We are interested in understanding how cells develop into organisms. We love the nematode C. elegans, because it allows us to readily combine a great number of useful techniques, including techniques of cell biology, direct manipulation of cells, forward and reverse genetics, biochemistry, molecular biology, biophysics, and live imaging of cells and their dynamic, cytoskeletal components. Current work in the lab addresses several fundamental questions in cell and developmental biology — how cells move to specific positions during development, how cells change shape, how developmental patterning mechanisms tell cell biological mechanisms what to do where and when, how intercellular signals act to polarize cells, and how the mitotic spindle is positioned in cells.

We have also been developing a relative of C. elegans and Drosophila, a water bear (tardigrade), to study how developmental mechanisms can evolve to produce organisms with different forms and how biological materials can survive unusual extremes.

• Bob Goldstein’s CV
• publications

Research Synopsis:

Appropriate allocation of cellular lipid stores is paramount to maintaining organismal energy homeostasis and is coordinated by a network of multi-tissue endocrine signals. Dysregulation of these pathways can manifest in human metabolic syndromes, including cardiovascular disease, obesity, diabetes, and cancer. The goal of my lab is to elucidate the molecular mechanisms that govern the storage, metabolism, and intercellular transport of lipids; as well as understand how these circuits interface with other cellular homeostatic pathways (e.g., growth and aging). We utilize C. elegans as a model system to interrogate these evolutionarily conserved pathways, combining genetic approaches (forward and reverse genetic screens, CRISPR) with genomic methodologies (ChIP-Seq, mRNA-Seq, DNA-Seq) to identify new components and mechanisms of metabolic regulation.

Recent Publications:

Dowen, RH. CEH-60/PBX and UNC-62/MEIS coordinate a metabolic switch that supports reproduction in C. elegans. Developmental Cell 2019 Apr 22;49(2):235-50. PMID: 30956009

Dowen, RH, Breen, PC, Tullius, T, Conery, AL, Ruvkun, G. A microRNA program in the C. elegans hypodermis couples to intestinal mTORC2/PQM-1 signaling to modulate fat transport. Genes & Development 2016 Jul 1;30(13):1515-28. PMID: 27401555

Riedel, CG, Dowen, RH, Lourenco, GF, Kirienko, NV, Heimbucher, T, West, JA, Bowman, SK, Kingston, RE, Dillin, A, Asara, JM, and Ruvkun, G. DAF-16 employs the chromatin remodeller SWI/SNF to promote stress resistance and longevity. Nature Cell Biology 2013 May;15(5):491-501. PMID: 23604319

Dowen, RH, Pelizzola, M, Schmitz, RJ, Lister, R, Dowen, JM, Nery, JR, Dixon, JE, and Ecker, JR. Widespread dynamic DNA methylation in response to biotic stress. Proc Natl Acad Sci USA 2012 Aug 7;109(32):E2183-91. PMID: 22733782

Lister, R*, Pelizzola, M*, Dowen, RH, Hawkins, RD, Hon, G, Tonti-Filippini, J, Nery, JR, Lee, L, Ye, Z, Ngo, Q, Edsall, L, Antosiewicz-Bourget, J, Stewart, R, Ruotti, V, Millar, AH, Thomson, JA, Ren, B, and Ecker, JR. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009 Nov 19;462(7271):315-322. *Equal contribution. PMID: 19829295

Macrophages are highly dynamic and widespread blood cells that play many important functions in vertebrates. They are the main phagocytes throughout the body, responsible for clearing away dying cells, damaged tissue, and pathogens, to maintain tissue integrity. Macrophages circulate in the bloodstream as monocytes or are stationed in strategic locations of the body as tissue macrophages where their phagocytic roles are critical, such as microglia in the brain, Kupffer cells in the liver, Langerhans cells in the skin, and osteoclasts in the bone.

Of particular interest are the normal roles and mechanisms of macrophages and microglia in the development and maintenance of the nervous system that remain far less understood than their functions in disease and injury. In the healthy brain, microglia have been implicated in shaping brain circuitry and neuronal development as well as in possibly affecting behavioral outcomes. They have unique embryonic origins from primitive macrophages that migrate into the brain and remain thereafter through life. These versatile glial cells provide the first line of defense and respond to a wide variety of environmental factors, such as protein aggregates, apoptotic cells, injured tissue, and pathogens, as well as to intracellular dysfunctions. Overall, the developmental process by which macrophages take residence and differentiate into tissue macrophages, and the contribution of macrophages to normal animal development remain not well understood.  We are addressing these two fundamental areas of macrophage biology in the context of how macrophages participate in the nervous system.

Research in the lab focuses on how a single genome gives rise to a variety of cell types and body parts during development. We use Drosophila as a model organism to investigate (1) how transcription factors access DNA to regulate complex patterns of gene expression, and (2) how post-translational modification of histones contributes to maintenance of gene expression programs over time. We combine genomic approaches (e.g. chromatin immunoprecipitation followed by high-throughput sequencing) with Drosophila genetics and transgenesis to address both of these questions. Defects in cell fate specification and maintenance of cell identity often occur in human diseases, including cancer. (website)

Curriculum vitae

The research in our lab is centered on understanding the mechanisms and principles of cellular movement. Cytoskeletal filaments – composed of actin and microtubules – serve as a structural scaffolding that defines the architecture of the cytoplasm and gives cells the ability to divide, crawl, and change their shapes. We are interested in understanding how cells regulate cytoskeletal dynamics to produce motility. Our primary model system is the fruit fly, Drosophila melanogaster as it allows us to use functional genomic tools and classical genetic techniques to study gene function at the level of individual cells and during development. Current projects in the lab address mechanisms of microtubule dynamic instability, crosstalk between the actin and microtubule cytoskeletal networks, and the regulation of cellular contractility during Drosophila gastrulation.

At a Glance

• Combining genetics with real-time analysis of living cells by video or digital enhanced microscopy to examine the role of dynein and other microtubule motor proteins in spindle and nuclear dynamics.
• Using specific chromosomal or cytoskeletal perturbations to understand cell cycle control of late mitotic events.

Synopsis

Accurate chromosome segregation at each cell division is one of the most fundamental processes in a living organism. This complex process requires the coordination of cytoskeletal components such as microtubules and microtubule motor proteins that form the mitotic spindle with the replication and attachment of chromosomes to the segregation apparatus. Both the high fidelity of chromosome segregation and genome integrity are essential for normal development and cellular propagation. The ease of genetic and molecular manipulations to address the mechanism of chromosome segregation n the context of a live cell makes the budding yeast an excellent model system to address the mechanism of spindle assembly and the maintenance of genome integrity in mitosis. Our lab takes a broad approach to understanding mitosis in yeast. Recent projects in the lab have addressed the role of plus end microtubule binding proteins such as Bim1 and microtubule motor proteins on spindle integrity and the contribution of pericentric chromatin to regulating spindle length.

The site of microtubule attachment to the chromosome is the kinetochore, a complex of over 60 proteins assembled at a specific site on the chromosome, the centromere. Almost every kinetochore protein identified in yeast is conserved throughout phylogeny and the organization of the kinetochore in yeast may serve as the fundamental unit of attachment for mammalian cells. More recently we have become interested in the role of two different classes of ATP binding proteins, cohesions (Smc3, Scc1) and chromatin remodeling factors (Cac1, Hir1, Rdh54), in the structural organization of the kinetochore and how these classes of proteins contribute to the fidelity of chromosome segregation.

Yeast Cell (MPEG Viewer – 635K)
Yeast-dynein (Quick Time Viewer – 6912K)

Chromatin and Gene Regulation

Chromosomes are compacted into increasingly complex chromatin structures within eukaryotic nuclei. High-throughput sequence-based assays have been developed to identify regions of nucleosome-depleted open chromatin that mark all types of regulatory elements genome-wide in tissues and cell-types. The computational integration of these data with related gene expression, transcription factor binding, and epigenetic data provide a more complete picture of the complex process of gene transcription and regulation. With these data, we are also investigating the effects of genetic variation on regulation, as can been seen through allelic imbalance in signal from chromatin and transcription factor data, as well as in quantitative trait loci (QTL)-based analyses of these data across individuals. Our computational biology lab both applies established analysis tools to data generated in collaboration with other labs as well as develops new analytical techniques to make novel associations.

Inflammatory Bowel Disease

Inflammatory bowel disease (IBD), primarily consisting of Crohn’s disease and ulcerative colitis, is the result of an inappropriate immune response to the intestinal microbiota in a genetically susceptible individual. We have partnered with Dr. Shehzad Sheikh, MD, PhD (Dept of Medicine, CGIBD) to uncover molecular and microbial characteristics of IBD disease phenotypes. We hypothesize that changes in the chromatin landscape in key intestinal cell types such as macrophages, are influenced by the host genetic background and significantly contribute to aberrant intestinal inflammation. Using both human tissue and mouse models, we seek to identify where chromatin is altered, the impacts on gene expression, the contributions of genetic variation, and the relationship to the microbial community in tissues and cells from affected individuals.

Environmental Toxicogenomics

Exposure to naturally occurring toxicants or by-products of manufacturing process can result in serious health challenges. We hypothesize that toxicant exposure can alter normal cellular function through changes in chromatin architecture and transcriptional profiles in tissues or cells contributing to the onset of medical complications. In a collaboration with Dr. Samir Kelada, PhD (Dept of Genetics), we are investigating the effects of exposure to ozone on the lung inflammatory response in the genetically diverse Collaborative Cross mouse model resource. In particular, we are assaying how ozone-induced chromatin structure and gene expression changes in alveolar macrophages, along with genetic variation, explain variability in ozone response.

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Teaching   |   Undergraduate Research

Developmental Biology at UNC  |  Cytoskeletal research at UNC

Cell adhesion, cytoskeletal regulation and Wnt signaling

in development and cancer

Biomedical science has twin goals; to explain the many amazing properties of our own bodies and those of other animals, and to use this information to reveal the causes of disease and to suggest possible treatments. We work at the interface between cell and developmental biology, focusing on the epithelial tissues that form the basic architectural unit of our bodies and of those of other animals.  We explore how the machinery mediating cell adhesion, cytoskeletal regulation and Wnt signaling regulates cell fate and tissue architecture in development and disease.  Epithelial tissues like skin, lung, colon, and breast are affected in many cancers. Cancer results from alterations in normal cell behaviors. To explore underlying causes of epithelial tumors, we need to understand the basic cellular machinery that links cell adhesion, signal transduction and cytoskeletal regulation during normal development.

We focus on the machinery that modulates cell-cell adhesion and connects cell junctions to the actin cytoskeleton, thus shaping the architecture of epithelial tissues.  We also explore the machinery that transduces and regulates Wnt signaling, which helps determine cell fates.  Wnt signaling is inappropriately activated in colon and other cancers, while the cell adhesion machinery is inactivated in most metastatic tumors.  We study these processes in the fruit fly Drosophila, combining classical and modern genetic tools with state-of-the-art cell biology, microscopy, and biochemistry,  thus capitalizing on the speed of this model system and its synergy with vertebrate cell biology, and supplement this with work on cultured Drosophila cells and mammalian cells.  Like all good science, our work sometimes leads us in unexpected directions–our recent wor on the roles of centrosomes in genome stability is an example.

To learn more about our work, visit our wpcf-lab-website via the link above, where you can meet the people in the lab and learn more about their work. It’s an exciting time to be working at the interface between cell and developmental biology, and we are always looking for talented and enthusiastic graduate students and postdocs to add to our group.  You can also follow us on Facebook or check out our videos on Vimeo.

Obtaining Armadillo Antibody

The anti-Armadillo antibody is now available from the Developmental Studies Hybridoma Bank, an NIH funded facility that produces antibodies for the research community at cost. They will sell you anti-Armadillo 7A1 mouse monoclonal antibody at $10/ml. You can reach them by phone at 319-335-3826 or by wpcf-emailfaculty at dshb@uiowa.edu. Perhaps the easiest way to reach them is at their home page at http://dshb.biology.uiowa.edu/.

If you need more information about the use of the antibody, feel free to contact us. We use it at 1:40 in situ on embryos, 1:20 for immunoprecipitations, and at 1:400 on Westerns.

Good luck with your experiments.