Abstract Long non-coding RNAs have emerged as highly versatile players in the regulation of gene expression in development and human disease, particularly cancer. Hundreds of lncRNAs become ...dysregulated across tumor types, and multiple lncRNAs have demonstrated functions as tumor-suppressors or oncogenes. Furthermore, studies have demonstrated that dysregulation of lncRNAs results in alterations of the epigenome in cancer cells, potentially providing a novel mechanism for the massive epigenomic alterations observed in many tumors. Here, we highlight and provide some illustrious examples of lncRNAs in various epigenetic regulatory processes, including coordination of chromatin dynamics, regulation of DNA methylation, modulation of other non-coding RNAs and mRNA stability, and control of epigenetic substrate availability through altered tumor metabolism. In light of all these known and emerging functions in epigenetic regulation of tumorigenesis and cancer progression, lncRNAs represent attractive targets for future therapeutic strategies in cancer.
A remarkable Pd-catalyzed diamination of unactivated alkenes using N-fluorobenzenesulfonimide (NFBS) as an aminating reagent is described. The reaction occurs in an intra/intermolecular fashion, ...incorporating one nitrogen donor from the substrate and the other from the NFBS, thereby generating cyclic diamine derivatives in a single step. The products are differentially protected at both nitrogens, allowing for maximal synthetic flexibility. The intermediacy of the Pd(IV) species is proposed to be responsible for the unusual reactivity of NFBS.
Messenger RNA (mRNA) degradation plays a critical role in regulating transcript levels in the cell and is a major control point for modulating gene expression. In yeast and other model organisms, ...codon identity is a powerful determinant of transcript stability, contributing broadly to impact half-lives. General principles governing mRNA stability are poorly understood in mammalian systems. Importantly, however, the degradation machinery is highly conserved, thus it seems logical that mammalian transcript half-lives would also be strongly influenced by coding determinants. Herein we characterize the contribution of coding sequence towards mRNA decay in human and Chinese Hamster Ovary cells. In agreement with previous studies, we observed that synonymous codon usage impacts mRNA stability in mammalian cells. Surprisingly, however, we also observe that the amino acid content of a gene is an additional determinant correlating with transcript stability. The impact of codon and amino acid identity on mRNA decay appears to be associated with underlying tRNA and intracellular amino acid concentrations. Accordingly, genes of similar physiological function appear to coordinate their mRNA stabilities in part through codon and amino acid content. Together, these results raise the possibility that intracellular tRNA and amino acid levels interplay to mediate coupling between translational elongation and mRNA degradation rate in mammals.
The Diels-Alder reaction is a cornerstone in organic synthesis, forming two carbon-carbon bonds and up to four new stereogenic centers in one step. No naturally occurring enzymes have been shown to ...catalyze bimolecular Diels-Alder reactions. We describe the de novo computational design and experimental characterization of enzymes catalyzing a bimolecular Diels-Alder reaction with high stereoselectivity and substrate specificity. X-ray crystallography confirms that the structure matches the design for the most active of the enzymes, and binding site substitutions reprogram the substrate specificity. Designed stereoselective catalysts for carbon-carbon bond-forming reactions should be broadly useful in synthetic chemistry.
Mechanistic studies of the intramolecular hydroamination of unactivated aminoalkenes catalyzed by a dicationic bis(diphenylphosphinomethyl)pyridinepalladium complex highlight the important role that ...protonolysis plays in this reaction. Coordination of the aminoalkene substrate to this complex activates the alkene toward intramolecular nucleophilic attack to form a dicationic palladium alkyl complex (6). A stable monocationic palladium alkyl complex (7) was isolated by in situ deprotonation of 6 with mild base, and its structure was confirmed by X-ray crystallography. Complex 7 reacted rapidly with a variety of strong acids to undergo protonolysis, resulting in formation of hydroamination product 3 and regenerating the active catalyst. Evidence that formation of the palladium alkyl complex is reversible under the catalytic conditions was obtained from observation of the protonolysis at low temperature. During the course of all catalytic reactions, the resting state of the catalyst was palladium alkyl complex 7, indicating that protonolysis of the Pd-C bond was the turnover-limiting step. Kinetic studies reveal an unusual inverse dependence of the reaction rate on the concentration of the aminoalkene substrate. This effect can be accurately explained by a model in which the carbamate protecting group of the aminoalkene acts as a Brønsted base to remove free protons from the catalytic cycle and thereby inhibits the turnover-limiting protonolysis step. Formation of a 2:1 complex (12) between the carbamate and the proton is most consistent with the kinetic data.
The mechanisms and rates of mercury methylation in the Florida Everglades are of great concern because of potential adverse impacts on human and wildlife health through mercury accumulation in ...aquatic food webs. We developed a new PCR primer set targeting hgcA, a gene encoding a corrinoid protein essential for Hg methylation across broad phylogenetic boundaries, and used this primer set to study the distribution of hgcA sequences in soils collected from three sites along a gradient in sulfate and nutrient concentrations in the northern Everglades. The sequences obtained were distributed in diverse phyla, including Proteobacteria, Chloroflexi, Firmicutes, and Methanomicrobia; however, hgcA clone libraries from all sites were dominated by sequences clustering within the order Syntrophobacterales of the Deltaproteobacteria (49 to 65% of total sequences). dsrB mRNA sequences, representing active sulfate-reducing prokaryotes at the time of sampling, obtained from these sites were also dominated by Syntrophobacterales (75 to 89%). Laboratory incubations with soils taken from the site low in sulfate concentrations also suggested that Hg methylation activities were primarily mediated by members of the order Syntrophobacterales, with some contribution by methanogens, Chloroflexi, iron-reducing Geobacter, and non-sulfate-reducing Firmicutes inhabiting the sites. This suggests that prokaryotes distributed within clades defined by syntrophs are the predominant group controlling methylation of Hg in low-sulfate areas of the Everglades. Any strategy for managing mercury methylation in the Everglades should consider that net mercury methylation is not limited to the action of sulfate reduction.
Mercury (Hg) methylation in the Florida Everglades is of great environmental concern because of its adverse effects on human and wildlife health through biomagnification in aquatic food webs. ...Periphyton and flocculant materials (floc) overlaying peat soil are important ecological compartments producing methylmercury (MeHg) in this ecosystem. These compartments retain higher concentrations of MeHg than did soil at study sites across nutrient and/or sulfate gradient(s). To better understand what controls Hg methylation in these compartments, the present study explored the structures and abundances of Hg methylators using genes
as biomarkers. The
sequences indicated that these compartments hosted a high diversity of Hg methylators, including
,
,
, and
, with community compositions that differed between these habitats. The copy numbers of
quantified by quantitative PCR revealed that floc and soil supported higher numbers of Hg methylators than periphyton in the Everglades ecosystem. The abundance of Hg methylators was strongly positively correlated with concentrations of carbon and nutrients (e.g., phosphorus and nitrogen) according to redundancy analysis. Strong correlations were also observed among numbers of sulfate reducers, methanogens, and the dominant
-carrying groups, suggesting that
would spread primarily through the growth of those assemblages. The abundances of Hg methylators were weakly negatively correlated to MeHg concentrations, suggesting that the size of this population would not solely determine the final concentrations of MeHg in the ecological compartments studied. This study extends the knowledge regarding the distribution of diverse potential mercury methylators in different environmental compartments in a wetland of national concern.
Methylmercury is a potent neurotoxin that impacts the health of humans and wildlife. Most mercury in wetlands such as the Florida Everglades enters as inorganic mercury via atmospheric deposition, some of which is transformed to the more toxic methylmercury through the activities of anaerobic microorganisms. We investigated the numbers and phylogenetic diversity of
, genes that are linked to mercury methylation, in the soil, floc, and periphyton in areas of the Everglades with different sulfate and nutrient concentrations. Soil harbored relatively high numbers of cells capable of methylating mercury; however, little detectable methylmercury was present in soil. The greatest concentrations of methylmercury were found in floc and periphyton. The dominant methylators in those compartments included methanogens and
This work provides significant insight into the microbial processes that control methylation and form the basis for accumulation through the food chain in this important environment.
A mild palladium-catalyzed cross-coupling of unsubstituted and 2-alkyl-substituted aziridines with arylboronic acid nucleophiles is presented. The reaction is highly regioselective and compatible ...with diverse functionality. A catalytic amount of base, a sterically demanding triarylphosphine ligand, and a phenol additive are critical to the success of the reaction. Coupling of a deuterium-labeled substrate established that ring opening of the aziridine occurs with inversion of stereochemistry.
A new selenophosphoramide-catalyzed diamination of terminal- and
trans
-1,2-disubstituted olefins is presented. Key to the success of this transformation was the introduction of a fluoride scavenger, ...trimethylsilyl trifluoromethanesulfonate (TMSOTf), to prevent a competitive
syn
-elimination pathway, as was the use of a phosphoramide ligand on selenium to promote the desired substitution reaction. A screen of catalysts revealed that more electron-rich phosphine ligands resulted in higher yields of the desired product, with selenophosphoramides giving the optimal results. A broad range of substrates and functional groups were tolerated and yields were generally good to excellent. For (
E
)-1,2-disubstituted olefins, diastereoselectivities were always high, giving exclusively anti products. The conditions were also applied to substrates bearing internal nucleophiles such as esters and carbonates, giving rise to 1,2-aminoesters and cyclic carbonates, respectively.
Scavenging fluoride from a selenophosphoramide-catalyzed alkene oxidation reaction suppresses the known
syn
-elimination pathway, enabling alkene diamination/oxyamination reactions
via
substitution.
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