THE DUNCAN LABORATORY

Research

How do animals (re)create new tissues?
How do some maintain this capacity as adults?

We are interested in these questions at the
molecular and genomic levels.

Overview

from T.H. Morgan's "Experimental studies of the regeneration of Planaria maculata." (1898)

Planarians are flatworms with an abundant adult stem cell population and an astounding regenerative capacity. As described by Nobel Prize winner and UK alumnus T.H. Morgan himself, even a small fragment of an adult worm can regenerate into a new, fully-formed animal!

These features make planarians an excellent model for studying both stem cell differentiation and animal regeneration.

Planarian stem cells are both highly similar to other types of stem cells and yet also unique. Much like pluripotent stem cells in early mammalian embryos, planarian stem cells are highly "plastic"; they both self-renew their own population AND differentiate into all the cell lineages that comprise a mature worm. Yet unlike mammalian stem cells, which are only pluripotent very briefly during early embryogenesis, planarian stem cells maintain their "stemness" indefinitely.

In the Duncan lab, we are particularly interested in how regulation of the planarian genome and chromatin state contribute to these powerful biological features.

Projects

anti-acetylated tubulin IF (cilia marker)

tissue specificity of mll1/2 function

MLL1 and MLL2 are chromatin modifying enzymes best known for regulating the expression of Hox genes, transcription factors that specify the animal body plan during development. Interestingly, RNAi of mll1/2 in the planarian species Schmidtea mediterranea (Smed) does NOT prevent — or grossly distort — regeneration.

mll1/2(RNAi) worms DO exhibit abnormal motility, i.e. "inch-worming" vs gliding. Closer examination reveals that mll1/2(RNAi) worms progressively lose their epidermal cilia. However, preliminary data suggests that other ciliated tissues (e.g. pharynx, kidney units, sperm) are NOT obviously affected, despite the fact that SmedMLL1/2 targets cilia genes in the stem cells.

This project aims to characterize and dissect the tissue specificity of the mll1/2(RNAi) phenotype.

ventral cilia (SEM)

cilia, signaling, and stem cells

We were surprised to observe that SmedMLL1/2 targets cilia gene loci in stem cells given that planarian stem cells are not ciliated. We hypothesize that this targeting serves to "prime" these loci for later expression, i.e. upon differentiation to ciliated cell types.

We are interested in understanding the nature of this "priming". Is SmedMLL1/2 priming a stem cell autonomous mechanism, independent of external signals? Or a non-autonomous mechanism, dependent on external signals? If the latter, what are those signals? What are their source(s)?

This project addresses whether gene targeting by SmedMLL1/2 in stem cells is dynamically regulated by their organismal context.

double whole-mount in situ hybridization: cyan = SmedMLL1/2 target gene, magenta = stem cell marker

silencing and activation of mll1/2 targets

Another aspect of SmedMLL1/2 priming we want to understand is how the expression of these target genes is regulated. Given that MLL1/2 catalyzes a post-translational modification normally found on actively transcribing genes (histone H3 lysine 4 trimethylation), it's interesting that SmedMLL1/2 preferably targets non-expressed and/or lowly-expressed genes in planarian stem cells.

Moreover, the genes targeted by SmedMLL1/2 in stem cells ARE highly expressed in differentiated cells. We are interested in the mechanisms controlling these divergent states. How are SmedMLL1/2 genes kept inactive in planarian stem cells? How are they activated in differentiated cell types, e.g. epidermal cells?

This project aims to address the molecules and mechanisms regulating the expression of SmedMLL1/2 target genes in a cell-type specific manner.

Students and Staff:

Shishir Biswas, Postdoc, Added 08/02/2021

Zachary Baker, Undergrad

Whitney Combs, Undergrad

Makayla Dean, Undergrad

Ekaterina (Katya) S Lundberg, Staff

Prince Verma, Graduate

Pallob Barai, Graduate

Courtney Waterbury, Added on MCC cluster 04/17/2023

Saima Rahman, Gradulate Added on MCC cluster 09/07/2023

Publications:

Duncan, E.M., Chitsazan A.D., Seidel C.W, and Sánchez Alvarado, A. (2015). Set1 and MLL1/2 Target Distinct Sets of Functionally Different Genomic Loci In Vivo. Cell Reports, 13, 2741-55.

Duncan, E.M. and Allis, C.D. (2011). Errors in erasure: links between histone lysine methylation removal and disease. Prog Drug Res. 67, 69-90. (Review)

Duncan, E.M., Muratore-Schroeder, T.L., Cook, R.G., Garcia, B.A., Shabanowitz, J., Hunt, D.F., Allis, C.D. (2008). Cathepsin L Proteolytically Processes Histone H3 During Mouse Embryonic Stem Cell Differentiation. Cell, 135, 284-294.

Li, H., Fischle, W., Wang, W., Duncan, E.M., Liang, L., Murakami-Ishibe, S., Allis, C.D., Patel, D.J. (2007). Structural basis for lower lysine methylation state-specific readout by MBT repeats of L3MBTL1 and an engineered PHD finger. Mol Cell, 28, 677-691.

Sehayek, E., Hagey, L.R., Fung, Y.Y., Duncan, E.M., Yu, H.J., Eggertsen, G., Björkhem, I., Hofmann, A.F., Breslow, J.L. (2006). Two loci on chromosome 9 control bile acid composition: evidence that a strong candidate gene, Cyp8b1, is not the culprit. J Lipid Res. 47, 2020-2027.

Li, H., Ilin, S., Wang, W., Duncan, E.M., Wysocka, J., Allis, C.D., Patel, D.J. (2006). Molecular basis for site/state-specific readout of histone lysine-methylation marks by the PHD domain of BPTF. Nature, 442, 91-95.

Bernstein, E., Duncan, E.M., Masui, O., Gil, J., Heard, E., Allis, C.D. (2006). Mouse polycomb proteins bind differentially to methylated histone H3 and RNA and are enriched in facultative heterochromatin. Mol Cell Biol., 26, 2560-2569.

Hake, S.B., Garcia, B.A., Duncan, E.M., Kauer, M., Dellaire, G., Shabanowitz, J., Bazett-Jones, D.P., Allis, C.D., Hunt, D.F. (2006). Expression patterns and post-translational modifications associated with mammalian histone H3 variants. J Biol Chem., 281, 559-568.

Sehayek, E., Yu, H.J., von Bergmann, K., Lutjohann, D., Stoffel, M., Duncan, E.M., Garcia-Naveda, L., Salit, J., Blundell, M.L., Friedman, J.M., Breslow, J.L. (2004). Phytosterolemia on the island of Kosrae: founder effect for a novel ABCG8 mutation results in high carrier rate and increased plasma plant sterol levels. J Lipid Res., 45, 1608-1613.

Maxwell, K.N., Soccio, R.E., Duncan, E.M., Sehayek, E., Breslow, J.L. (2003). Novel putative SREBP and LXR target genes identified by microarray analysis in liver of cholesterol-fed mice. J Lipid Res., 44, 2109-2119.

Sehayek, E., Duncan, E.M., Yu, H.J., Petukhova, L., Breslow, J.L. (2003). Loci controlling plasma non-HDL and HDL cholesterol levels in a C57BL /6J x CASA/Rk intercross. J Lipid Res., 44, 1744-1750.

Sehayek, E., Wang, R., Ono, J.G., Zinchuk, V.S., Duncan, E.M., Shefer, S., Vance, D.E., Ananthanarayanan, M., Chait, B.T., Breslow, J.L. (2003). Localization of the PE methylation pathway and SR-BI to the canalicular membrane: evidence for apical PC biosynthesis that may promote biliary excretion of phospholipid and cholesterol. J Lipid Res., 44, 1605-1613.

Rudner, L.A., Lin, J.T., Park, I.K., Cates, J.M., Dyer, D.A., Franz, D.M., French, M.A., Duncan, E.M., White, H.D., Gorham, J.D. (2003). Necroinflammatory liver disease in BALB/c background, TGF-beta 1-deficient mice requires CD4+ T cells. J Immunol., 170, 4785-4792.

Sehayek E., Duncan E.M., Lutjohann D., Von Bergmann K., Ono J.G., Batta A.K., Salen G., Breslow J.L. (2002). Loci on chromosomes 14 and 2, distinct from ABCG5/ABCG8, regulate plasma plant sterol levels in a C57BL/6J x CASA/Rk intercross. Proc Natl Acad Sci., 99, 16215-16219.

Sehayek E., Ono J.G., Duncan E.M., Batta A.K., Salen G., Shefer S., Neguyen L.B., Yang K., Lipkin M., Breslow J.L. (2001). Hyodeoxycholic acid efficiently suppresses atherosclerosis formation and plasma cholesterol levels in mice. J Lipid Res., 42, 1250-1256.

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