Deciphering 3'ss selection in the yeast genome reveals an RNA thermosensor that mediates alternative splicing

Poor understanding of the spliceosomal mechanisms to select intronic 3' ends (3'ss) is a major obstacle to deciphering eukaryotic genomes. Here, we discern the rules for global 3'ss selection in yeast. We show that, in contrast to the uniformity of yeast splicing, the spliceosome uses all available 3'ss within a distance window from the intronic branch site (BS), and that in 70% of all possible 3'ss this is likely to be mediated by pre-mRNA structures. Our results reveal that one of these RNA folds acts as an RNA thermosensor, modulating alternative splicing in response to heat shock by controlling alternate 3'ss availability. Thus, our data point to a deeper role for the pre-mRNA in the control of its own fate, and to a simple mechanism for some alternative splicing.

Deletion of the RNA-binding proteins ZFP36L1 and ZFP36L2 leads to perturbed thymic development and T lymphoblastic leukemia.

ZFP36L1 and ZFP36L2 are RNA-binding proteins (RBPs) that interact with AU-rich elements in the 3' untranslated region of mRNA, which leads to mRNA degradation and translational repression. Here we show that mice that lacked ZFP36L1 and ZFP36L2 during thymopoiesis developed a T cell acute lymphoblastic leukemia (T-ALL) dependent on the oncogenic transcription factor Notch1. Before the onset of T-ALL, thymic development was perturbed, with accumulation of cells that had passed through the beta-selection checkpoint without first expressing the T cell antigen receptor beta-chain (TCRbeta). Notch1 expression was higher in untransformed thymocytes in the absence of ZFP36L1 and ZFP36L2. Both RBPs interacted with evolutionarily conserved AU-rich elements in the 3' untranslated region of Notch1 and suppressed its expression. Our data establish a role for ZFP36L1 and ZFP36L2 during thymocyte development and in the prevention of malignant transformation.

Tumor necrosis factor and transforming growth factor β regulate clock genes by controlling the expression of the cold inducible RNA-binding protein (CIRBP).

The circadian clock drives the rhythmic expression of a broad array of genes that orchestrate metabolism, sleep wake behavior, and the immune response. Clock genes are transcriptional regulators engaged in the generation of circadian rhythms. The cold inducible RNA-binding protein (CIRBP) guarantees high amplitude expression of clock. The cytokines TNF and TGFβ impair the expression of clock genes, namely the period genes and the proline- and acidic amino acid-rich basic leucine zipper (PAR-bZip) clock-controlled genes. Here, we show that TNF and TGFβ impair the expression of Cirbp in fibroblasts and neuronal cells. IL-1β, IL-6, IFNα, and IFNγ do not exert such effects. Depletion of Cirbp is found to increase the susceptibility of cells to the TNF-mediated inhibition of high amplitude expression of clock genes and modulates the TNF-induced cytokine response. Our findings reveal a new mechanism of cytokine-regulated expression of clock genes.

Welcoming New Iowans: A Guide for Managers and Supervisors; The Best Practices of Iowa Employers with Immigrants and efugees in the Workplace, 2002

This guidebook has been published by the University of Northern Iowa New Iowans Program to assist employers, managers and supervisors with the unique challenges associated with hiring, training and integrating immigrant and refugee workers. Its purpose is to promote proactive engagement of newcomer workers to assure the vitality of Iowa businesses. Successful integration of immigrants and refugees in our workplaces and communities is essential to insure Iowa’s long-term economic and social health. This book provides essential information for human resource directors, trainers, supervisors and others as they meet the challenges and rewards of hiring immigrants and refugees. Of course, no guidebook can provide simple solutions to complex issues in a great variety if workplaces. This is not a “cookbook” with recipes that provide easy answers to challenges facing every company and worker. All employers are unique and approach problems differently. What works in one company might not work as well in another.

Welcoming New Iowans; A Guide for Christians and Churches, 2002

Immigrant and refugee newcomers have an important role in Iowa. These newcomers have revitalized many Iowa communities, workplaces and faith-based institutions. The arrival of immigrants and refugees poses challenges as well as rewards; understanding and addressing these issues is vital to welcoming and accommodating new Iowans and assuring their part in the long-term economic and social health of our state. This handbook represents a unique collaboration between the University of Northern Iowa (UNI) and Ecumenical Ministries of Iowa (EMI). The goal of this collaboration is to create a guidebook for Iowans to learn more about Iowa’s growing immigrant and refugee population and discover ways to welcome these newcomers and accommodate them in our communities and churches. The unique nature of this joint publication between a public university and Christian churches acknowledges that both institutions have a stake in accommodating immigrants in Iowa. UNI and all institutions of higher education need to support population growth to assure future enrollments. Churches and many other community institutions need immigrants and other newcomers to help maintain their viability. Universities and churches also need healthy local economies. Newcomers can provide much needed skills and labor to make this happen. In short, His collaboration recognizes that making immigration in Iowa work has important long-term implications for us all. This book was written and compiled by two university faculty members, but it is not an official university endorsement of Christianity as the only religion practiced and accepted by Iowans, and no university funds were used to print or distribute this handbook. This handbook is written for Iowa’s Christian community and is based on the Biblical mandate to welcome newcomers, but we acknowledge Iowa’s other religious groups and their role in accommodating newcomers as well. We readily acknowledge that other faith-based organizations also welcome newcomers and have a stake in making immigration a positive experience. In order to accommodate the perspectives and needs of these groups, the UNI New Iowans Program is planning to develop similar handbooks for Iowa’s Jewish and Muslim communities. This handbook includes a number of resource lists for individuals, newcomers, churches and others. Of course, as soon as these lists are printed, they may become out-of-date. In order to obtain the most up-to-date information, please visit the UNI New Iowans Web site: www.bcs.uni.edu/idm/newiowans/ The UNI New Iowans website also makes this handbook available in a PDF format.

Implementing the Mechanistic-Empirical Pavement Design Guide: Technical Report, May 2005

With the release of the new Mechanistic-Empirical Pavement Design Guide (MEPDG), pavement design has taken a “quantum” leap forward. The current 1993 design guide is solidly based on the empirical interpretation of the results of the 1960 American Association of State Highway and Transportation Officials (AASHTO) Road Test. This report seeks to outline the technical aspects of the new MEPDG. Full detail is essentially impossible and impractical, since the release of the MEPDG was accompanied by eighteen volumes of technical justification and background. Consequently, this report seeks only to provide a potential user with a practical understanding of the workings of the new guide, with only sufficient technical depth to aid in understanding.

Direct detection of a BRAF mutation in total RNA from melanoma cells using cantilever arrays.

Malignant melanoma, the deadliest form of skin cancer, is characterized by a predominant mutation in the BRAF gene. Drugs that target tumours carrying this mutation have recently entered the clinic. Accordingly, patients are routinely screened for mutations in this gene to determine whether they can benefit from this type of treatment. The current gold standard for mutation screening uses real-time polymerase chain reaction and sequencing methods. Here we show that an assay based on microcantilever arrays can detect the mutation nanomechanically without amplification in total RNA samples isolated from melanoma cells. The assay is based on a BRAF-specific oligonucleotide probe. We detected mutant BRAF at a concentration of 500 pM in a 50-fold excess of the wild-type sequence. The method was able to distinguish melanoma cells carrying the mutation from wild-type cells using as little as 20 ng µl(-1) of RNA material, without prior PCR amplification and use of labels.

A sensitized RNA interference screen identifies a novel role for the PI3K p110γ isoform in medulloblastoma cell proliferation and chemoresistance.

Medulloblastoma is the most common malignant brain tumor in children and is associated with a poor outcome. We were interested in gaining further insight into the potential of targeting the human kinome as a novel approach to sensitize medulloblastoma to chemotherapeutic agents. A library of small interfering RNA (siRNA) was used to downregulate the known human protein and lipid kinases in medulloblastoma cell lines. The analysis of cell proliferation, in the presence or absence of a low dose of cisplatin after siRNA transfection, identified new protein and lipid kinases involved in medulloblastoma chemoresistance. PLK1 (polo-like kinase 1) was identified as a kinase involved in proliferation in medulloblastoma cell lines. Moreover, a set of 6 genes comprising ATR, LYK5, MPP2, PIK3CG, PIK4CA, and WNK4 were identified as contributing to both cell proliferation and resistance to cisplatin treatment in medulloblastoma cells. An analysis of the expression of the 6 target genes in primary medulloblastoma tumor samples and cell lines revealed overexpression of LYK5 and PIK3CG. The results of the siRNA screen were validated by target inhibition with specific pharmacological inhibitors. A pharmacological inhibitor of p110γ (encoded by PIK3CG) impaired cell proliferation in medulloblastoma cell lines and sensitized the cells to cisplatin treatment. Together, our data show that the p110γ phosphoinositide 3-kinase isoform is a novel target for combinatorial therapies in medulloblastoma.