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.

The lab studies how genes function within the three-dimensional context of the nucleus to control development and prevent disease. We combine genomic approaches (ChIP-Seq, ChIA-PET) and genome editing tools (CRISPR) to study the epigenetic mechanisms by which transcriptional regulatory elements control gene expression in embryonic stem cells.  Our current research efforts are divided into 3 areas: 1) Mapping the folding pattern of the genome 2) Dynamics of three-dimensional genome organization as cells differentiate and 3) Functional analysis of altered chromosome structure in cancer and other diseases.

Plants contain discrete populations of self-renewing stem cells that give rise to the diverse differentiated cell types found throughout the plant. Stem cell function is therefore ultimately responsible for the aesthetic and economic benefits plants provide us. My lab uses multiple approaches to dissect plant stem cell signaling networks including genetics, genomics, live tissue imaging, and cell biological and biochemical methods.  

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)