Transcriptomic-wide discovery of direct and indirect HuR RNA targets in activated CD4+ T cells

Due to poor correlation between steady state mRNA levels and protein product, purely transcriptomic profiling methods may miss genes posttranscriptionally regulated by RNA binding proteins (RBPs) and microRNAs (miRNAs). RNA immunoprecipitation (RIP) methods developed to identify in vivo targets of RBPs have greatly elucidated those mRNAs which may be regulated via transcript stability and translation. The RBP HuR (ELAVL1) and family members are major stabilizers of mRNA. Many labs have identified HuR mRNA targets; however, many of these analyses have been performed in cell lines and oftentimes are not independent biological replicates. Little is known about how HuR target mRNAs behave in conditional knock-out models. In the present work, we performed HuR RIP-Seq and RNA-Seq to investigate HuR direct and indirect targets using a novel conditional knock-out model of HuR genetic ablation during CD4+ T activation and Th2 differentiation. Using independent biological replicates, we generated a high coverage RIP-Seq data set (>160 million reads) that was analyzed using bioinformatics methods specifically designed to find direct mRNA targets in RIP-Seq data. Simultaneously, another set of independent biological replicates were sequenced by RNA-Seq (>425 million reads) to identify indirect HuR targets. These direct and indirect targets were combined to determine canonical pathways in CD4+ T cell activation and differentiation for which HuR plays an important role. We show that HuR may regulate genes in multiple canonical pathways involved in T cell activation especially the CD28 family signaling pathway. These data provide insights into potential HuR-regulated genes during T cell activation and immune mechanisms

Inappropriate Antidiuresis: Examples of an Hyponatremic Syndrome Resembling Exogenous Vasopressin Administration in Man

We have reviewed some of the features of hyponatremic syndromes, unassociated with sodium retention and edema, but associated with primary water retention. The syndromes were probably caused by excessive vasopressin activity, in the presence of normal circulatory, renal and adreno-cortical function. Underlying diseases, including bronchogenic carcinoma, head injury, and tuberculous meningitis, illustrated the diverse etiologic bases of this condition

Physiological Basis of the Radioisotope Renogram

A model elucidating the relationships between blood radioactivity, the renogram curve, and urine radioactivity, as a function of time, is derived. Estimation procedures have been devised which use the data from three curves at once to estimate parameters common to the three curves, and which also estimate parameters unique to the individual curves. A program has been written for the RPC 4000 computer to perform the estimation. It was found that some model in which six different exponential parameters could be justified instead of the two proposed by the model could provide a significantly better fit of the data (P \u3c .001), but that the fit under the hypothesis was still quite good

Overexpression of the RNA-binding protein HuR impairs tumor growth in triple negative breast cancer associated with deficient angiogenesis [abstract]

Breast cancer is the second most common cancer in women and causes the death of 519,000 people worldwide. Many cancer genes are posttranscriptionally regulated by RNA-binding proteins (RBPs) and microRNAs. The RBP HuR binds to the AU-rich (ARE) regions of labile mRNAs, such as proto-oncogenes, stabilizing their mRNA and facilitating their translation into protein. HuR has been described to control genes in multiple areas of the acquired capabilities model of cancer and has been hypothesized to be a tumor maintenance gene, allowing for cancers to proliferate once they are established. We investigated the role of HuR in aggressive and difficult to treat triple-negative breast cancer

Simulating the one‐dimensional structure of Titan's upper atmosphere: 1. Formulation of the Titan Global Ionosphere‐Thermosphere Model and benchmark simulations

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/94638/1/jgre2819.pd

Simulating the one‐dimensional structure of Titan's upper atmosphere: 3. Mechanisms determining methane escape

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/94596/1/jgre2822.pd

Coordinate regulation of GATA3 and CD4+ T-helper 2 (TH2) cytokine gene expression by the RNA-binding protein HuR [abstract]

Asthma and other allergic inflammation diseases are major contributors to hospitalizations and deaths worldwide. These diseases are the result of over reactive immune responses initiating pro inflammatory mediators. These CD4+ T helper type 2 (Th2) mediated diseases are driven by the transcription factor GATA3 as well as the cytokines IL-4 and IL-13. HuR, an RNA binding protein (RBP), has been shown to posttranscriptionally regulate many early response genes, including these critical allergy mediators

Simulating the one‐dimensional structure of Titan's upper atmosphere: 2. Alternative scenarios for methane escape

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/94984/1/jgre2821.pd

The Parasexual Cycle in Candida albicans Provides an Alternative Pathway to Meiosis for the Formation of Recombinant Strains

Candida albicans has an elaborate, yet efficient, mating system that promotes conjugation between diploid a and α strains. The product of mating is a tetraploid a/α cell that must undergo a reductional division to return to the diploid state. Despite the presence of several “meiosis-specific” genes in the C. albicans genome, a meiotic program has not been observed. Instead, tetraploid products of mating can be induced to undergo efficient, random chromosome loss, often producing strains that are diploid, or close to diploid, in ploidy. Using SNP and comparative genome hybridization arrays we have now analyzed the genotypes of products from the C. albicans parasexual cycle. We show that the parasexual cycle generates progeny strains with shuffled combinations of the eight C. albicans chromosomes. In addition, several isolates had undergone extensive genetic recombination between homologous chromosomes, including multiple gene conversion events. Progeny strains exhibited altered colony morphologies on laboratory media, demonstrating that the parasexual cycle generates phenotypic variants of C. albicans. In several fungi, including Saccharomyces cerevisiae and Schizosaccharomyces pombe, the conserved Spo11 protein is integral to meiotic recombination, where it is required for the formation of DNA double-strand breaks. We show that deletion of SPO11 prevented genetic recombination between homologous chromosomes during the C. albicans parasexual cycle. These findings suggest that at least one meiosis-specific gene has been re-programmed to mediate genetic recombination during the alternative parasexual life cycle of C. albicans. We discuss, in light of the long association of C. albicans with warm-blooded animals, the potential advantages of a parasexual cycle over a conventional sexual cycle