Nucleo-cytoplasmic relationships of high-molecular-weight ribonucleic acid, including polyadenylated species, in the developing rat brain

Nucleolar Enrichment of Brain Proteins with Critical Roles in Human Neurodevelopment

To study nucleolar involvement in brain development, the nuclear and nucleolar proteomes from the rat cerebral cortex at postnatal day 7 were analyzed using LC-MS/iTRAQ methodology. Data of the analysis are available via ProteomeXchange with identifier PXD002188. Among 504 candidate nucleolar proteins, the overrepresented gene ontology terms included such cellular compartmentcategories as "nucleolus", "ribosome" and "chromatin". Consistent with such classification, the most overrepresented functional gene ontology terms were related to RNA metabolism/ribosomal biogenesis, translation, and chromatin organization. Sixteen putative nucleolar proteins were associated with neurodevelopmental phenotypes in humans. Microcephaly and/or cognitive impairment were the most common phenotypic manifestations. Although several such proteins have links to ribosomal biogenesis and/or genomic stability/chromatin structure (e.g. EMG1, RPL10, DKC1, EIF4A3, FLNA, SMC1, ATRX, MCM4, NSD1, LMNA, or CUL4B), others including ADAR, LARP7, GTF2I, or TCF4 have no such connections known. Although neither the Alazami syndrome-associated LARP7nor the Pitt-Hopkins syndrome-associated TCF4 were reported in nucleoli of non-neural cells, in neurons, their nucleolar localization was confirmed by immunostaining. In cultured rat hippocampal neurons, knockdown of LARP7 reduced both perikaryal ribosome content and general protein synthesis. Similar anti-ribosomal/anti-translation effects were observed after knockdown of the ribosomal biogenesis factor EMG1 whose deficiency underlies Bowen-Conradi syndrome. Finally, moderate reduction of ribosome content and general protein synthesis followed overexpression of two Pitt-Hopkins syndrome mutant variants of TCF4. Therefore, dysregulation of ribosomal biogenesis and/or other functions of the nucleolus may disrupt neurodevelopment resulting in such phenotypes as microcephaly and/or cognitive impairment.

Differential effects of axotomy on immature and mature hamster facial neurons: a tritiated-uridine autoradiographic study

In this study, tritiated-uridine incorporation was autoradiographically examined following axotomy of hamster facial motor neurons (HFMN) at the critical development age of 15 days postnatal and in the adult. The postoperative times selected were 0.5, 1, 2, and 4 days. In the 15-day operative series, no changes in incorporation were observed at any of the postoperative times, except at 4 days postoperative, when there was a decrease in tritiated-uridine incorporation in the axotomized neurons relative to the controls. In the adult operative series there were no changes in incorporation at 0.5 or 1 day postoperative, relative to the controls. At 2 days postoperative in the adult, there was a transient increase in tritiated-uridine incorporation that returned to control levels by 4 days postoperative. When axotomized and control cytoplasmic/nuclear grain densities were compared, no changes were found in either operative series. These results of the time course of axotomy-induced changes in RNA synthesis in HFMN corroborate our previous findings of an age-dependent reactive sequence in HFMN and lend support to the hypothesis that the young neurons are synthesizing at peak capacity related to final growth and cannot be stimulated further by axotomy. As discussed, the transient increase in RNA levels in the adult, the lack of any changes in the rate of transfer of RNA from the nucleus to the cytoplasm, and the decrease in RNA levels in the 15-day neurons may be related to the presence of an unusual intranucleolar body within the nucleolus of HFMN that contains ribosomal precursors.

Ultrastructural changes in the nucleoplasm of hamster facial neurons during a postnatal maturation period

Changes in the characteristics of the nucleoplasm were examined in young hamster facial motoneurons of 15 and 20 days postnatal age and in the adult (100 days postnatal age) at both the light and electron microscope levels. In toluidine-blue stained 1-micron thick sections, a progressive increase in basophilic islands within the nucleoplasm occurred during maturation. Ultrastructural changes that were observed during final development included a transition from a homogeneous, 'filled-in' appearing nucleoplasm to a clumped-appearing nucleoplasm. This process principally involved the formation of distinct clusters of interchromatin granules that was associated with a loss of fine fibrils, an increase in clear spaces between intervening fibrillar and granular material, and an increase in small scattered clumps of heterochromatin. These changes in both ribonucleoprotein (RNP)-and DNA-containing nuclear constituents (interchromatin granules and heterochromatin, respectively) occurred during a postnatal maturational period previously demonstrated to involve other alterations in nuclear structures. It is interpreted that these cytomorphic changes in the nucleoplasm reflect an underlying metabolic shift at the transcriptional level during the transition from an actively growing neuron to an adult functioning neuron.

Ribosome biogenesis and nucleolar ultrastructure in neuronal and oligodendroglial rat brain cells

The absolute amounts of precursor to ribosomal RNA (pre-rRNA) and ribosomal RNA (rRNA) in isolated rat brain neuronal and oligodendroglial nuclei were determined. The amount of the major pre-rRNA and rRNA species in neuronal nuclei was about twofold higher than in oligodendroglial nuclei. The relative rate of pre-rRNA synthesis in vivo was 2.3- to 2.7-fold higher in neuronal as compared with oligodendroglial nuclei. This corresponds to a 2.7-fold higher activity of the "template-bound" RNA polymerase I in isolated neuronal nuclei, whereas the activity of the "free" enzyme in both neuronal and glial nuclei was almost identical. The higher transcription rates of rRNA genes correlated with the markedly more prominent fibrillar component in neuronal nucleoli. The turnover times of the major pre-rRNA and rRNA species in neuronal and oligodendroglial nuclei were similar, except for 45S pre-rRNA, which turned over at an approximately 1.5-fold slower rate in neuronal nuclei. The relative rates of processing of pre-rRNA and of nucleocytoplasmic transport of rRNA in neuronal cells were approximately 2.7-fold higher than in oligodendroglial cells and corresponded to the differences in rRNA gene transcription rates. The established ribosome formation features correlated with an abundant (neurons) or exceedingly scarce (oligodendrocytes) nucleolar granular component. The turnover rate of cytoplasmic ribosomes in rat brain neurons was twofold slower than in oligodendrocytes, largely because of the about fivefold higher amount of ribosomes in the cytoplasm of neurons. We conclude that ribosome formation and turnover in neuronal and oligodendroglial cells are adapted to the protein synthetic levels in these two types of brain cells.

Age-related changes in the structure and function of chromatin: a review

Due to rapid advancement in biochemical and biophysical techniques during the last decade, extensive studies have been undertaken to understand the structure and function of chromatin. Several interesting results have been reported regarding the changes in basic organization and function of chromatin during the life time of a eukaryotic cell. The data accumulated so far have been obtained with different organs and organisms and widely differing methods, and the conclusions drawn from them are sometimes contradictory. In this paper, therefore, the available data on the age-associated alterations in the composition, structure and function of chromatin have been discussed, and an attempt has been made to correlate the structural changes in chromatin with alteration in gene expression during aging.

RNA synthesis in neuronal and glial cell nuclei from rat cerebral hemispheres during early postnatal development

RNA synthesis in rat cerebral hemispheres at 1, 5, and 10 days of age and the relative contribution brought by neuronal and glial nuclei to RNA synthesis was investigated. The experiments were carried out both in vivo (by i.p. injection of [3H]uridine) and in vitro (either by incubation of tissue slices with [3H]uridine or by determination of RNA polymerase activities). The labeling of RNA decreases from 1 to 10 days of age both in vivo and in vitro; the decrease is of the same extent in neuronal and glial nuclei. RNA polymerase activity Mg2+-dependent does not change significantly from 1 to 10 days of age either in total, in neuronal, or in glial nuclei, whereas the Mn2+-dependent activity increases significantly over the same developmental period studied. The significance of RNA polymerase assay as an index of in vivo RNA synthesis is discussed.

Different Rates of Synthesis and Turnover of Ribosomal RNA in Rat Brain and Liver

The kinetics of in vivo labeling of cellular free UMP and nucleolar, nucleoplasmic, and cytoplasmic rRNA with [14C]orotate in rat brain and liver were investigated. Evaluation of the experimental data shows: (a) The rate of nucleolar precursors of ribosomal RNA (pre-rRNA) synthesis and the deduced rate of ribosome formation in brain is about fivefold lower than in liver and corresponds to 220-260 ribosomes/min/nucleus. (b) The lower rate of in vivo pre-rRNA synthesis is correlated with a lower activity of RNA polymerase I in isolated brain nuclei. (c) The half-lives of nucleolar rRNA in brain and liver are 210 and 60 min, respectively, thus showing a slower rate of processing of pre-rRNA in brain nucleoli. (d) The nucleo-cytoplasmic transport of ribosomes in brain is also markedly slower than in liver and reflects the lower rates of synthesis and processing of pre-rRNA. (e) Cytoplasmic ribosomes in brain and liver turn over with half-lives of about 6 and 4 days, respectively. It is concluded that the markedly lower rate of ribosome biogenesis in brain is specified mainly at the level of transcription of rRNA genes.

Labeling of RNA in young and adult rat brain: evidence for different RNA processing

The labeling of RNA in young and adult rat brain has been studied by measuring in vitro (tissue slices incubation) the incorporation of labeled uridine into RNA of total tissue and of the various subcellular fractions purified from cerebral hemispheres of 1- and 10-month-old rats. Gel electrophoretic analysis of the newly synthesized nuclear and microsomal RNA was also accomplished. An active metabolism of RNA in adult animals was found; moreover, distinct differences in ribosomal RNA processing in cerebral hemispheres of 1- and 10-month-old rats, with a more rapid processing in the brain of adult animals, were obtained.

In vivo studies on the age-dependent decrease of the rates of total and mRNA synthesis in the brain cortex of rats

The membrane hypothesis of aging (Zs.-Nagy, I., 1978, J. Theor. Biol. 75, 189-195) attributes the primary role in cellular aging to an age-dependent decrease of the passive potassium permeability of the cell membrane which is due most probably to free-radical damage of the membrane components. As a consequence, the intracellular and intranuclear ionic strength increases resulting in a condensation of the chromatin and a slowing down of the synthetic processes performed by the nucleus. In this concept it was of importance to reveal whether the rates of total and mRNA synthesis display any age-dependent alteration parallel with the change of membrane permeability of the brain nerve cells. Experiments were performed using tritiated uridine incorporation measurements and suitable preparation techniques in young, adult and old rats (1.5, 13 and 25 mth of age, respectively). Comparisons of the incorporation rates revealed a very considerable decrease in the rate of synthesis of both the total and polyadenylated RNA (polyA + RNA) between the ages of 13 and 26 mth. The old animals displayed only about 55 and 67% of the rate of synthesis for the 2 classes of RNA, respectively, as compared to the young and adult rats, if the results are expressed as dpm/mg RNA. However, the decreases are even more pronounced (34 and 41%) if the results are expressed on a dry weight basis. The results obtained are compatible with the membrane hypothesis of aging.

Developmental changes in the composition of polyadenylated RNA isolated from free and membrane-bound polyribosomes of the rat forebrain, analysed by translation in vitro

Free and membrane-bound polyribosomes were isolated from the rat forebrain during its development. Polyadenylated RNA [poly(A)+ RNA] was isolated from both fractions, by using oligo(dT)-cellulose chromatography, and its composition studied by translating the poly(A)+ RNA in vitro in reticulocyte lysates. Electrophoretic analysis of the translation products showed that both free and membrane-bound polyribosomal poly(A)+ RNA gave many common components, but that there were also distinct differences in the protein composition of the products of the two fractions. Several proteins, of mol.wts. 39 000, 37 000, 31 000, 27 000 and 17 000, appeared to be products predominantly of free polyribosomal poly(A)+ RNA, whereas others, of mol.wt. 47 000, 33 000, 24 000 and 21 000 were specific to the membrane-bound polyribosomal poly(A)+ RNA fraction. More developmental changes were observed in the translational products of the membrane-bound poly(A)+ RNA fraction. Proteins of mol.wts. 33 000 and 21 000, which were predominant components of the translational products of this fraction when isolated from 10-day and older rats, were not present in translational products derived from preparations isolated from 3-day-old rats. The developmental appearance of these proteins as translational products of the membrane-bound poly(A)+ RNA suggests the appearance of new mRNA species. These transcriptional changes are discussed in relation to processes involved in brain differentiation, including myelination.

Developmental changes in the protein and ribonucleic acid components of rat brain messenger ribonucleic acid-protein particles isolated from free polyribosomes by oligo(dT)-cellulose chromatography

A study has been made of the developmental changes that occur in the RNA and protein moieties of mRNA-protein particles isolated from newborn and adult rat forebrain free polyribosomes. mRNA-protein particles were isolated by oligo(dT)-cellulose chromatography from salt-washed polyribosomes dissociated by puromycin/0.5 M-KCl treatment as two fractions (E1 and E2) by using Tris/HCl/NaCl eluting buffers containing respectively 25 and 50% (v/v) formamide. Isopycnic centrifugation on CsCl gradients showed that the newborn-derived fractions E1 and E2 has buoyant densities of 1.48--1.50 and 1.41--1.43 g/cm3. Adult-derived E1 and E2 fractions had corresponding values of 1.47 and 1.42 g/cm3. The pooled mRNA-protein particles from the E1 and E2 fractions after deproteinization with proteinase K sedimented with a mean size of approx. 18 S on a sucrose gradient containing 85% formamide with little differences between mRNA molecules from newborn and adult. The mean lengths of the poly(A) segments were similar, being about 130 nucleotides long. Distinct changes were found in the protein composition of the mRNA-protein particles. Fractions E1 and E2 from the newborn contained two major proteins of mol.wts. 74 000 and 52 000 with differences in the relative proportions in each fraction. In contrast, adult fractions E1 and E2 contained predominantly the larger protein. However, the adult fraction E2 contained a more heterogeneous population of minor bands of proteins, including that of mol.wt. 52 000. The findings are discussed briefly in relation to other changes in the developing brain.

Poly(A)- and nonpoly(A)-RNA associated with rat brain microsomal fractions: in vivo labelling studies

The time course of incorporation of radiolabelled precursor into RNA associated with rat brain free polyribosomes, rough membranes, and smooth membranes was measured following a single intracranial injection of [3H] orotic acid. Polyadenylated RNAs were separated from nonpolyadenylated RNAs by affinity chromatography on oligo (dT)-cellulose columns. Poly(A)-RNA associated with each of the microsomal fractions became more rapidly labelled than did the nonpoly(A)-RNA of the same fractions. While the labelling profiles of the nonpoly(A)-RNA isolated from the polyribosomes and rough membranes are similar from one fraction to another, the specific radioactivity of the poly(A)-RNA isolated from free polyribosomes increased much more drastically than that of the poly(A)-RNA associated with rough membranes. The labelling profiles of RNA species isolated from smooth membranes were very different in this respect from the two ribosomal fractions. There was a lag of more than four hours before significant label appeared in the RNA associated with the smooth membrane fraction. These studies demonstrate that the different populations of brain microsomal RNA are labelled at different rates, perhaps reflecting differences in the turnover of these RNAs and differences in their function.

The metabolism of high-molecular-weight ribonucleic acid in hypothalamic and cortical regions of the developing female rat brain

The regional metabolism of high-molecular-weight RNA in the developing female rat brain was investigated after the intracranial injection of [32P]P1. The synthesis of polyadenylated RNA relative to high-molecular-weight RNA was determined after oligo(dT)-cellulose chromatography of total cellular high-molecular-weight RNA labelled after 4h. In both hypothalamus and cortex this synthesis was significantly higher during the first 10 days post partum than at subsequent ages. In both regions apparently more mRNA is synthesized in the young. The ratio of the specific radioactivity of cytoplasmic high-molecular-weight RNA relative to that of the nucleus, measured after a 48 h period of labelling, was considered to be an index of the nucleocytoplasmic transport of newly synthesized RNA [Berthold & Lim (1976) Biochem. J. 154, 529--539]. In the cortex, nucleo-cytoplasmic RNA transport in rats aged up to 20 days was significantly higher than in older rats, with the maximal value being attained between 16 and 19 days post partum. In contrast, in the hypothalamus, nucleo-cytoplasmic transport of RNA was low during the neonatal period and comparable with that of the mature animal. However, there were two periods of increased transport at later stages of development, the first between 15 and 19 days post partum and the second between 25 and 29 days post partum. These prepubertal changes in the nucleo-cytoplasmic transport of RNA in the female hypothalamus during weeks 3 and 4 post partum are coincident with other reported changes occurring during sexual differentiation. Differences in the timing of the maturational changes of the two brain regions thus appear to be reflected in developmental changes in RNA transport.

The metabolism of high-molecular-weight ribonucleic acid including polyadenylated species, in the developing rat brain

High-molecular-weight RNA was isolated from rat brain at various times after the intracranial administration of [32P]Pi. The synthesis of 28S and 18S rRNA could be detected within 1h of the injection of the radioactive precursor and appeared to be more pronounced, relative to other high-molecular-weight RNA, in the brains of older rats compared with those of newborn rats. Polyadenylated RNA, representing most mRNA and their precursors, was isolated by chromatography on oligo(dT)-cellulose. The contribution of this polyadenylated RNA to total RNA synthesis was investigated in the cerebral cortex and the phylogenetically older brain stem at different stages in the development of the rats by using a 5h period of labelling as an arbitrary index of transcription. In the brain stem the proportion of labelled polyadenylated RNA comprised 27-30% of the total RNA. The corresponding values for the cortex decreased from 34% in newborn rats to 23% in 40-150-day-old rats. These data indicated that proportionately more polyadenylated RNA is synthesized in the cortex of the newborn than in the adult rat and that there is a progressive decrease in the synthesis of polyadenylated RNA relative to rRNA during development.