The 3' untranslated region of the new rat synaptic vesicle protein 2B mRNA transcript inhibits translational efficiency

All-or-(N)One - an epistemological characterization of the human tumorigenic neuronal paralogous FAM72 gene loci

FAM72 is a novel neuronal progenitor cell (NPC) self-renewal supporting protein expressed under physiological conditions at low levels in other tissues. Accumulating data indicate the potential pivotal tumourigenic effects of FAM72. Our in silico human genome-wide analysis (GWA) revealed that the FAM72 gene family consists of four human-specific paralogous members, all of which are located on chromosome (chr) 1. Unique asymmetric FAM72 segmental gene duplications are most likely to have occurred in conjunction with the paired genomic neighbour SRGAP2 (SLIT-ROBO Rho GTPase activating protein), as both genes have four paralogues in humans but only one vertebra-emerging orthologue in all other species. No species with two or three FAM72/SRGAP2 gene pairs could be identified, and the four exclusively human-defining ohnologues, with different mutation patterns in Homo neanderthalensis and Denisova hominin, may remain under epigenetic control through long non-coding (lnc) RNAs.

Characterizing the new transcription regulator protein p60TRP

Active cell death ('apoptosis' or 'programmed cell death') is essential in the development and homeostasis of multicellular organisms and abnormal inhibition of apoptosis is an indicator of cancer and autoimmune diseases, whereas excessive cell death might be implicated in neurodegenerative disorders such as Alzheimer's disease (AD). Using bioinformatics-, Western-blotting-, yeast-two-hybrid-system-, polymerase chain reaction (PCR)-, and fluorescence microscopy-analyses, we demonstrate here that the neuroprotective protein p60TRP (p60-transcription-regulator-protein) is a basic helix-loop-helix (bHLH) domain-containing member of a new protein family that interacts with the Ran-binding-protein-5 (RanBP5) and the protein-phosphatase-2A (PP2A). The additional findings of its influence on NNT1 and p48ZnF (new-neurotrophin-1, p48-zinc-finger-protein)-signaling and its down-regulation in the brain of AD subjects point to a possible pivotal role of p60TRP in the control of cellular aging and survival.

Glutathione S-transferase 8-8 expression is lower in alcohol-preferring than in alcohol-nonpreferring rats

OBJECTIVE

A primary focus of alcohol research is to provide novel targets for alcohol treatment by identifying genes that predispose individuals to drink alcohol. Animal models of alcoholism developed by selective breeding are invaluable tools to elucidate both the genetic nature and the underlying biological mechanisms that contribute to alcohol dependence. These selected lines (high alcohol preferring and low alcohol preferring) display phenotypic and genetic differences that can be studied to further our understanding of alcohol preference and related genetic traits. By combining molecular techniques, genetic and physiological factors that underlie the cause of alcoholism can be identified.

METHODS

Total gene expression analysis was used to identify genes that are differentially expressed in specific brain regions between alcohol-naive, inbred alcohol-preferring (iP) and -nonpreferring (iNP) rats. Quantitative reverse transcriptase-polymerase chain reaction, in situ hybridization, Western blot, and sequence analysis were used to further characterize rat glutathione S-transferase 8-8 (rGST 8-8).

RESULTS

Lower expression of rGST 8-8 mRNA was observed in discrete brain regions of iP compared with iNP animals, and these expression differences were confirmed. To determine additional expression patterns of rGST 8-8, we used in situ hybridization. Rat GST 8-8 was highly expressed in hippocampus, the choroid plexus of the dorsal third ventricle and the lateral ventricle, and ependymal cells along the dorsal third ventricle and the third ventricle. Western blot analysis showed that rGST 8-8 protein levels were lower in the hippocampus and the amygdala of iP compared with iNP. A silent single-nucleotide polymorphism in the coding region and three single-nucleotide polymorphisms in the 3'-UTR were identified in the rGST 8-8 cDNA.

CONCLUSION

There is regional variation of rGST 8-8 expression in the brain, at both the mRNA and protein level, and the iP strain has lower innate rGST 8-8 levels than the iNP strain in discrete brain regions.

Structure and expression of the murine calcyon gene

Calcyon was recently identified as a D1 dopamine receptor (DR1) interacting protein. Previous studies show that calcyon can potentiate DR1 mediated intracellular Ca(2+) release in transfected HEK293 cells, and may play an important role in DR1 Ca(2+) signaling in brain. We report that similar to the genomic structure of the human gene, the mouse calcyon gene contains six relatively short exons, with a large intron (about 8.4 kb) between exons one and two. The mouse and human calcyon genes exhibit a high level of sequence homology (77.5% at the nucleotide level) within coding regions. Northern blot and RT-PCR analyses reveal that mouse calcyon transcripts are most abundant in brain, but also present in testis and ovary, as well as in kidney and heart at much lower levels. The most distal of the transcript initiation sites identified by 5' RACE is located 159 nucleotides upstream of the putative start of translation. BLAST search of the NCBI mouse EST database and RT-PCR analysis uncovered two differentially spliced transcripts, "mcal-A" and "mcal-B." The two transcripts are identical, except that mcal-B contains a longer 3' untranslated region due to retention of a short intron (I5) between exons five and six. However, mcal-A represents the predominant calcyon transcript in mouse tissue. Further, the presence of I5 produced no detectable differences in the biosynthesis of calcyon polypeptide when expressed in HEK293, MDCK and Neuro2a cells.

Comparative gene identification-94--a pivotal regulator of apoptosis

Apoptosis is an active form of cell death that is carried out by proteins that are designed to kill the cell during normal mammalian development and tissue homeostasis. Cell death by apoptosis comprises a sequence of events leading to the activation of caspases which execute the fragmentation of the cellular protein and DNA leading to disintegration of the cell. This physiological neuronal apoptosis allows the nervous system to eliminate excess neurons. In addition, apoptotic cell death occurs in a variety of neuronal degeneration such as Alzheimer's disease. Here we describe second mitochondria-derived activator of caspases/Diablo as a new interacting protein of CGI-94 (comparative gene identification-94) which itself is probably involved in degenerative processes of Alzheimer's disease. Our findings that CGI-94 interacts with second mitochondria-derived activator of caspases/Diablo, inhibits nerve growth factor-induced neurite outgrowth and that its neuronal expression leads to cell death point to its pivotal role in the control of cellular survival. In conclusion, CGI-94 appears to be involved in processes of neuronal degeneration.

alpha-Synuclein maps to a quantitative trait locus for alcohol preference and is differentially expressed in alcohol-preferring and -nonpreferring rats

Total gene expression analysis (TOGA) was used to identify genes that are differentially expressed in brain regions between the alcohol-naive, inbred alcohol-preferring (iP), and -nonpreferring (iNP) rats. alpha-Synuclein, expressed at >2-fold higher levels in the hippocampus of the iP than the iNP rat, was prioritized for further study. In situ hybridization was used to determine specific brain regions and cells expressing alpha-synuclein in the iP and iNP rats. Similar to alpha-synuclein mRNA levels, protein levels in the hippocampus were higher in iP rats than iNP rats. Higher protein levels were also observed in the caudate putamen of iP rats compared with iNP rats. Sequence analysis identified two single nucleotide polymorphisms in the 3' UTR of the cDNA. The polymorphism was used to map the gene, by using recombination-based methods, to chromosome 4, within a quantitative trait locus for alcohol consumption that was identified in the iP and iNP rats. A nucleotide exchange in the iNP 3' UTR reduced expression of the luciferase reporter gene in SK-N-SH neuroblastoma cells. These results suggest that differential expression of the alpha-synuclein gene may contribute to alcohol preference in the iP rats.