 | Jean-Paul Armache's Lab |
| The Armache Lab uses cryo-EM and other techniques to understand the mechanisms of ATP-dependent chromatin remodeling complexes, their functions and roles in eukaryotic genome regulation. Cryo-EM structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome. Armache, J.-P., Gamarra, N., Johnson, S.L., Wu, S., Leonard, J., Narlikar, G. and Cheng, Y. (Jun 18, 2019). Elife. 8: e46057 MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Zheng, S.Q., Palovcak, E., Armache, J.-P., Verba, K.A., Cheng, Y. and Agard, D.A. (April 17, 2017). Nature Methods. 14(4): 331–332. Structure of the TRPA1 ion channel suggests regulatory mechanisms. Paulsen, C. E.*, Armache J.-P.*, Gao Y., Cheng Y., Julius D. (April 8, 2015). Nature. 520(7548): 511–517. To view a list of all of Jean-Paul Armache's Publications please click here |
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 | Lucy Bai's Lab |
| The Bai Lab uses a variety of strategies to understand the mechanism of gene regulation by chromatin structure at different levels. Basic helix-loop-helix pioneer factors interact with the histone octamer to invade nucleosomes and generate nucleosome depleted regions. Donovan BT, Chen HY, Eek P, Meng ZY, Jipa C, Tan S, Bai L, Poirier MG, Molecular Cell, 83:1251, 2023. Partitioned Usage of Chromatin Remodelers by Nucleosome-Displacing Factors, Chen HY, Kharerin H, Dhasarathy A, Kladde M, Bai L, Cell Reports, 40(8):111250, 2022. Chemically Induced Chromosomal Interaction (CICI) method to study chromosome dynamics and its biological roles, Du MY, Zou F, Li Y, Yan YJ, Bai L, Nat Communication, 13:757, 2022. To view a list of all of Lucy Bai's Publications please click here |
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 | Marina Feric's Lab |
| The Feric lab investigates the principles underlying cellular organization and how anomalies contribute to aging and age-related diseases. Within the context of phase transitions, we take an interdisciplinary approach to interrogate droplet-like structures in live cells and in reconstituted systems in vitro, including advanced super-resolution light microscopy and quantitative image analysis; genetic and sequencing techniques; and biophysical modeling. Mesoscale structure-function relationships in mitochondrial transcriptional condensates, Feric, M., A. Sarfallah, F. Dar, D. Temiakov, R. Pappu, and T. Misteli. PNAS, 119(41):e2207303119, 2022. Self-assembly of multi-component mitochondrial nucleoids via phase separation, Feric, M., Demarest, T.G., Tian, J., Croteau, D.L., Bohr, V.A., Misteli, T., The EMBO Journal, 40(6): e107165, 2021. Coexisting liquid phases underlie nucleolar sub-compartments, Feric M., Vaidya N., Harmon T. S., Mitrea D. M., Zhu L., Richardson T. M., Kriwacki R. W., Pappu R. V., & Brangwynne C.P., Cell, 165(7): 1686-1697, 2016. To view a list of all of Marina Feric's Publications please click here |
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 | Ross Hardison's Lab |
| Ross and his co-workers measure transcriptome profiles and use epigenetic marks and comparative genomics to predict gene regulatory modules. Accurate and reproducible functional maps in 127 human cell types via 2D genome segmentation. Zhang Y, Hardison RC. (2017 Sept 29) Nucleic Acids Res. 45:9823-9836. Establishment of regulatory elements during erythro-megakaryopoiesis identifies hematopoietic lineage-commitment points. Heuston EF, Keller CA, Lichtenberg J, Giardine B, Anderson SM; NIH Intramural Sequencing Center, Hardison RC, Bodine DM.. (2018 May 28) Epigenetics Chromatin 11(22). The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries. Hsu SC, Gilgenast TG, Bartman CR, Edwards CR, Stonestrom AJ, Huang P, Emerson DJ, Evans P, Werner MT, Keller CA, Giardine B, Hardison RC, Raj A, Phillips-Cremins JE, Blobel GA. (2017 Apr 6) Mol Cell. 66(1):102-116.e7. To view a list of all of Ross Hardison's Publications please click here |
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 | Scott Lindner's Lab |
| The Lindner Laboratory is focused on understanding how malaria parasites prepare themselves for an unpredictable moment: the chance to transmit to and from mosquitoes. Plasmodium parasites (the causative agent of malaria) rely upon translational repression for this preparation, whereby they proactively make, store, and silence mRNAs that are only needed after the transmission event. The Lindner Laboratory uses comparative transcriptomics, proteomics, structural biology, Nanopore sequencing and reverse genetics approaches to study the essential features of this essential control mechanism. Long-Read Genome Assembly and Gene Model Annotations for the Rodent Malaria Parasite Plasmodium yoelii 17XNL, Godin, M.J., Sebastian, A., Albert, I, & Lindner, S.E., Journal of Biological Chemistry, 27:104871, 2023. Specialized Ribosomes of Plasmodium Parasites, McGee, J.M., Armache, J.P., & Lindner, S.E., PLoS Pathogens..19:e1011267, 2023. The Plasmodium NOT1-G paralogue is an essential regulator of sexual stage maturation and parasite transmission, Hart, K.J., Power, B.J., Rios, K.T., Sebastian, A., & Lindner, S.E., PLoS Biology, 19:e3001434, 2021. To view a list of all of Scott Lindner's Publications please click here |
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 | Manuel Llinás' Lab |
| Research in our laboratory is focused on understanding the mechanisms of gene regulation in Plasmodium. Inhibitors of ApiAP2 protein DNA binding exhibit multistage activity against Plasmodium parasites. Russell TJ, De Silva EK, Crowley VM, Shaw-Saliba K, Dube N, Josling G, Pasaje CFA, Kouskoumvekaki I, Panagiotou G, Niles JC, Jacobs-Lorena M, Denise Okafor C, Gamo FJ, Llinás M., PLoS Pathogens, 18(10):e1010887, 2022. A heat-shock response regulated by the PfAP2-HS transcription factor protects human malaria parasites from febrile temperatures. Tintó-Font E, Michel-Todó L, Russell TJ, Casas-Vila N, Conway DJ, Bozdech Z, Llinás M, Cortés A. (2017 Jun 14) Nature Microbiology, 6(9):1163, 2021 Dissecting the role of PfAP2-G in malaria gametocytogenesis. Josling GA, Russell TJ, Venezia J, Orchard L, van Biljon R, Painter HJ, Llinás M. Nature Communications, 11(1):1503, 2020. To view a list of all of Manuel Llinás' Publications please click here |
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 | Shaun Mahony's Lab |
| We are computational biologists who develop machine-learning methods for understanding gene regulation. In particular, we aim to understand where transcription factors bind in the genome, and what they do once they get there. Domain adaptive neural networks improve cross-species prediction of transcription factor binding, K Cochran, D Srivastava, A Shrikumar, A Balsubramani, RC Hardison, A Kundaje, S Mahony, Genome Research 32(3):512-523, 2022 High resolution protein architecture of the budding yeast genome, MJ Rossi, PK Kuntala, WKM Lai, N Yamada, N Badjatia, C Mittal, G Kuzu, K Bocklund, NP Farrell, TR Blanda, JD Mairose, AV Basting, KS Mistretta, DJ Rocco, ES Perkinson, GD Kellogg, S Mahony, BF Pugh, Nature, 592(7853):309-314, 2021 An interpretable bimodal neural network characterizes the sequence and preexisting chromatin predictors of induced transcription factor binding, D Srivastava, B Aydin, EO Mazzoni, S Mahony, Genome Biology 22(1):20, 2021 To view a list of all of Shaun Mahony's Publications please click here |
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 | Joseph Reese's Lab |
| We are interested in understanding chromatin structure, gene expression, and DNA damage resistance pathways. Ccr4-Not maintains genomic integrity by controlling the ubiquitylation and degradation of arrested RNAPII. Jiang, H., Wolgast, M., Beebe, L.M. and Reese, J.C. (4 Apr 2019) Genes and Development. 33:705-717 Genome-Wide Mapping of Decay Factor-mRNA Interactions in Yeast Identifies Nutrient Responsive Transcripts as Targets of the Deadenylase Ccr4. Miller, J.E., L. Zhang, H. Jiang, Y. Li, B.F. Pugh and J.C. Reese (4 Jan 2018). G3. 8:315-330. To view a list of all of Joseph Reese's Publications please click here |
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 | Scott Showalter's Lab |
| We apply biophysical chemistry techniques to understand the function of partially disordered proteins that regulate transcription. Phosphorylation Induces Sequence-Specific Conformational Switches in the RNA Polymerase II C-Terminal Domain. Gibbs, EB, Lu, F, Portz, B, Fisher, MJ, Medellin, BP, Laremore, TN, Zhang, YJ, Gilmour, DS, Showalter, SA. (2017 May 12) Nat Commun. 8: 15233. Application of NMR to Studies of Intrinsically Disordered Proteins. Gibbs, EB, Cook, EC, Showalter, SA. (2017 Aug 15) Arch Biochem Biophys. 628: 57-70. The Solution Ensemble of the C-Terminal Domain from the Transcription Factor Pdx1 Resembles an Excluded Volume Polymer. Cook, EC, Sahu, D, Bastidas, M, Showalter, SA. (2019 Jan 10) J. Phys. Chem. B. 123: 106-116. To view a list of all of Scott Showalter's Publications please click here |
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 | Song Tan's Lab |
| Our goal is to understand how gene expression is regulated. We study the molecular mechanism of gene regulation chromatin enzymes, in particular, the structural basis for how chromatin enzymes recognize and act on their nucleosome substrate. Cryo-EM structure of the human Sirtuin 6-nucleosome complex, U.S. Chio, O. Rechiche, A.R. Bryll, J. Zhu, J.L. Feldman, E.M. Leith, C.L. Peterson, S. Tan, J.-P. Armache, Science Advances, 9:eadf7586, 2023. Basic helix-loop-helix pioneer factors interact with the histone octamer to invade nucleosomes and generate nucleosome depleted regions, B.T. Donovan, H. Chen, P. Eek,, Z. Meng, C. Jipa, S. Tan, Lu Bai, M.G. Poirier, Mol. Cell., 83:1-13, 2023 Principles of nucleosome recognition by chromatin factors and enzymes function, R.K. McGinty and S. Tan, Curr. Opin. Struct. Biol., 71:16-26, 2021. To view a list of all of Song Tan's Publications please click here |