Isolation of a library of target-sites for sequence specific DNA binding proteins from chick embryonic heart: a potential tool for identifying novel transcriptional regulators involved in embryonic development

Enormity of the metazoan genomes and divergence in their regulation impose a serious constraint on the comprehensive understanding of context specific gene regulation. DNA elements located in the promoter, enhancer, and other regulatory regions of the genome dictate the temporal and spatial patterns of gene activities. However, owing to the diminutive and variable nature of the regulatory DNA elements, their identification and location remains a major challenge. We have developed an efficient strategy for isolating a repertoire of target sites for sequence specific DNA binding proteins from embryonic chick heart. A comprehensive library of such sequences was constructed and authenticated using various parameters including in silico determination of functional binding sites. This approach, therefore, for the first time, established an experimental and conceptual framework for defining the entire repertoire of functional DNA elements in any cellular context.     

A soluble and active form of Wnt-3a protein is involved in myogenic differentiation after cholesterol depletion

Cholesterol is one of the major lipids of plasma membranes. Recently, we have shown that cholesterol depletion by methyl-beta-cyclodextrin (M beta CD) induces the activation of the Wnt/beta-catenin pathway and enhances myogenic differentiation. Here, we show that M beta CD-conditioned media accelerates myogenesis in a similar way as M beta CD does, suggesting that the effects induced by M beta CD could be caused by soluble factors present in the culture medium. Soluble Wnt-3 protein is significantly enhanced in M beta CD-conditioned medium. Wnt-3a-enriched media induces myogenesis as much as M beta CD does, whereas Wnt-5a-enriched media inhibits. We suggest that Wnt-3a is involved in the myogenic induction observed after cholesterol depletion.     

The conserved Ala37 in the ERF/AP2 domain is essential for binding with the DRE element and the GCC box

Four AP2/EREBP genes encoding putative ethylene-responsive element binding factor (ERF)/AP2 domains were cloned from Brassica napus, and these genes could be induced by low temperature, ethylene, drought, high salinity, abscisic acid and jasmonate treatments. These four genes, named BnDREBIII-1 to BnDREBIII-4, were highly homologous and the 37th amino acid was the only difference among their ERF/AP2 domains. BnDREBIII-1 was demonstrated to be able to bind to both dehydration-responsive element and the GCC box and transactivate the expression of downstream genes, while BnDREBIII-4 could bind neither. Further results suggested that Ala37 might play a crucial role in the DNA binding or the stability of the ERF/AP2 domain.     

Molecular and structural analysis of C4-specific PEPC isoform from Pennisetum glaucum plays a role in stress adaptation

As an activator of adenylate cyclase, the neuropeptide Pituitary Adenylate Cyclase Activating Peptide (PACAP) impacts levels of cyclic AMP, a key second messenger available in brain cells. PACAP is involved in certain adult behaviors. To elucidate PACAP interactions, a compendium of microarrays representing mRNA expression in the adult mouse whole brain was pooled from the Phenogen database for analysis. A regulatory network was computed based on mutual information between gene pairs using gene expression data across the compendium. Clusters among genes directly linked to PACAP, and probable interactions between corresponding proteins were computed. Database “experts” affirmed some of the inferred relationships. The findings suggest ADCY7 is probably the adenylate cyclase isoform most relevant to PACAP's action. They also support intervening roles for kinases including GSK3B, PI 3-kinase, SGK3 and AMPK. Other high-confidence interactions are hypothesized for future testing. This new information has implications for certain behavioral and other disorders.