Genetic expression in the developing brain

Toward Best Practices for Imaging Transcriptomics of the Human Brain

Modern brainwide transcriptional atlases provide unprecedented opportunities for investigating the molecular correlates of brain organization, as quantified using noninvasive neuroimaging. However, integrating neuroimaging data with transcriptomic measures is not straightforward, and careful consideration is required to make valid inferences. In this article, we review recent work exploring how various methodological choices affect 3 main phases of imaging transcriptomic analyses, including 1) processing of transcriptional atlas data; 2) relating transcriptional measures to independently derived neuroimaging phenotypes; and 3) evaluating the functional implications of identified associations through gene enrichment analyses. Our aim is to facilitate the development of standardized and reproducible approaches for this rapidly growing field. We identify sources of methodological variability, key choices that can affect findings, and considerations for mitigating false positive and/or spurious results. Finally, we provide an overview of freely available open-source toolboxes implementing current best-practice procedures across all 3 analysis phases.

Social Networking of Quasi-Species Consortia drive Virolution via Persistence

The emergence of cooperative quasi-species consortia (QS-C) thinking from the more accepted quasispecies equations of Manfred Eigen, provides a conceptual foundation from which concerted action of RNA agents can now be understood. As group membership becomes a basic criteria for the emergence of living systems, we also start to understand why the history and context of social RNA networks become crucial for survival and function. History and context of social RNA networks also lead to the emergence of a natural genetic code. Indeed, this QS-C thinking can also provide us with a transition point between the chemical world of RNA replicators and the living world of RNA agents that actively differentiate self from non-self and generate group identity with membership roles. Importantly the social force of a consortia to solve complex, multilevel problems also depend on using opposing and minority functions. The consortial action of social networks of RNA stem-loops subsequently lead to the evolution of cellular organisms representing a tree of life.

Developmental influence of the cellular prion protein on the gene expression profile in mouse hippocampus

The conversion of the cellular prion protein (PrP(C)) to an abnormal and protease-resistant isoform is the key event in prion diseases. Mice lacking PrP(C) are resistant to prion infection, and downregulation of PrP(C) during prion infection prevents neuronal loss and the progression to clinical disease. These results are suggestive of the potential beneficial effect of silencing PrP(C) during prion diseases. However, the silencing of a protein that is widely expressed throughout the central nervous system could be detrimental to brain homeostasis. The physiological role of PrP(C) remains still unclear, but several putative functions (e.g., neuronal development and maintenance) have been proposed. To assess the influence of PrP(C) on gene expression profile in the mouse brain, we undertook a microarray analysis by using RNA isolated from the hippocampus at two different developmental stages: newborn (4.5-day-old) and adult (3-mo-old) mice, both from wild-type and Prnp(0/0) animals. Comparing the different datasets allowed us to identify "commonly" co-regulated genes and "uniquely" deregulated genes during postnatal development. The absence of PrP(C) affected several biological pathways, the most representative being cell signaling, cell-cell communication and transduction processes, calcium homeostasis, nervous system development, synaptic transmission, and cell adhesion. However, there was only a moderate alteration of the gene expression profile in our animal models. PrP(C) deficiency did not lead to a dramatic alteration of gene expression profile and produced moderately altered gene expression levels from young to adult animals. Thus, our results may provide additional support to silencing endogenous PrP(C) levels as therapeutic approach to prion diseases.

Developmental regulation of prion protein mRNA in brain

During development of the hamster brain, synthesis of the cellular isoform of the scrapie prion protein (PrPC) was found to be regulated. Low levels of PrP poly(A)+ mRNA were detectable one day after birth. PrP poly(A)+ mRNA reached maximal levels between 10 and 20 days post-partum; thereafter, no change in its level could be detected at ages up to 13 months. In contrast, myelin basic protein poly(A)+ mRNA was shown to reach maximal levels by 30 days of age and thereafter steadily declined in adult brain. Using monospecific PrP antisera, immunoprecipitable cell-free translation products were detected at low levels two days after birth and progressively increased up to 10 days of age. How the PrP mRNA participates in brain development and its function in scrapie prion infection are being investigated.

Targeted cDNA differential display (TcDD)

Targeted cDNA differential display (TcDD) was developed to study expression of a different selected gene families especially those at low copy numbers per cell. This method is an adaptation of our previously described targeted genomic differential display method (TGDD). In TcDD, the expression of genes containing target sequences such as CAG repeating sequences or genes encoding for zinc-finger binding proteins were followed in an experimental rat model with salt-induced hypertension. DNA sequencing experiments demonstrated that the effectiveness of targeting was greater than 99%.

DNA-polymerase alpha, beta, delta and epsilon activities in isolated neuronal and astroglial cell fractions from developing and aging rat cerebral cortex

The relative proportions of DNA-polymerases alpha, beta, delta and epsilon (pols alpha, beta, delta and epsilon ) activities in isolated neuronal and astroglial cell fractions from developing, adult and aging rat brain cerebral cortex, were examined. This was achieved through a protocol that takes advantage of the reported differential sensitivities of different DNA-polymerases towards certain inhibitors like butylphenyl and butylanilino nucleotide analogs, 2',3'-dideoxythymidine triphosphate (ddTTP), monoclonal antibody of human alpha polymerase and the use of two template primers as substrates. The results indicate that while DNA-polymerase beta (pol beta) is the predominant enzyme, significant levels of DNA-polymerases alpha and delta/epsilon (pols alpha and delta/epsilon ) are also present in both cell types at all the post-natal ages studied. A notable difference regarding the relative abundance of DNA-polymerases other than beta is the higher percentage of pol delta/epsilon in neurons and a more sustained pol alpha activity through the life span in astroglia. The presence of detectable proportion of DNA-polymerases other than beta (particularly the delta/epsilon type) may be taken to indicate their role in long patch base excision repair as well as in other modes of DNA repair.

Expression profiling with oligonucleotide arrays: technologies and applications for neurobiology

DNA microarrays have been used in applications ranging from the assignment of gene function to analytical uses in prognostics. However, the detection sensitivity, cross hybridization, and reproducibility of these arrays can affect experimental design and data interpretation. Moreover, several technologies are available for fabrication of oligonucleotide microarrays. We review these technologies and performance attributes and, with data sets generated from human brain RNA, present statistical tools and methods to analyze data quality and to mine and visualize the data. Our data show high reproducibility and should allow an investigator to discern biological and regional variability from differential expression. Although we have used brain RNA as a model system to illustrate some of these points, the oligonucleotide arrays and methods employed in this study can be used with cell lines, tissue sections, blood, and other fluids. To further demonstrate this point, we provide data generated from total RNA sample sizes of 200 ng.

DEPD, a high resolution gene expression profiling technique capable of identifying new drug targets in the central nervous system

Digital expression pattern display (DEPD) is an open, automated, PCR-based system of gene expression profiling that is capable of resolving as many as 100,000 transcripts from a single brain tissue cDNA sample. It has a detection sensitivity of better than 1 in 750,000 and it can reliably detect differences in RNA expression levels of less than two-fold. Digital expression pattern display presently is the most sensitive and therefore the only expression profiling method available that is capable of monitoring, in a semi-quantitative fashion, the expression of even the rarest of transcripts found in human brain tissue. Biofrontera applies this proprietary technique, together with state-of-the-art bioinformatics, for the purposes of elucidating pathology pathways of major brain diseases, of analysing the target profiles of drugs presently applied or in development, and of identifying novel targets for drug action.

Effect of gestational age and hypoxia on activity of ribonucleic acid polymerase in fetal guinea pig brain

OBJECTIVE

The aim of this study was to determine the effect of gestational age and hypoxia on the activity of ribonucleic acid polymerase in fetal guinea pig brain.

STUDY DESIGN

Fetal cerebral cortical neuronal nuclei were isolated at 40, 50, and 60 days (term) of gestation to determine the effect of gestational age on the activity of ribonucleic acid polymerase I, II, and III. Pregnant guinea pigs at 60 days' gestation were randomly assigned to a normoxic or hypoxic group to determine the effect of hypoxia on ribonucleic acid polymerase activity. The fetal neuronal nuclei were pooled from 6 pregnant animals in each group. In the normoxic group the pregnant guinea pigs were exposed to room air before delivery. In the hypoxic group delivery occurred after the pregnant guinea pig had been exposed to 7% oxygen for 60 minutes. The fetuses were delivered by cesarean, and the fetal cerebral cortical neuronal nuclei were isolated immediately. Ribonucleic acid polymerase activity was determined with nuclei suspended in a buffer containing adenosine triphosphate, guanosine triphosphate, cytidine triphosphate, and tritiated uridine triphosphate. Dactinomycin (actinomycin D) and polydeoxyadenylic-thymidylic acid were used to determine the activity of bound and free ribonucleic acid polymerase. alpha-Amanitin was used to determine the activity of ribonucleic acid polymerase II.

RESULTS

The activity of total (bound and free) ribonucleic acid polymerase I and III increased from 85.4 +/- 9.4 fmol of tritiated uridine triphosphate incorporated per milligram of protein per hour at 40 days' gestation to 233.3 +/- 82.1 fmol at 50 days and to 343.4 +/- 231.6 fmol at 60 days (P =.02). Total ribonucleic acid polymerase II activity increased from 19.9 +/- 6.0 fmol of tritiated uridine triphosphate incorporated per milligram of protein per hour at 40 days to 123.8 +/- 53.0 fmol at 50 days and to 200.9 +/- 77.8 fmol at 60 days (P <.01). In the term fetal guinea pig brain the activity of bound ribonucleic acid polymerase I and III decreased from 116.8 +/- 107.2 fmol of tritiated uridine triphosphate incorporated per milligram of protein per hour under normoxic conditions to 92.8 +/- 76.0 fmol in hypoxic fetal brain, a decrease of 20.5%. Free ribonucleic acid polymerase I and III activity decreased from 199.2 +/- 115.2 fmol of tritiated uridine triphosphate incorporated per milligram of protein per hour in normoxic fetal brain to 132.0 +/- 66.4 fmol in hypoxic fetal brain, a decrease of 33.8%. Free ribonucleic acid polymerase II activity decreased from 62.4 +/- 70.4 fmol of tritiated uridine triphosphate incorporated per milligram of protein per hour in normoxic fetuses to 13.6 +/- 9.6 fmol in hypoxic fetal brain, a decrease of 78.2%. In contrast, however, in term fetal guinea pig brain, bound ribonucleic acid polymerase II activity increased from 8.0 +/- 10.4 fmol of tritiated uridine triphosphate incorporated per milligram of protein per hour under normoxic conditions to 35.2 +/- 8.8 fmol in hypoxic fetal brain, an increase of 340% (P <.01).

CONCLUSION

The activity of ribonucleic acid polymerases I, II, and III increases throughout the latter half of gestation, from 40 to 60 days, in the fetal guinea pig brain. Hypoxia in utero is associated with a decrease in ribonucleic acid polymerase I and III activity. Although hypoxia is associated with a decrease in free ribonucleic acid polymerase II activity, we observed a marked increase in bound ribonucleic acid polymerase II activity, which may represent a hypoxia-induced alteration of gene expression.

The sequence of the human genome

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

Bacteriophage lambda display of complex cDNA libraries: a new approach to functional genomics

We describe the construction and characterization of two lambda surface displayed cDNA expression libraries derived from human brain and mouse embryo. cDNA inserts were obtained by tagged random-priming elongation of commercially available cDNA libraries and cloned into a novel lambda vector at the 3' end of the D capsid protein gene, which produced highly complex repertoires (1x10(8) and 2x10(7) phage). These libraries were affinity selected with a monoclonal antibody against the neural specific factor GAP-43 and with polyclonal antibodies that recognize the EMX1 and EMX2 homeoproteins. In both cases rapid identification of specific clones was achieved, which demonstrates the great potential of the lambda display system for generating affinity selectable cDNA libraries from complex genomes.

Regulation of the neuron-specific exon of clathrin light chain B

Clathrin light chain B (LCB) is a major component of clathrin coated vesicles, which are structures involved in intracellular transport. A neuron-specific isoform of LCB is generated by incorporation of a single exon (EN) using an alternative splicing mechanism that reflects the special demands of neurons, such as axonal transport and synaptic neurotransmission. Here, we demonstrate that this neuron-specific exon is developmentally regulated and is excluded in non-neuronal cells because its 5' and 3' splice sites deviate from the mammalian consensus sequences. A gel retardation assay indicated the presence of a developmentally regulated factor in brain that binds to the neuronal exon. In addition, EN usage is repressed by increasing the concentration of htra2-beta1, a splice factor whose isoform expression is influenced by neuronal activity. We propose that a brain-specific factor is involved in EN recognition during development and adulthood. In addition, ubiquitously expressed splicing factors such as htra2-beta1 are involved in regulating EN expression in the adult brain.

Biology of the congenitally hypothyroid hyt/hyt mouse

The hyt/hyt mouse has an autosomal recessive, fetal onset, characterized by severe hypothyroidism that persists throughout life and is a reliable model of human sporadic congenital hypothyroidism. The hypothyroidism in the hyt/hyt mouse reflects the hyporesponsiveness of the thyroid gland to thyrotropin (TSH). This is attributable to a point mutation of C to T at nucleotide position 1666, resulting in the replacement of a Pro with Leu at position 556 in transmembrane domain IV of the G protein-linked TSH receptor. This mutation leads to a reduction in all cAMP-regulated events, including thyroid hormone synthesis. The diminution in T3/T4 in serum and other organs, including the brain, also leads to alterations in the level and timing of expression of critical brain molecules, i.e. selected tubulin isoforms (M beta 5, M beta 2, and M alpha 1), microtubule associated proteins (MAPs), and myelin basic protein, as well as to changes in important neuronal cytoskeletal events, i.e. microtubule assembly and SCa and SCb axonal transport. In the hyt/hyt mouse, fetal hypothyroidism leads to reductions in M beta 5, M beta 2, and M alpha 1 mRNAs, important tubulin isoforms, and M beta 5 and M beta 2 proteins, which comprise the microtubules. These molecules are localized to layer V pyramidal neurons in the sensorimotor cortex, a site of differentiating neurons, as well as a site for localization of specific thyroid hormone receptors. These molecular abnormalities in specific cells and at specific times of development or maturation may contribute to the observed neuroanatomical abnormalities, i.e. altered neuronal process growth and maintenance, synaptogenesis, and myelination, in hypothyroid brain. Abnormal neuroanatomical development in selected brain regions may be the factor underlying the abnormalities in reflexive, locomotor, and adaptive behavior seen in the hyt/hyt mouse and other hypothyroid animals.

Detection of lamprin mRNA in the anadromous sea lamprey using in situ hybridization

An optimal in situ hybridization protocol is described for the detection of gene expression of a structural protein unique to lampreys, lamprin, in the cartilages of prolarval, metamorphic and adult sea lamprey, Petromyzon marinus. A 156 bp antisense RNA probe labeled with (35)S-UTP was transcribed in vitro from a recombinant plasmid containing a cDNA insert homologous to the largest (1.8 kb) of three known mRNAs for the lamprin gene and hybridized to 6 mu m paraffin sections. Optimal signal to noise ratio was achieved by fixing tissues 30 min in 4% paraformaldehyde and prehybridizing with a probe incorporating a nonradioactive S-UTP. Strong signals were visualized in all cartilaginous elements of the lamprey neurocranium; however, lamprin mRNA transcripts were not detected in branchial and pericardial cartilages suggesting differential expression of the lamprin gene. No signals were observed in tissue sections that had been treated with RNase A prior to hybridization or in sections hybridized with sense RNA probes. This technique has great potential for use in studies of the spatial and temporal distribution of cartilaginous components during developmental stages of lampreys.

Structure and expression of the guinea pig preproenkephalin gene: site-specific cleavage in the 3' untranslated region yields truncated mRNA transcripts in specific brain regions

We isolated the guinea pig preproenkephalin gene from a genomic library by hybridization to a rat cDNA probe. The entire nucleotide sequence of the gene was determined. Genomic Southern blot hybridization demonstrated that the gene exists in a single copy within the genome. On the basis of RNase protection transcript mapping and homology comparisons with known preproenkephalin sequences from other species and assuming a poly(A) tail length of 100 residues, we predicted an mRNA transcript of approximately 1,400 nucleotides encoded by three exons. Northern (RNA) blot analysis of total RNA from several brain regions showed high levels of preproenkephalin mRNA in the caudate putamen, nucleus accumbens, and hypothalamus, with detectable levels in the amygdala, ventral tegmental area, and central gray and also in the pituitary. Unexpectedly, in several brain regions, the mRNA appeared not only in the 1,400-nucleotide length but also in a shorter length of approximately 1,130 bases. Significant amounts of the shorter mRNA were found in the caudate putamen, nucleus accumbens, and amygdala. The longer, but not the shorter, transcripts from the caudate putamen were found to be polyadenylated, but the difference in size was not due solely to the presence of poly(A) tails. Northern gel analysis of total RNA from the caudate putamen with probes from each exon, together with RNase protection mapping of the 3' end of the mRNA demonstrated that the 1,400-base preproenkephalin mRNA transcripts are cleaved in a site-specific manner in some brain regions, yielding a 1,130-base transcript and a 165-base polyadenylated fragment derived from the terminal end of the 3' untranslated region of the mRNA. This cleavage may serve as a preliminary step in RNA degradation and provide a mechanism for control of preproenkephalin mRNA abundance through selective degradation.

Hormonal regulation of hypothalamic gene expression: identification of multiple novel estrogen induced genes

Estrogen (E) has been shown to play a major role in hypothalamic function and is a prerequisite for progesterone (P) induced sexual behavior in female rats. In the course of studies in search of steroid induced hypothalamic genes, we discovered a surprisingly large number of E-induced genes (21 mRNAs in total). This is the largest number of E-induced genes ever identified in a single organ. Many of these mRNAs exhibit considerable magnitudes of induction and their levels were maintained typically during subsequent P treatment. Among the induced genes, several encode metabolic enzymes and may account for some of the morphological changes observed in hypothalamic neurons in response to E. Since E appears to play a major role in defining the pattern of hypothalamic gene expression in conjunction with its capacity for behavioral modulation, these newly identified cDNAs may serve as genetic markers for correlative studies of E-induced central nervous system behavior.

Enhancer trapping by a human mid-sized neurofilament transgene reveals unexpected patterns of neuronal enhancer activity

In ten transgenic lines, expression of a human mid-sized (M) neurofilament (NF) transgene was restricted to neurons in the central and peripheral nervous systems. However, no two lines gave identical expression patterns and none exactly matched the expression of mouse NF(M). These varied expression patterns within the neural compartment likely result from interactions of the transgene with enhancer elements located in the regions flanking the insertion site. Unexpected patterns of enhancer activity included an enhancer active in subsets of cerebellar basket cells as well as others preferentially active in subsets of motor or sensory neurons.

Construction and characterization of a normalized cDNA library

We have developed a simple procedure based on reassociation kinetics that can reduce effectively the high variation in abundance among the clones of a cDNA library that represent individual mRNA species. For this normalization, we used as a model system a library of human infant brain cDNAs that were cloned directionally into a phagemid vector and, thus, could be easily converted into single-stranded circles. After controlled primer extension to synthesize a short complementary strand on each circular template, melting and reannealing of the partial duplexes at relatively low C0t, and hydroxyapatite column chromatography, unreassociated circles were recovered from the flow through fraction and electroporated into bacteria, to propagate a normalized library without a requirement for subcloning steps. An evaluation of the extent of normalization has indicated that, from an extreme range of abundance of 4 orders of magnitude in the original library, the frequency of occurrence of any clone examined in the normalized library was brought within the narrow range of only 1 order of magnitude.

Expression of polyadenylated and non-polyadenylated trkC transcripts in the rodent central nervous system

We have previously isolated a full-length cDNA clone encoding rat TrkC, a member of the Trk family of tyrosine kinase receptors, that specifically mediates biological responses to neurotrophin-3. Here, we report the identification of five major trkC transcripts in the adult and developing rat and mouse brain suggesting the presence of several TrkC receptors. Northern blot hybridizations revealed that three of these trkC transcripts (of 14, 3.9 and 4.8 kb) were poly(A)+ messenger RNAs, while the two others, of shorter size (1.1 and 0.7 kb), were poly(A)- messenger RNAs. All transcripts were expressed in 11 brain regions but poly(A)- messenger RNAs were found at much higher levels than poly(A)+ messenger RNAs in the cerebellum. Hybridization with five oligonucleotide and two complementary DNA probes, corresponding to different parts of the full-length trkC complementary DNA, revealed that the two poly(A)- transcripts may encode for receptors truncated in their extracellular and kinase intracellular domains. During ontogeny, poly(A)- trkC messenger RNAs were found at low amounts at prenatal and early postnatal ages with a drastic increase in the cerebellum at postnatal day 30. No poly(A)- transcript was identified for the trk B gene. In situ hybridization revealed that trkC messenger RNAs are expressed both in granular and Purkinje cells in the cerebellum. Northern blot on RNA extracted from mice mutant strains with degeneration of either granular or both granular and Purkinje cells suggested that poly(A)- and poly(A)+ trkC messenger RNAs are expressed within the same cells. We have demonstrated the existence of several trkC transcripts that differ both by their size and polyadenylation. This phenomenon could be of physiological relevance in regulating TrkC functions. To the best of our knowledge, this is an original feature for a mammalian gene expression. Studies focused on poly(A)- messenger RNAs could give rise to the identification of other genes expressed in a similar fashion.

A sequence compilation and comparison of exons that are alternatively spliced in neurons

Alternative splicing is an important regulatory mechanism to create protein diversity. In order to elucidate possible regulatory elements common to neuron specific exons, we created and statistically analysed a database of exons that are alternatively spliced in neurons. The splice site comparison of alternatively and constitutively spliced exons reveals that some, but not all alternatively spliced exons have splice sites deviating from the consensus sequence, implying diverse patterns of regulation. The deviation from the consensus is most evident at the -3 position of the 3' splice site and the +4 and -3 position of the 5' splice site. The nucleotide composition of alternatively and constitutively spliced exons is different, with alternatively spliced exons being more AU rich. We performed overlapping k-tuple analysis to identify common motifs. We found that alternatively and constitutively spliced exons differ in the frequency of several trinucleotides that cannot be explained by the amino acid composition and may be important for splicing regulation.

Molecular genetic approaches to understanding brain development and behaviour

An understanding of brain development and brain function at the level of the genome is developing rapidly, because of the availability of new technologies in molecular and cellular biology. This understanding can be further enhanced by an interactive exchange between the disciplines of behavioural neuroscience and molecular genetics. New genes are being cloned almost daily, but their function remains an enigma. The purpose of this review is to illustrate how reporter genes can be used to map the brain's genetic activity in developmental time and anatomical space. The production of mutants in the homozygous condition may further lead to a morphological or behavioural phenotype. A knowledge of behavioural neuroscience can provide a prescreen of the reporter distribution and thereby make predictions concerning the type of behavioural analysis required. This approach allows selective cloning and sequencing of those genes which have either a morphological or behavioural phenotype but are transcribed at low levels. It is known that genomic imprinting influences brain development, and also that human genetic mutations and deletions influence imprinting in mental retardation as well as certain behavioural disorders. Precisely how such imprinted genes influence brain development and behaviour is being pursued by the use of chimeras. The distribution of maternal or paternal disomy cells in the brain and the way they influence behaviour may reveal the phenotype and how this is brought about.

Suppression of protein synthesis in the reperfused brain

BACKGROUND

Brain ischemia and reperfusion produce profound protein synthesis alterations, the extent and persistence of which are dependent on the nature of the ischemia, the brain region, the cell layer within a region, and the particular proteins studied. After transient ischemia, most brain regions recover their protein synthesis capability; however, recovery in the selectively vulnerable areas is poor. It is unknown whether this phenomenon itself provokes or is a consequence of the process of neuronal death.

SUMMARY OF REVIEW

Protein synthesis suppression during ischemia is due to energy depletion, but this is quickly reversed upon recirculation. Reperfusion does not appear to damage DNA or transcription mechanisms, although there are changes in the profile of transcripts being made. Similarly, purified ribosomes isolated from reperfused brains can make the normal repertoire of proteins and heat-shock proteins. However, during early reperfusion, newly synthesized messenger RNAs appear to accumulate in the nucleus; this alteration in RNA handling could reflect disruption at any of several steps, including posttranscriptional processing, nuclear pore transport, cytoskeletal binding, or formation of the translation initiation complex. Another mechanism that may be responsible for protein synthesis suppression during late reperfusion is progressive membrane destruction, with consequent shifts in the concentration of ions crucial for ribosomal function.

CONCLUSIONS

Protein synthesis suppression after ischemia likely involves a progression of multiple mechanisms during reperfusion. Although the recent work reviewed here offers new insight into the potential mechanisms disrupting protein synthesis, detailed understanding will require further investigation.

Genomic damage and its repair in young and aging brain

A brief review of the available information concerning age-related genomic (DNA) damage and its repair, with special reference to brain tissue, is presented. The usefulness of examining the validity of DNA-damage and repair hypothesis of aging in a postmitotic cell like neuron is emphasized. The limited number of reports that exist on brain seem to overwhelmingly support the accumulation of DNA damage with age. However, results regarding the age-dependent decline in DNA-repair capacity are conflicting and divided. The possible reasons for these discrepancies are discussed in light of the gathering evidence, including some human genetic disorders, to indicate how complex is the DNA-repair system in higher animals. It is suggested that assessment of repair potential of neurons with respect to a specific damage in a specific gene might yield more definitive answers about the DNA-repair process and its role in aging.

Brain non-adenylated mRNAs

Most eukaryotic messenger RNA (mRNA) species contain a 3'-poly(A) tract. The histone mRNAs are a notable exception although a subclass of histone-encoding mRNAs is polyadenylated. A class of mRNAs lacking a poly(A) tail would be expected to be less stable than poly(A)+ mRNAs and might, like the histones, have a half-life that varied in response to changes in the intracellular milieu. Brain mRNA exhibits an unusually high degree of sequence complexity; studies published ten years ago suggested that a large component of this complexity might be present in a poly(A)- mRNA population that was expressed postnatally. The question of the existence of a complex class of poly(A)- brain mRNAs is particularly tantalizing in light of the heterogeneity of brain cells and the possibility that the stability of these poly(A)- mRNAs might vary with changes in synaptic function, changing hormonal stimulation or with other modulations of neuronal function. The mRNA complexity analyses, although intriguing, did not prove the existence of the complex class of poly(A)- brain mRNAs. The observed mRNA complexity could have resulted from a variety of artifacts, discussed in more detail below. Several attempts have been made to clone members of this class of mRNA. This search for specific poly(A)- brain mRNAs has met with only limited success. Changes in mRNA polyadenylation state do occur in brain in response to specific physiologic stimuli; however, both the role of polyadenylation and de-adenylation in specific neuronal activities and the existence and significance of poly(A)- mRNAs in brain remain unclear.

Novel brain-specific bovine cDNA for a developmentally regulated mRNA encoding a putative new member of the leucine-rich glycoprotein (LRG) family

We have isolated a bovine cDNA which hybridized to a 2 kb mRNA specifically expressed in the rat and human brain. The mRNA was abundantly expressed in adult but not 21-week old human brain. In the rat brain, there was very little of the transcript in 15-day old fetus but it increased in abundance with development, being most abundant in the adult and expressed in all brain regions. Genomic analysis showed that the sequence is single copy and conserved in all vertebrates examined, including chicken. The 702 bp partial cDNA encoded an amino acid sequence for a putative member of the leucine-rich glycoprotein (LRG) family known to be involved in cell adhesion/recognition. The predicted polypeptide displayed sequence identity with that recently reported for the human oligodendrocyte-myelin glycoprotein. This cDNA should prove useful in further investigations on brain-specific cell-cell interactions.

In situ Hybridization demonstrates the stability of mRNA in post-mortem rat tissues

In situ hybridization was used to detect messenger RNA (mRNA) in a variety of rat tissues which were fixed in formalin either immediately after death or after a 24 h period of storage at 5 degrees C. A synthetic polydeoxythymidine [poly d(T)] oligonucleotide probe was used to demonstrate polyadenylated [poly (A)] mRNA in the small intestine, pancreas, liver, cerebellum, and pituitary. Of these tissues, only the liver showed a small reproducible reduction in hybridization signal following delayed fixation. Synthetic oligonucleotide probes complementary to albumin and pro-opiomelanocortin (POMC) mRNAs were hybridized to liver and pituitary, respectively. There was no significant reduction in hybridization signal in post-mortem tissues. The results suggest that some mRNAs may be remarkably stable under certain post-mortem conditions and this should encourage the wider application of in situ hybridization techniques to post-mortem material.

Alterations in brain polyribosomal RNA translation and lymphocyte proliferation in prenatal ethanol-exposed rats

The long-term effects of prenatal ethanol exposure on the properties of brain polysomes and the proliferative responses of lymphocytes to mitogenic stimulation in adult offspring were assessed. Female Sprague-Dawley rats either ingested the control or 6.6% ethanol-containing Lieber-DeCarli liquid diet during the 3rd trimester of pregnancy. Controls were age-matched and pair-fed. At 42 to 72 days of age, ethanol effects were evaluated on the (1) polysomal properties in the cerebral hemispheres, cerebellum, and hippocampal regions of the brain after translation in a messenger RNA (mRNA)-dependent rabbit reticulocyte lysate system and (2) immunologic functions of lymphocytes cultured from spleen cells by measuring their responses to mitogenic stimulation. Results showed long-term adverse effects of in utero ethanol exposure on the polysomal RNA translation in each of the three brain regions tested with free polysomal mRNAs affected more than the bound polysomal mRNAs. Of these, the hippocampal region appeared to sustain the most injurious effects. In addition, a suppression of the mitogen-induced lymphocyte proliferative responses were present under these conditions. The degree of suppression varied with the specific mitogen used. Data suggest that the ethanol effects on the CNS and lymphocyte proliferation are most possibly irreversible, and in the case of the CNS, a post-translational modification by ethanol is indicated. The reduced lymphocyte responses are suggestive of a possible interference by ethanol of the synthesis of interleukin-2 (IL-2) and/or a reduced binding of IL-2 with its receptor (IL-2 receptors).

Gene expression in cells of the central nervous system

This review summarized a part of our studies over a long period of time, relating them to the literature on the same topics. We aimed our research toward an understanding of the genetic origin of brain specific proteins, identified by B. W. Moore and of the high complexity of the nucleotide sequence of brain mRNA, originally investigated by W. E. Hahn, but have not completely achieved the projected goal. According to our studies, the reason for the high complexity in the RNA of brain nuclei might be the high complexity in neuronal nuclear RNA as described in the Introduction. Although one possible explanation is that it results from the summation of RNA complexities of several neuronal types, our saturation hybridization study with RNA from the isolated nuclei of granule cells showed an equally high sequence complexity as that of brain. It is likely that this type of neuron also contains numerous rare proteins and peptides, perhaps as many as 20,000 species which were not detectable even by two-dimensional PAGE. I was possible to gain insight into the reasons for the high sequence complexity of brain RNA by cloning the cDNA and genomic DNA of the brain-specific proteins as described in the previous sections. These data provided evidence for the long 3'-noncoding regions in the cDNA of the brain-specific proteins which caused the mRNA of brain to be larger than that from other tissues. During isolation of such large mRNAs, a molecule might be split into a 3'-poly(A)+RNA and 5'-poly(A)-RNA. In the studies on genomic DNA, genes with multiple transcription initiation sites were found in brain, such as CCK, CNP and MAG, in addition to NSE which was a housekeeping gene, and this may contribute to the high sequence complexity of brain RNA. Our studies also indicated the presence of genes with alternative splicing in brain, such as those for CNP, MAG and NGF, suggesting a further basis for greater RNA nucleotide sequence complexity. It is noteworthy that alternative splicing of the genes for MBP and PLP also produced multiple mRNAs. Such a mechanism may be a general characteristic of the genes for the myelin-specific proteins produced by oligodendrocytes. In considering the high nucleotide sequence complexity, it is interesting that MAG and S-100 beta genes etc. possess two additional sites for poly(A).(ABSTRACT TRUNCATED AT 400 WORDS)

Transforming growth factor-beta 1 (TGF-beta 1) expression and regulation in rat cortical astrocytes

Transforming growth factor-beta 1 (TGF-beta 1) is a potent modulator of immune and glial cells' functions and thus, could play an important role in neuro-immune interaction. However, published reports disagree on whether or not TGF-beta 1 is expressed in normal brain. We demonstrate here the constitutive expression of TGF-beta 1 mRNA but not protein in both cerebral cortex and primary rat cortical astrocytes. Steady-state TGF-beta 1 mRNA level increased 2-fold in adult compared to neonatal cortex and during proliferation and differentiation of astrocytes in primary culture. This response was not accompanied by the appearance of detectable TGF-beta protein either in vivo or in vitro. However, both intracellular immunoreactive TGF-beta and extracellular TGF-beta 1 activity were detected upon in vitro stimulation of astrocytes with interleukin-1 (IL-1). The extracellular TGF-beta 1 increased with time of exposure to and concentration of IL-1. In contrast, the amount of TGF-beta 1 mRNA remained unchanged during stimulation of astrocytes with IL-1. These results suggest that the production of TGF-beta 1 in astrocytes is regulated at both mRNA and protein levels. The former may occur during astrocytic development, and the latter during astrocytic response to injury in association with elevation of IL-1.

Isolation and characterization of a library of cDNA clones that are preferentially expressed in the embryonic telencephalon

In order to isolate genes involved in development of the mammalian telencephalon we employed an efficient cDNA library procedure. By subtracting an adult mouse telencephalic cDNA library from an embryonic day 15 (E15) mouse telencephalic cDNA library we generated two subtracted libraries (ES1 and ES2). We estimate that ES1 contains between 200 and 600 different cDNA clones, which approximates the number of genes that are preferentially expressed in the E15 telencephalon, compared to the adult telencephalon. Northern analysis of 20 different cDNA clones shows that 14 of these are expressed at least 5-fold more in the E15 telencephalon than the adult telencephalon. Limited sequencing of the 14 differentially expressed clones reveals that 10 have no significant identity to sequences in GenBank and EMBL databases, whereas the other 4 have significant sequence identity to vimentin, histone 3.3, topoisomerase I and the B2 repeat element. In situ hybridization using one of the differentially expressed cDNAs, TES-1, demonstrates that it is transiently expressed in the anlage of the basal ganglia. In situ hybridization with another differentially expressed cDNA clone, TES-4, shows that it is specifically expressed in differentiating cells of the neural axis with a distinctive rostral-caudal temporal pattern. These findings, and the methods that we have developed, provide a framework for future investigations of the genetic control of telencephalon development.

Regional and neuronal reductions of polyadenylated messenger RNA in Alzheimer's disease

Messenger RNA (mRNA) is the key intermediate in the gene expression pathway. The amount of mRNA in Alzheimer's disease (AD) brains has been determined using in situ hybridization histochemistry (ISHH) to detect the poly(A) tails of polyadenylated mRNA (poly(A) + mRNA). On a regional basis, AD cases had significantly less poly(A) + mRNA than controls in hippocampus (field CA3) and cerebellum (granule cell layer). Analysis of constituent pyramidal neurons showed mean reductions per cell within AD hippocampus (field CA3) and temporal cortex, but not in visual cortex. Similar changes were seen in a small group of non-AD dementias. The finding of reduced poly(A) + mRNA content is another indication of the altered brain gene expression occurring in AD. It is proposed that measurement of poly(A) + mRNA may be valuable in identifying functionally impaired neuronal populations. The methodology also provides a means by which changes in the quantitative distribution of individual mRNAs can be determined relative to that of poly(A) + mRNA as a whole.

Cloning of non-polyadenylated RNAs from rat brain

Rodent brain has been reported to contain a fraction of non-polyadenylated (poly(A)-) mRNA that includes about 100,000 different sequences, most of which are not found in the poly(A)+ fraction. We have prepared a cDNA library of low-abundance poly(A)- RNAs from rat brain polysomes, and have characterized three clones in detail. Two of the clones hybridize on Northern blots to poly(A)+ RNAs from brain. Dot blot hybridization and RNase protection assays demonstrate that although the bulk of the RNA complementary to these clones is present in the poly(A)- fraction, a small portion (7-21%) is present in the poly(A)+ fraction. Our results suggest that the poly(A)-mRNA fraction from rat brain may not contain sequences that are different from those in the poly(A)+ fraction.

Gene expression in different cell types of aging rat brain

"Bound" and "free" RNA polymerase activities were assessed in the nuclear fraction of cerebral cortical, neuronal, astroglial, and oligodendroglial cells obtained from rats of young, adult, and old ages. Significant decreases in both the bound and free polymerase II activities were noticed in old brain, as compared to adult brain, in neuronal and oligodendroglial nuclei. In astroglia, only the free polymerase II was found to be affected. No effect of aging could be seen on the activity of bound RNA polymerase I + III. The free RNA polymerase I + III activity was increased from adult to old age in neuronal nuclei, but unchanged in oligodendroglial and astroglial nuclei. The age-dependent reduction in RNA polymerase II was maximum in oligodendroglial cells, whereas it was least, although still significant, in neuronal cells. DNA isolated from old brain was unable to enhance the transcriptional activity when added to chromatin preparations obtained from rat brains of any of the above ages and the "old" chromatin was unable to accept even the "young" DNA as additional exogenous template. It is concluded that the reduced gene expression noticed in old brain nuclei is due to both altered chromatin/DNA structure and inadequate levels of free RNA polymerase II.

A position-dependent transgene reveals patterns of gene expression in the developing brain

We have made a detailed analysis of the developing mouse brain using a transgene (HSVtk-lacZ), whose expression is dependent on its unique site of integration. The position-dependent transgene expression defines a novel pattern of gene expression in the developing mouse brain. The transgene is first transcribed on day 10 of gestation in a small cluster of cells in the developing hind brain. Extensive expression is subsequently seen in a number of developing brain structures (cortex, cerebellum, hippocampus), but postnatally this becomes restricted to cell types within distinct anatomical foci principally associated with the olfactory system. Expression in the olfactory system is maintained even into adulthood. Hence, the expression of this transgene is confined to cell types which are known from other studies to sustain developmental plasticity in embryos and in adults. It will be of interest to analyse the transgene pre-integration site and determine if endogenous genes at this locus are also expressed in these cells and if they have a role in maintaining their developmental potential.

Use of avidin-biotin subtractive hybridization to characterize mRNA common to neurons destroyed by the selective neurotoxicant trimethyltin

Trimethyltin (TMT), a selective neurotoxicant, destroys a distinct subpopulation of neurons which possess no known biochemical or anatomic linkage. However, TMT-sensitive neurons may share common gene products related to susceptibility. In an effort to isolate mRNAs common to TMT-sensitive neurons, avidin/biotin based-subtractive hybridization was used to generate a cDNA library specifically related to TMT-toxicity. Out of 50 cDNAs, two clones hybridized only to poly(A+) mRNA isolated from the brains of saline-treated rats. Two of these cDNAs, p9T10 and p9T19, were used for in situ hybridization; both hybridized to hippocampus, limbic cortex, amygdala and other regions destroyed by TMT, suggesting that these probes identified mRNA enriched in TMT-sensitive neurons. The patterns of in situ hybridization coupled with the loss of p9T10 and p9T19 hybridization to mRNA isolated from the brains of TMT-treated rats suggests that one or both of these two clones may represent mRNA found in neurons damaged by TMT. The combination of selective neurotoxic lesions followed by cDNA subtractive hybridization should prove to be a useful strategy for the isolation of gene products from specific neuronal populations.

Low-abundance 32-kilodalton nuclear protein specifically enriched in the central nervous system

Recently, a low-abundance nuclear protein, p32/6.3, has been identified in brain tissue (Egle and Shelton: Journal of Biological Chemistry 261:2294-2298, 1986). Using a Western blot procedure, we describe its distribution in the nervous system, determine its relative enrichment in brain versus liver, kidney, and certain other tissues, and describe an isolation procedure from brain. Selective enrichment occurs in basal ganglia, diencephalon, hippocampus, cerebellum, brainstem, spinal cord, and cerebral cortex but not in retina, dorsal root ganglia, and sympathetic ganglia. Thus, enrichment is limited to areas of the central nervous system. p32/6.3 appears to be preferentially enriched in neurons, because in bulk-isolated fractions from rat grey matter it is more abundant in neuron-enriched fractions than in astrocyte-enriched fractions. p32/6.3 is approximately 20-fold more concentrated in an insoluble nuclear protein or matrix fraction from forebrain than from kidney, liver, adrenal gland, or retina. This degree of enrichment is an ancient trait, detectable in the chicken as well as mammals.

Poly(A) metabolism and aging: a current view

Polyadenylation of mRNA is a key step in post-transcriptional control of gene expression. Therefore, age-dependent changes in poly(A) synthesis have to play a crucial role in the course of cellular aging. In this review, the importance of the signal sequence, poly(A), in determining mRNA stability and intracellular distribution of mRNA during aging is discussed.

Genes expressed in cortical neurons--chromatin conformation and DNase I hypersensitive sites

DNase I sensitivity experiments were performed utilizing DNA probes to genes which are either transcribed in rat cortical neurons (the 68 kDa neurofilament gene and the neuron-specific enolase gene) or are transcriptionally silent (albumin). Results suggest that unlike liver, in which a hierarchy in chromatin conformation exists between transcribed and nontranscribed genes, the majority of protein coding sequences in cortical neurons may be relatively sensitive to nuclease digestion. This supports our previous observation of an increased DNase I sensitivity of total chromatin in cortical neurons. Nuclease sensitivity experiments also revealed the presence of brain-specific DNase I hypersensitive sites associated with the two neuron-specific genes.

In situ transcription: specific synthesis of complementary DNA in fixed tissue sections

A technique, in situ transcription, is described, in which reverse transcription of mRNAs is achieved within fixed tissue sections. An oligonucleotide complementary to proopiomelanocortin (POMC) mRNA was used as a primer for the specific synthesis of radiolabeled POMC cDNA in fixed sections of rat pituitary, thus permitting the rapid anatomical localization of POMC mRNA by autoradiography. Intermediate lobe signal intensities were sensitive to dopaminergic drugs, demonstrating that the method can be used for studies of mRNA regulation. The transcripts may also be eluted from tissue sections for a variety of uses, including the identification and cloning of autoradiographically localized cDNAs from small amounts of tissue.