Studies by DNA-RNA hybridization of transcriptional diversity in human brain

A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17

We report progress assembling the parts list for chromosome 17 and illustrate the various processes that we have developed to integrate available data from diverse genomic and proteomic knowledge bases. As primary resources, we have used GPMDB, neXtProt, PeptideAtlas, Human Protein Atlas (HPA), and GeneCards. All sites share the common resource of Ensembl for the genome modeling information. We have defined the chromosome 17 parts list with the following information: 1169 protein-coding genes, the numbers of proteins confidently identified by various experimental approaches as documented in GPMDB, neXtProt, PeptideAtlas, and HPA, examples of typical data sets obtained by RNASeq and proteomic studies of epithelial derived tumor cell lines (disease proteome) and a normal proteome (peripheral mononuclear cells), reported evidence of post-translational modifications, and examples of alternative splice variants (ASVs). We have constructed a list of the 59 "missing" proteins as well as 201 proteins that have inconclusive mass spectrometric (MS) identifications. In this report we have defined a process to establish a baseline for the incorporation of new evidence on protein identification and characterization as well as related information from transcriptome analyses. This initial list of "missing" proteins that will guide the selection of appropriate samples for discovery studies as well as antibody reagents. Also we have illustrated the significant diversity of protein variants (including post-translational modifications, PTMs) using regions on chromosome 17 that contain important oncogenes. We emphasize the need for mandated deposition of proteomics data in public databases, the further development of improved PTM, ASV, and single nucleotide variant (SNV) databases, and the construction of Web sites that can integrate and regularly update such information. In addition, we describe the distribution of both clustered and scattered sets of protein families on the chromosome. Since chromosome 17 is rich in cancer-associated genes, we have focused the clustering of cancer-associated genes in such genomic regions and have used the ERBB2 amplicon as an example of the value of a proteogenomic approach in which one integrates transcriptomic with proteomic information and captures evidence of coexpression through coordinated regulation.

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.

Analysis of brain and pituitary RNA metabolism: a review of recent methodologies

Recent characterization of brain and pituitary RNA metabolism is reviewed. Relative to other tissues, the brain transcribes more of the unique, single-copy DNA. This transcriptional diversity reflects the inherent heterogeneity in organization and development of the brain. The end product of transcriptional regulation in the brain is a population of functional cytoplasmic mRNAs with multiple components, differing in complexity and abundance. Analysis of nuclear and cytoplasmic RNA provides evidence that both brain-specific synthesis and processing may determine the final mRNA population. Both polyadenylated and non-polyadenylated RNA classes contribute significantly to the total brain polysomal mRNA fraction. Characterizations of individual species of mRNA from both brain and pituitary are described. One possible transcriptional modulator in both the pituitary and brain is the presence of steroid hormone at responsive sites. Functional consequences of steroid accumulation within the brain may be (1) interactions with neurotransmitter, especially catecholamine, metabolism and function, (2) developmental interactions with neuronal systems, and (3) differentiation of glial cell function. The pleiotropic nature of steroid hormone effects (both transcriptional and non-transcriptional) within one brain region is considered by examining the biochemical effects of glucocorticoids in the hippocampus.

Analysis of messenger RNA coding for S100 protein in the mammalian brain

S100 protein is a brain-specific protein which is absent at birth and first appears in rabbit brain 2-3 days after birth. To determine how the synthesis of this brain-specific protein is regulated, mRNA was isolated from brain polysomes and assayed for S100 protein mRNA activity by in vitro translation in a heterologous cell-free system and immunoprecipitation of released polypeptides with rabbit anti-S100 protein antiserum. S100 protein mRNA was detected primarily in small polysomes containing five to eight ribosomes, and virtually no S100 protein mRNA was present in polysomes containing more than eight ribosomes. S100 protein mRNA was not detected in brain polysomes at stages prior to the induction of synthesis of S100 protein, i.e., in fetal brain or in 1-day neonates. The amount of S100 protein mRNA in polysomes of the cerebral cortex and cerebellum was measured to see if it correlated with the level of S100 protein in the two regions of adult brain. The cerebellum, which contained three to four times the level of S100 protein in the cerebral cortex, contained four times more S100 protein mRNA.

Fate of mRNA following disaggregation of brain polysomes after administration of (+)-lysergic acid diethylamide in vivo

Intravenous injection of (+)-lysergic acid diethylamide into young rabbits induced a transient brain-specific disaggregation of polysomes to monosomes. Investigation of the fate of mRNA revealed that brain poly(A+)mRNA was conserved. In particular, mRNA coding for brain-specific S100 protein was not degraded, nor was it released into free ribonucleoprotein particles. Following the (+)-lysergic acid diethylamide-induced disaggregation of polysomes, mRNA shifted from polysomes and accumulated on monosomes. Formation of a blocked monosome complex, which contained intact mRNA and 40-S plus 60-S ribosomal subunits but lacked nascent peptide chains, suggested that (+)-lysergic acid diethylamide inhibited brain protein synthesis at a specific stage of late initiation or early elongation.

Coordinate transcription within families of related DNA sequences in human colon and rat liver

An assay has been developed to determine the fraction of members of active families of related base sequences which are being transcribed into RNA. In normal human colon mucosa and in normal rat liver, essentially all members of the active families are being transcribed.

Analysis of rabbit brain polysomal poly (A+) mRNA by DNA excess hybridization

DNA sequence representation in rabbit brain mRNA was examined by DNA excess hybridization. purified polysomal poly (A+) mRNA was labeled in vitro with [3H] dimethyl sulfate and reacted at DNA: RNA ratios of 5000 : 1 and 30 000 : 1. Poly(A+) mRNA hybridizied mainly to nonrepeated DNA with a smaller kinetic component which was complementary to repeated DNA sequences. The latter component was not due to nuclear or ribosomal RNA contamination. Poly(A-) RNA purified from brain polysomes hybridized to excess DNA as a single repeated component. Thermal denaturation profiles of the RNA - DNA hybrids indicated a high degree of fidelity in base pairing.

The genetics, if any, of infantile autism and childhood schizophrenia

A critical examination of the data for and against genetic factors in early infantile autism and childhood schizophrenia is presented. The extreme rareness of both disorders made analysis difficult. No strong evidence exists implicating genetics in the development of childhood psychoses that begin before the age of 5. Family pedigree data fail to support psychogenic transmission because very few siblings of early onset cases are affected. Biological but not genetic etiological agents are more likely. Genetic factors are implicated in the development of psychoses that begin near pubescence and such factors appear to overlap with those for adult schizophrenia. Reevaluation of the minimum age of onset for adult-type schizophrenia is suggested.

Synthesis of the brain-specific S-100 protein in a cell-free system from wheat embryo programmed with poly(A)-containing RNA from rabbit brain

Polyadenylated polysomal RNA was prepared from rabbit cerebral hemispheres using phenol extraction and chromatography on oligo(dT)-cellulose. This RNA directed the synthesis of the brain-specific S-100 protein in cell-free extracts from wheat embryo. S-100 protein was absent from the products of endogenous incorporation and from a reaction programmed with kidney mRNA. These results suggest that S-100 protein mRNA contains a poly(adenylic acid) sequence and rule out the necessity of a brain-specific factor for translation of -S100 protein mRNA.

RNA synthesis in isolated brian nuclei after administration of d-lysergic acid diethylamide (LSD) in vivo

RNA synthesis in isolated brain nuclei was analyzed 2.5 hr after the intravenous administration of d-lysergic acid diethylamide (LSD) to young rabbits. The drug stimulated transcription by 54% in brain stem nuclei and by 13% in cerebral hemisphere nuclei expressed over saline controls. Both nucleoplasmic and nucleolar RNA synthesis were increased. The main activity in the isolated nuclei assay was due to nucleoplasmic RNA polymerase, since alpha-amanitin reduced synthesis by over 70% in either drug or control treatments.