Publications

Journal Articles


  • Oscillations in supercoiling drive circadian gene expression in cyanobacteria PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Vijayan, V., Zuzow, R., O'Shea, E. K. 2009; 106 (52): 22564-22568

    Abstract

    The cyanobacterium Synechococcus elongatus PCC 7942 exhibits oscillations in mRNA transcript abundance with 24-h periodicity under continuous light conditions. The mechanism underlying these oscillations remains elusive--neither cis nor trans-factors controlling circadian gene expression phase have been identified. Here, we show that the topological status of the chromosome is highly correlated with circadian gene expression state. We also demonstrate that DNA sequence characteristics of genes that appear monotonically activated and monotonically repressed by chromosomal relaxation during the circadian cycle are similar to those of supercoiling-responsive genes in Escherichia coli. Furthermore, perturbation of superhelical status within the physiological range elicits global changes in gene expression similar to those that occur during the normal circadian cycle.

    View details for DOI 10.1073/pnas.0912673106

    View details for Web of Science ID 000273178700093

    View details for PubMedID 20018699

  • Gene expression profiling in Daphnia magna, part II: Validation of a copper specific gene expression signature with effluent from two copper mines in California ENVIRONMENTAL SCIENCE & TECHNOLOGY Poynton, H. C., Zuzow, R., Loguinov, A. V., Perkins, E. J., Vulpe, C. D. 2008; 42 (16): 6257-6263

    Abstract

    Genomic technologies show great potential for classifying disease states and toxicological impacts from exposure to chemicals into functional categories. In environmental monitoring, the ability to classify field samples and predict the pollutants present in these samples could contribute to monitoring efforts and the diagnosis of contaminated sites. Using gene expression analysis, we challenged our custom Daphnia magna cDNA microarray to determine the presence of a specific metal toxicant in blinded field samples collected from two copper mines in California. We compared the gene expression profiles from our field samples to previously established expression profiles for Cu, Cd, and Zn. The expression profiles from the Cu-containing field samples clustered with the laboratory-exposed Cu-specific gene expression profiles and included genes previously identified as copper biomarkers, verifying that gene expression analysis can predict environmental exposure to a specific pollutant. In addition, our study revealed that upstream field samples containing undetectable levels of Cu caused the differential expression of only a few genes, lending support for the concept of a no observed transcriptional effect level (NOTEL). If confirmed by further studies, the NOTEL may play an important role in discriminating polluted and nonpolluted sites in future monitoring efforts.

    View details for DOI 10.1021/es800262k

    View details for Web of Science ID 000258439600067

    View details for PubMedID 18767696

  • The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans NATURE King, N., Westbrook, M. J., Young, S. L., Kuo, A., Abedin, M., Chapman, J., Fairclough, S., Hellsten, U., Isogai, Y., Letunic, I., Marr, M., Pincus, D., Putnam, N., Rokas, A., Wright, K. J., Zuzow, R., Dirks, W., Good, M., Goodstein, D., Lemons, D., Li, W., Lyons, J. B., Morris, A., Nichols, S., Richter, D. J., Salamov, A., Bork, P., Lim, W. A., Manning, G., Miller, W. T., McGinnis, W., Shapiro, H., Tjian, R., Grigoriev, I. V., Rokhsar, D. 2008; 451 (7180): 783-788

    Abstract

    Choanoflagellates are the closest known relatives of metazoans. To discover potential molecular mechanisms underlying the evolution of metazoan multicellularity, we sequenced and analysed the genome of the unicellular choanoflagellate Monosiga brevicollis. The genome contains approximately 9,200 intron-rich genes, including a number that encode cell adhesion and signalling protein domains that are otherwise restricted to metazoans. Here we show that the physical linkages among protein domains often differ between M. brevicollis and metazoans, suggesting that abundant domain shuffling followed the separation of the choanoflagellate and metazoan lineages. The completion of the M. brevicollis genome allows us to reconstruct with increasing resolution the genomic changes that accompanied the origin of metazoans.

    View details for DOI 10.1038/nature06617

    View details for Web of Science ID 000253191400033

    View details for PubMedID 18273011

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