in the glial cell-specific expression of PLP lie between 1400 and 5400 bp upstream of the gene.

Major chromatin changes accompany extinction of alpha-fetoprotein gene in hepatoma x fibroblast hybrids

The sensitivity of the alpha-fetoprotein (AFP) gene to digestion by the enzyme DNaseI, and the presence of hypersensitive sites in the 5' region of this gene, were examined in hepatoma x fibroblast hybrid cells that exhibit extinction of AFP gene expression. Major changes occur in the extinguished gene, i.e., loss of long-range sensitivity to DNase digestion and of the hypersensitive sites. In this respect, the extinguished gene resembles the corresponding silent gene present in fibroblasts, but differs from the silent gene present in normal adult hepatocytes. These observations suggest that extinguisher factors acting on the AFP gene alter its conformation.

Effect of differentiating agents on nucleolar organizer region activity in human melanoma cells

A human cell line established from a metastatic melanoma had both multiple numerical and structural chromosome aberrations including one to two copies of a submetacentric marker chromosome with an insertion of an active nucleolar organizer region (NOR). Treatment of this cell line with retinoic acid (RA) induced morphologic differentiation and reduced the cellular saturation density concomitant with a significant decrease in Ag-NOR activity. RA-treated cells grown in the absence of this differentiating agent, however, displayed a return to normal Ag-NOR activity, indicating the effect of this chemical on ribosomal genes is reversible.

Cellular factor affecting the stability of beta-globin mRNA

Messenger RNAs in eukaryotic cells exhibit a broad range of stabilities in vivo. Globin mRNA has a half life in excess of 50 h, but the half life of the c-myc oncogene mRNA is less than 20 min. Regulation of gene expression may be accomplished by a variety of mechanisms, including altering mRNA stability. We have examined the nuclear and cytoplasmic fractions of cells for factors affecting the metabolism of mRNA. Here we report that a HeLa whole-cell extract contains a factor that protects beta-globin mRNA from attack by RNases in a mouse erythroleukemia cell cytoplasmic extract. The factor is non-dialysable, inactivated by proteinase K and heat treatment, and resistant to RNase and DNase digestion. The HeLa cell factor resembles placental RNase inhibitor in that the mRNA-protecting activity is effective against RNase A and that treatment of the extract with N-ethylmaleimide completely destroys the protective activity. However, purified placental RNase inhibitor was unable to inhibit the RNase activity in the MELC cytoplasmic extract. These results suggest that the HeLa cell extract contains an RNase inhibitor (or inhibitors) with an activity or specificity that is distinct from that of placental RNase inhibitor.

Ontogenetic changes in helminth membrane function

During their life-cycle many parasites experience a wide range of environments including free living and those provided by a variety of intermediate and final hosts. The nutritional requirements of parasites are met by physiological processes adapted to exploit the physicochemical characteristics provided by different hosts. In helminth parasites these adaptations are frequently expressed on the tegumentary surface. As an example of adaptations within the Trematoda, the control of monosaccharide transport in Proterometra sp. is described. Environmental sodium, although not directly involved in the uptake process, nevertheless regulates the expression of transport capabilities. In the Cestoda, the uptake of monosaccharides and amino acids is described for Hymenolepis diminuta. The metacestode of this tapeworm inhabits the blood system of an arthropod, and the adult the gut of a mammal. There are quantitative and qualitative differences in the amino acids and monosaccharides in these two environments and these are reflected in the transport mechanisms exhibited by the two forms of the life-cycle. In Echinococcus granulosus the transfer of amino acids, sugars and macromolecules across the membranes of hydatid cysts and protoscoleces is described. The major difference between these two stages in the life-cycle relates to the ability of hydatid cysts to absorb macromolecules, whereas protoscoleces are impermeable to these compounds. The potential for future work is emphasized.

Phenobarbital-mediated modulation of gene expression in rat liver. Analysis of cDNA clones

Phenobarbital evokes a pleiotypic response in the liver characterized by cell hypertrophy and mono-oxygenase induction. These phenomena arise through complex modulation mechanisms changing the pattern of protein synthesis, distinct from those triggered by other well known inducers, like steroid hormones or polycyclic hydrocarbons. To investigate the mechanisms involved in regulating the expression of the phenobarbital-inducible tissue-specific genes, we constructed two libraries of recombinant bacterial plasmids pBR322 in Escherichia coli. Each library contains cDNA copies of polysomal poly(A)-rich RNA obtained from control and 16-h phenobarbital-induced rat liver. A thousand cloned sequences from each library were screened by double-cross colony hybridization using [32P]cDNA prepared from homologous and heterologous poly(A)-rich RNAs as the probes. The statistical analysis of the results revealed that phenobarbital treatment significantly changes the relative abundance of different polysomal mRNA classes in rat liver. Clones corresponding to mRNAs clearly induced following phenobarbital treatment have been further selected by plasmid DNA dot hybridization, and used as probes for measuring the changes in each mRNA concentration in the whole cell and in the polysomal RNAs from rat livers, at different times after phenobarbital treatment. The fact that changes in the concentration of each specific mRNA in the polysomes does not parallel the variation of its total concentration in the cell indicates that the induced modulation of protein synthesis in the liver is brought about by mechanisms involving both transcriptional and translational regulation, since besides the increases in whole cellular mRNA concentration a marked mobilization of mRNA into active polysomes could be demonstrated during the onset of the adaptive response to phenobarbital.

Programmed gene rearrangements altering gene expression

Programmed gene rearrangements are used in nature to to alter gene copy number (gene amplification and deletion), to create diversity by reassorting gene segments (as in the formation of mammalian immunoglobulin genes), or to control the expression of a set of genes that code for the same function (such as surface antigens). Two major mechanisms for expression control are DNA inversion and DNA transposition. In DNA inversion a DNA segment flips around and is rejoined by site-specific recombination, disconnecting or connecting a gene to sequences required for its expression. In DNA transposition a gene moves into an expression site where it displaces its predecessor by gene conversion. Gene rearrangements altering gene expression have mainly been found in some unicellular organisms. They allow a fraction of the organisms to preadapt to sudden changes in environment, that is, to alter properties such as surface antigens in the absence of an inducing stimulus. The antigenic variation that helps the causative agents of African trypanosomiasis, gonorrhea, and relapsing fever to elude host defense is controlled in this way.

Synapse formation in retina is influenced by molecules that identify cell position

Molecules that identify cell type and position in the nervous system were detected by monoclonal antibodies. One molecule, TOP, is distributed in a 35-fold topographic gradient from the dorsoposterior margin to the ventroanterior margin of avian retina. The gradient is present in young embryos, increases with retinal growth, and persists in the adult. TOP molecules are present on most or all cells of retina. The number of TOP molecules detected per cell varies continuously along the axis of the antigen gradient. Thus, TOP can be used to identify position in the plane of retina along that axis. Other antigens that identify cell type and position across the thickness of retina also were detected. Molecules that mark such cellular organization may represent a neuronal recognition system. Antibodies were used to examine the role of markers of cell position in development of the nervous system. Antibody to TOP from hybridoma cells that were injected into in vivo embryo eyes diffused into the retina and bound in a topographic gradient of Ab.TOP complexes. Synapse formation in retina was inhibited in the presence of anti-TOP antibody. This suggests that TOP is involved in synapse formation and that recognition of position by neurons is necessary for normal synapse formation.

Membrane and cytoplasmic proteins are transported in the same organelle complex during nematode spermatogenesis

During the development of pseudopodial spermatozoa of the nematode, Caenorhabditis elegans, protein synthesis stops before differentiation is completed. Colloidal gold conjugates of monoclonal antibody SP56, which binds to the surface of spermatozoa, and TR20, which recognizes the major sperm cytoplasmic protein (MSP), were used to label thin sections of testes embedded in Lowicryl K4M in order to follow polypeptides from their synthesis early in spermatogenesis to their segregation to specific compartments of the mature cell. Both antigens are synthesized in primary spermatocytes and are assembled into a unique double organelle, the fibrous body-membranous organelle (FB-MO) complex. However, the antigens are localized in different regions of this FB-MO complex. As described in detail, the assembly of proteins into the FB-MO complex allows both membrane and cytoplasmic components to be concentrated in the spermatids after meiosis. Then, the stepwise disassembly of this transient structure ensures delivery of each component to its final destination in the mature spermatozoan: MSP filaments in the fibrous body depolymerize, releasing MSP into the cytoplasm and the membranous organelles fuse with the plasma membrane, delivering SP56 antigen to the surface.

Decreased methylation rates of DNA in SV40-transformed human fibroblasts

The rates of methylation of total cellular DNA and newly synthesized DNA were measured in four unrelated SV40-transformed human fibroblast lines and in four control parent fibroblast lines. Rates of methylation of total cellular DNA were decreased by a factor of 1.8-2.3 in the transformed cells relative to control cells. Methylation was largely (75%-87%) restricted to newly synthesized DNA in control and transformed fibroblasts, and methylation rates of newly synthesized DNA were diminished in transformed cells by 12- to 19-fold relative to control cells. Growth rates were similar in the normal and transformed cells. The cellular uptake of methionine and conversion to S-adenosylmethionine were similar in the normal and transformed cells, suggesting no major differences between the normal and transformed cells in the cellular transport of methionine, methionine S-adenosyltransferase activity, or the intracellular concentrations of methionine and S-adenosylmethionine. The diminished rates of DNA methylation that we have observed suggest a possible mechanism for altered gene expression and growth control in transformed cells.

Alternative processing of sequences during macronuclear development in Tetrahymena thermophila

DNA is eliminated during development of the somatic MACronucleus from the germinal MICronucleus in the ciliated protozoan, Tetrahymena thermophila. Facultatively persistent sequences are a class of sequences that persist in the MAC DNA of some cell lines but are eliminated from the MAC DNA of other cell lines. One cloned MAC fragment contains a persistent sequence as well as sequences normally retained in the MAC. When this cloned fragment was used to construct MAC restriction maps of this region in cell lines whose MAC DNAs do, or do not, contain the persistent sequence, extensive variation in the map flanking this region was observed. The different DNA rearrangements of this MIC segment are epigenetically determined during or soon after MAC development. Moreover, different rearrangements may occur among the 45 copies of this MIC segment as a MAC is formed, resulting in polymorphisms that are later resolved by phenotypic assortment.

Lysosomal enzyme inactivation associated with defects in post-translational modification during development in Dictyostelium discoideum

The developmental accumulation of lysosomal alpha-mannosidase-1 activity in Dictyostelium discoideum is controlled at the level of de novo enzyme precursor biosynthesis. Aggregation-deficient mutants are defective with regard to the accumulation of alpha-mannosidase-1 activity beyond 8-16 h of development. We used enzyme-specific monoclonal antibodies to show that the activity defect in aggregation-deficient strains is not due to a lack of alpha-mannosidase-1-precursor synthesis or processing, or to preferential degradation of the mature enzyme protein. Instead, the defect is a result of enzyme inactivation: cells of aggregation-deficient strains contain significant amounts of inactive alpha-mannosidase-1 protein late in development. The alpha-mannosidase-1 inactivation phenotype is associated with a more general defect in lysosomal enzyme modification. A change in the post-translational modification system occurs during normal slime-mold development, as shown by differences in enzyme isoelectric point, antigenicity, and thermolability. We found that this change in modification does not occur in mutant strains blocked early in development. We propose a model in which pleiotropic mutations in early aggregation-essential genes can indirectly affect the accumulation of alpha-mannosidase-1 activity by preventing the expression of a developmentally controlled change in the post-translational modification system, a change which is required for the stability of several lysosomal enzymes late in development.

The role of tobacco smoke, iron ore mine dusts, viruses, and chemicals in experimental cancer

Assessment of long-term studies on the carcinogenic potential of certain environmental agents has indicated that all of the following appear to activate and/or promote the inherent tumors of the host strains of the animals used irrespective of the extent of additional immunological modulation accompanying the agents: tobacco smoke inhalation, the implantation and inhalation of the respirable fraction of iron ore mine dusts, acute neonatal reovirus 3 infection, urethane, and tobacco smoke inhalation following urethane treatment. It is proposed that these environmental agents function at the onc-gene level as promoters/activators rather than carcinogens, and that this now requires an understanding of the means by which certain environmental agents function at the onc-gene level.

Apolipoprotein multigene family: tandem organization of human apolipoprotein AI, CIII, and AIV genes

The genes for two of the proteins of the plasma lipid transport system, apolipoprotein AI (apoAI) and CIII (apoCIII) are closely linked in the human genome. An approximately equal to 30-kilobase (kb) DNA segment containing these genes and their flanking sequences has been cloned and extensively characterized. Hybridization studies revealed that a DNA fragment located 12 kb 3' to the apoAI gene contains sequences homologous to a 1.8-kb mRNA transcript in human fetal intestine and adult liver but not in fetal liver, kidney, heart, brain, or muscle. This DNA fragment was used as a probe to isolate a clone from an adult human liver cDNA library. The nucleotide sequence of this clone is 74.8% homologous to the cDNA sequence of rat apolipoprotein AIV (apoAIV), another protein of the lipid transport system, and codes for a protein that is 58.6% identical to rat apoAIV. These results indicate that apoAI, apoCIII, and apoAIV genes are closely linked in the human genome and suggest that all three of them are derived from a common ancestral precursor.

Coordinate expression of MnSOD and CuZnSOD in human fibroblasts

The amount of manganese superoxide dismutase (MnSOD) and the activity of copper-zinc superoxide dismutase (CuZnSOD) have been studied in five karyotypically normal human fibroblast strains, using nuclear magnetic resonance (NMR) and polarographic methods. A significant correlation between the two enzyme activities, and a linear increase of MnSOD with the increase of CuZnSOD have been demonstrated. Both enzymes are present in nuclei, mitochondria, lysosome-microsome fraction and cytosol. These findings suggest that the two enzymes dismutate the O-2 cooperatively and that a common genetic control maintains the relative amounts of the two enzymes constant.

Regulation of polypeptide-hormone biosynthesis at the level of the genome

Understanding of gene control mechanisms has greatly accelerated largely due to the application of recombinant DNA techniques. Polypeptide hormone genes encode multiexonic-intronic transcriptional sequences, the exons of which in turn encode polyprotein precursors or prohormones from which the hormones are cleaved during posttranslational processing of the prohormones. Transcriptional processes are regulated by at least two qualitatively different modes of gene regulation. The first mode includes the factors and structural components of a gene that determine whether a gene can or cannot be expressed in a given tissue when the appropriate inducer is present. The second mode is the physiological induction and regulation of the gene that can normally be expressed in a particular tissue. Both cis and trans regulatory mechanisms appear to operate in both tissue-specific expression and physiological regulation. Tissue-specific enhancer sequences consisting of short nucleotide sequences of from 10 to 50 base pairs have been identified in or around genes that are expressed in specific tissues. In many instances trans-acting DNA binding proteins have been found to repress or activate the transcription of the genes. Physiological regulation of hormone genes involves at least two different classes of macromolecules, steroid hormone receptors and phosphoproteins that are formed in response to the binding of ligands to specific surface-located receptors. Although the precise mechanisms by which information encoded in cellular effectors is coupled to cellular responses is incomplete, continued investigations should lead to a more complete understanding of gene control mechanisms and the eventual ability to alter the expression of specific genes.

Dynamic aspects of cytoplasmic poly(A)+ RNA of Tetrahymena pyriformis

In the present work a study was made of the compartmentalization of the poly(A)+ RNA populations during the cultural development of cells of T. pyriformis that were pre-starved or derived from stationary cultures. It was found that the poly(A)+ RNA content increases when the cells change from stationary to lag phase. The increase in RNA poly(A)+ is manifested exclusively in the polysome compartment. The level of poly(A)+ RNA in the cytoplasmic non-polysomal compartment does not change. The increase in poly(A)+ RNA is concomitant with an expansion of the polysomes. Pre-starved cells initiate polysome formation soon after being transferred to a growing medium. During this time the poly(A)+ RNA content of the non-polysomal compartment decreases and that of polysomes increases in close proportion. Not only in the starved but also in stationary cells and in those that are beginning to grow, the proportion of poly(A)+ RNA in mRNP is higher than in the polysomes. These data are interpreted as indicating that cells of T. pyriformis, derived from stationary cultures are dependent on RNA synthesis for polysome formation; on the other hand, pre-starved cells use preformed non-polysomal poly(A)+ RNA for the same purpose, in the beginning of the cultural development.

Genetic modifications during cellular aging

We review evidence that biological aging is a genetic process related to development and cytodifferentiation and thus may involve alterations of DNA structure and gene expression. We conclude that although determined to a high degree aging also involves stochastic features which lead to progressive somatic cell diversification during the life span. These considerations may help to explain the unevenness of physiological decline and the clonal emergence of certain age-dependent diseases such as cancer.

Activation of dormant genes in specialized cells

In several experimental systems the genomic capacity in specialized cells can be assessed by examining the activation of dormant genes. Since some of these specialized cells can be induced to change cell phenotype, all cell specializations do not necessarily involve irreversible genetic changes.