Jean-Paul Armache

About Me

I joined Penn State University in April 2019 as a faculty at the Department of Biochemistry and Molecular Biology, Eberly College and the Huck Institutes of Life Sciences. I obtained my PhD in 2011 at the Ludwig-Maximilians-University in Munich, Germany. Subsequently, I left Europe for California to join University of California San Francisco as a postdoctoral scholar. Originally from Poland, I graduated as MSc in 2006 from the Technical University of Lodz in Computer Science.

Department or University Committees

• Seminar/Distinguished Lectures Committee
   
• Climate and Diversity Committee
   
• Faculty Search - Center for Eukaryotic Gene Regulation

Program or Departmental Affiliations

Centers

Research Summary

The Armache lab is interested in understanding the mechanisms and functions of ATP-dependent chromatin remodeling complexes and their place in genome regulation. 

The genome in eukaryotes is organized into chromatin, a condensed superstructure that evolved to keep DNA protected from damage and to tightly control gene expression. The basic unit of chromatin is the nucleosome, an octamer of proteins called histones wrapped by DNA. Cells evolved chromatin regulators to control critical steps in development and differentiation through processes such as DNA methylation, post-translational histone modifications, ATP-dependent remodeling, and mechanisms that establish a specific chromatin state. To this end, histones contain elongated tails that can be post-translationally modified. This is established, maintained, and interpreted mainly by non-histone chromosomal proteins. In turn, ATP-dependent chromatin remodelers modulate DNA accessibility by repositioning DNA with respect to the histones using energy from ATP hydrolysis.

These macromolecular machines are employed and influence a range of processes, such as transcription, replication and repair. To maintain or effectuate changes in chromatin, eukaryotic cells evolved several different families of ATP-dependent remodeling factors: SWI/SNF/, ISWI, Ino80 and CHD, that possess their own unique properties. They all share the ATPase core, but contain additional domains that affect their functionalities, behavior or time at which they are activated. These complexes can contain just a single ATP-ase or can employ additional accessory subunits that change their targeting and behavior. 

In the Armache lab, we are interested in structural and mechanistic studies of ATP-dependent chromatin remodeling complexes that are associated with human diseases. We probe the structures using a range of biochemical and biophysical approaches, using cryo-electron microscopy (cryo-EM) for structural determination.

At the same time, we also extend our techniques to a number of membrane protein targets that are relevant in human diseases.

We are also interested in pushing forward the technology in electron microscopy, hoping that our efforts will increase the adoption and decrease the amount of training required by scientists to use cryo-EM.

Selected Publications

• Armache, J.-P., Cheng, Y (2019). Single particle cryo-EM-beyond the resolution. National Science Review 
   
• Morris KL, Jones JR, Halebian M, Wu S, Baker M, Armache J.-P., Avila Ibarra A, Sessions RB, Cameron AD, Cheng Y, Smith CJ. (2019). Cryo-EM of multiple cage architectures reveals a universal mode of clathrin self-assembly. NAT. STRUCT. MOL. BIOL., Oct;26(10):890-898. PMID: 31582853
   
• Armache, J.-P.*, Gamarra, N.*, Johnson, S.L., Wu, S., Leonard, J., Narlikar, G. and Cheng, Y. (2019). Cryo-EM structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome. ELIFE. JUN 18; 8. (* equal contribution). PMID: 31210637
   
• Valencia-Sanchez, M.I., De Ioannes, P., Wang,M., Vasilyev,N. Chen, R. Nudler, E., Armache, J.-P. and Armache, K.-J. (2019). Structural Basis of Dot1L Stimulation by Histone H2B Lysine 120 Ubiquitination. MOLECULAR CELL BIOLOGY, JUN 6; 74(5):1010-1019. PMID: 30981630
   
• Kintzer, A.F., Green, E., Dominik, P., Bridges, M., Armache, J.-P., Deneka, D., Kim, S., Hubbell, W., Kossiakoff, A., Cheng, Y., Stroud, R. (2018). The structural basis for activation of voltage sensor domains in an ion channel TPC1. PROC. NATL. ACAD. SCI. U.S.A., SEP 25;115. PMID: 30190435
   
• Heymann, J.B., Marabini, R., Kazemi, M., Sorzano, C.O.S., Holmdahl, M., Mendez, J.H., Stagg, S.M., Jonic, S., Palovcak, E., Armache, J.-P., Zhao, J., Cheng, Y., Pintilie, G., Chiu, W., Patwardhan, A., Carazo, J.M. (2018). The first single particle analysis Map Challenge: A summary of the assessments. J. STRUCT. BIOL., NOV; 204(2):291-300. PMID: 30114512
   
• Armache, J.-P., Lee, C., Yang, Y., Zeng, W., Mootha, V.K., Cheng, Y., Bai, X.-C., Jiang, Y. (2018). Cryo-EM structure of the mitochondrial calcium uniporter. NATURE, JULY:1-19. PMID: 29995855
   
• Zheng, S.Q., Palovcak, E., Armache, J.-P., Verba, K.A., Cheng, Y. and Agard, D.A. (2017). MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. NATURE METHODS, APR;14(4):331-332. PMID: 28250466
   
• Frauenfeld J., Löving R., Armache J.-P., Sonnen, A.F.-P., Guettou, F., Moberg, P., Zhu, L., Jegerschöld, C., Flayhan, A., Briggs, J.A.G., Garoff, H., Löw, C., Cheng, Y. & Nordlund, P. A (2016). A saposin-lipoprotein nanoparticle system for membrane proteins. NATURE METHODS, MARCH 1-11. PMID: 26950744
   
• Wu S., Armache J.-P., Cheng Y. (2016). Single-particle cryo-EM data acquisition by using direct electron detection camera. MICROSCOPY, 65(1), 35-41. PMID: 26546989
   
• Paulsen, C. E.*, Armache J.-P.*, Gao Y., Cheng Y., Julius D. (2015). Structure of the TRPA1 ion channel suggests regulatory mechanisms. NATURE, 520 (7548), 511-517. (* equal contribution) PMID: 25855297
   
• Gogala, M., Becker, T., Beatrix, B., Armache, J.-P., Barrio-Garcia, C., Berninghausen, O., Beckmann, R. (2014). Structures of the Sec61 complex engaged in nascent peptide translocation or membrane insertion. NATURE, 506, 107-110. PMID: 24499919
   
• Anger, A.M.*, Armache, J.-P.*, Berninghausen, O., Habeck, M., Subklewe, M., Wilson, D.N., and Beckmann, R. (2013). Structures of the human and Drosophila 80S ribosome. NATURE, 497, 80–85. (* equal contribution) PMID: 23636399
   
• Armache, J.-P.*, Anger, A.M.*, Márquez, V., Franckenberg, S., Fröhlich, T., Villa, E., Berninghausen, O., Thomm, M., Arnold, G.J., Beckmann, R., and Wilson, D.N. (2013). Promiscuous behaviour of archaeal ribosomal proteins: implications for eukaryotic ribosome evolution. NUCLEIC ACIDS RES., 41, 1284–1293. (* equal contribution) PMID: 23222135
   
• Grela, P., Gajda, M.J., Armache, J.-P., Beckmann, R., Krokowski, D., Svergun, D.I., Grankowski, N., and Tchórzewski, M. (2012). Solution structure of the natively assembled yeast ribosomal stalk determined by small-angle X-ray scattering. BIOCHEM. J., 444, 205–209. PMID: 22458705
   
• Becker, T., Franckenberg, S., Wickles, S., Shoemaker, C.J., Anger, A.M., Armache, J.-P., Sieber, H., Ungewickell, C., Berninghausen, O., Daberkow, I., Karcher, A., Thomm, M. Hopfner, K.-P., Green, R., and Beckmann R. (2012). Structural basis of highly conserved ribosome recycling in eukaryotes and archaea. NATURE, 482, 501–506. PMID: 22358840
   
• Jarasch, A., Dziuk, P., Becker, T., Armache, J.-P., Hauser, A., Wilson, D.N., and Beckmann, R. (2012). The DARC site: a database of aligned ribosomal complexes. NUCLEIC ACIDS RES., 40, D495–D500. PMID: 22009674
   
• Becker, T., Armache, J.-P., Jarasch, A., Anger, A.M., Villa, E., Sieber, H., Motaal, B.A., Mielke, T., Berninghausen, O., and Beckmann, R. (2011). Structure of the no-go mRNA decay complex Dom34-Hbs1 bound to a stalled 80S ribosome. NAT. STRUCT. MOL. BIOL., 18, 715–720. PMID: 21623367
   
• Márquez, V., Fröhlich, T., Armache, J.-P., Sohmen, D., Dönhöfer, A., Mikolajka, A., Berninghausen, O., Thomm, M., Beckmann, R., Arnold, G.J., and Wilson, D.N. (2011). Proteomic characterization of archaeal ribosomes reveals the presence of novel archaeal-specific ribosomal proteins. J. MOL. BIOL., 405, 1215–1232. PMID: 21134383
   
• Armache, J.-P.*, Jarasch, A.*, Anger, A.M.*, Villa, E., Becker, T., Bhushan, S., Jossinet, F., Habeck, M., Dindar, G., Franckenberg, S., Márquez, V., Mielke, T., Thomm, M., Berninghausen, O., Beatrix, B., Söding, J., Westhof, E., Wilson, D.N., and Beckmann, R. (2010a). Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution. PROC. NATL. ACAD. SCI. U.S.A., 107, 19748–19753. (* equal contribution) PMID: 20980660
   
• Armache, J.-P.*, Jarasch, A.*, Anger, A.M.*, Villa, E., Becker, T., Bhushan, S., Jossinet, F., Habeck, M., Dindar, G., Franckenberg, S., Márquez, V., Mielke, T., Thomm, M., Berninghausen, O., Beatrix, B., Söding, J., Westhof, E., Wilson, D.N., and Beckmann, R. (2010b). Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome. PROC. NATL. ACAD. SCI. U.S.A., 107, 19754–19759. (* equal contribution) PMID: 20974910
   
• Gartmann, M., Blau, M., Armache, J.-P., Mielke, T., Topf, M., and Beckmann, R. (2010). Mechanism of eIF6-mediated inhibition of ribosomal subunit joining. J. BIOL. CHEM., 285, 14848–14851. PMID: 20356839
   
• Bhushan, S., Gartmann, M., Halic, M., Armache, J.-P., Jarasch, A., Mielke, T., Berninghausen, O., Wilson, D.N., and Beckmann, R. (2010). alpha-Helical nascent polypeptide chains visualized within distinct regions of the ribosomal exit tunnel. NAT. STRUCT. MOL. BIOL., 17, 313–317. PMID: 20139981
   
• Becker, T., Bhushan, S., Jarasch, A., Armache, J.-P., Funes, S., Jossinet, F., Gumbart, J., Mielke, T., Berninghausen, O., Schulten, K., Westhof, E., Gilmore, R., Mandon, E.C, and Beckmann R. (2009). Structure of monomeric yeast and mammalian Sec61 complexes interacting with the translating ribosome. SCIENCE, 326, 1369–1373. PMID: 19933108
   
• Seidelt, B., Innis, C.A., Wilson, D.N., Gartmann, M., Armache, J.-P., Villa, E., Trabuco, L.G., Becker, T., Mielke, T., Schulten, K., Steitz, T.A., and Beckmann R. (2009). Structural insight into nascent polypeptide chain-mediated translational stalling. SCIENCE, 326, 1412–1415. PMID: 19933110