Determinants of expression variability

The amount of tissue-specific expression variability (EV) across individuals is an essential characteristic of a gene and believed to have evolved, in part, under functional constraints. However, the determinants and functional implications of EV are only beginning to be investigated. Our analyses based on multiple expression profiles in 41 primary human tissues show that a gene’s EV is significantly correlated with a number of features pertaining to the genomic, epigenomic, regulatory, polymorphic, functional, structural and network characteristics of the gene. We found that (i) EV of a gene is encoded, in part, by its genomic context and is further influenced by the epigenome; (ii) strong promoters induce less variable expression; (iii) less variable gene loci evolve under purifying selection against copy number polymorphisms; (iv) genes that encode inherently disordered or highly interacting proteins exhibit lower variability; and (v) genes with less variable expression are enriched for house-keeping functions, while genes with highly variable expression tend to function in development and extra-cellular response and are associated with human diseases. Thus, our analysis reveals a number of potential mediators as well as functional and evolutionary correlates of EV, and provides new insights into the inherent variability in eukaryotic gene expression.     

The renal Na+/Ca2+ exchange system is located exclusively in the distal tubule.

The movement of Ca2+ across the basolateral plasma membrane was determined in purified preparations of this membrane isolated from rabbit proximal and distal convoluted tubules. The ATP-dependent Ca2+ uptake was present in basolateral membranes from both these tubular segments, but the activity was higher in the distal tubules. A very active Na+/Ca2+ exchange system was also demonstrated in the distal-tubular membranes, but in proximal-tubular membranes this exchange system was not demonstrable. The presence of Na+ outside the vesicles gradually inhibited the ATP-dependent Ca2+ uptake in the distal-tubular-membrane preparations, but remained without effect in those from the proximal tubules. The activity of the Na+/Ca2+ exchange system in the distal-tubular membranes was a function of the imposed Na+ gradient. These results suggest that the major differences in the characteristics of Ca2+ transport in the proximal and in the distal tubules are due to the high activity of a Na+/Ca2+ exchange system in the distal tubule and its virtual absence in the proximal tubule.     

Specificity of tyrosine protein kinases of the structurally related receptors for insulin and insulin-like growth factor I: Tyr-containing synthetic polymers as specific inhibitors or substrates

The receptors for insulin and insulin-like growth factor (IGF) I are structurally similar transmembrane proteins. Ligand binding to the extracellular domain of the receptor stimulates its cytoplasmic tyrosine protein kinase which phosphorylates its own beta subunit as well as exogenous substrates. It is believed, from several lines of evidence, that tyrosine-specific protein kinases are mediating some or all of the actions of insulin (or IGF-I). In order to gain insights into the substrate specificity of the structurally related insulin and IGF-I receptor kinases, we have studied the action of highly purified receptors isolated from human placental membranes. Present studies using selected tyrosine-containing polymers have revealed: (i) Polymers such as (Y,A,E)n and (Y-A-E)n inhibit beta subunit autophosphorylation and exogenous substrate phosphorylation by autophosphorylated receptors. (ii) Insulin receptor kinase is at least 10 times more sensitive to these inhibitors than IGF-I receptor kinase. (iii) (Y-A-E)n is approximately 8 times more potent an inhibitor than (Y,A,E)n toward both receptors. (iv) While (E4,Y1)n and (E6,A3,Y1)n are good substrates for both receptor kinases, the ratio of phosphate incorporation into the former to the latter is characteristically high (approximately 4) for the IGF-I receptor and low (approximately 1) for the insulin receptor. These results imply that the substrate specificity and enzymatic action of these two receptor kinases are distinct.     

Cloning of a cDNA encoding the smallest neurofilament protein from the rat

We have cloned a cDNA coding for the smallest rat neurofilament protein. The cDNA is 861 nucleotides long coding for 287 amino acids from the internal alpha-helical region and the carboxy-terminal tail domain of the neurofilament protein. Comparison of the porcine, mouse and rat neurofilament protein sequences shows that the protein is highly conserved (greater than 93% identity). Blot analysis indicates that the cDNA is derived from a single neurofilament gene that codes for two different poly(A)+ mRNA species.     

Spatial phase and frequency in motion capture of random-dot patterns

A square matrix of spots (A) was presented in rapid alternation with an uncorrelated matrix (B). If the square arrays are superimposed spatially one sees random incoherent motion. However, incoherent motion was seen only if the outer edges were exactly aligned. If the outline of matrix A is shifted horizontally by 1 degree in relation to B, then the edges are seen to oscillate to and fro. Surprisingly, all the dots in the matrix were seen to 'adhere' to the edges and to move horizontally (Ramachandran, 1981). We then aligned the edges again to produce incoherent motion and superimposed a sine-wave grating on the pattern. If the grating was moved horizontally then all the spots 'adhered' to it and moved horizontally as well. This illusion ('motion capture') was optimal (a) at a 90 degrees spatial phase shift of the grating; (b) at low spatial frequencies (less than 0.5 cycles); and (c) when the grating was alternated in step with the dot patterns. Density modulated gratings were just as effective. We conclude that the unambiguous motion signal derived from the grating is applied spontaneously to the dots as well.     

Amino acid sequence of retinal transducin at the site ADP-ribosylated by cholera toxin

Transducin was [32P]ADP-ribosylated by cholera toxin in bovine retinal rod outer segments and then partially purified on omega-amino octyl agarose to remove other ADP-ribosylated proteins. Trypsin digestion of the ADP-ribosylated transducin and further purification using boronate-polyacrylamide beads and high performance liquid chromatography yielded a single radiolabeled tetrapeptide, Ser-Arg-Val-Lys. The ADP-ribose is linked to the guanidinium group of arginine.