Karolin Luger

Karolin LugerUniversity Distinguished Professor, Howard Hughes Medical Institute Investigator
Office: MRB 341
Phone: 970-491-6405
Website: http://lugerlab.org
Education: Ph.D., University of Basel
Email: Karolin.Luger@ColoState.edu
Research Title: Structure and function of eukaryotic chromatin

We are investigating the structural biology of chromatin. Our overreaching goal is to refine the overall view of chromatin's architecture by understanding how the nucleosome interfaces with the cellular machinery based on sequence variations in its own proteins or interactions with outside molecules.

Our long-term goal research is to investigate the structural properties of chromatin, and to understand how transcription, replication, recombination, and repair take place within the context of highly compacted chromatin. We are particularly interested in mechanistic and structural aspects of these fundamental questions. We are using multipronged approaches including x-ray crystallography, small-angle x-ray scattering, fluorescence resonance energy transfer, analytical ultracentrifugation, and atomic force microscopy, conventional biochemistry, molecular biology, and yeast genetics to investigate fundamental questions of chromatin structure control.

Interaction of Nucleosomes with Transcription Factors and other cellular proteins.
The nucleosome is the elemental repeating unit in chromatin, consisting of two copies each of the four histone proteins (the histone octamer) around which 146 base pairs of DNA are wrapped in nearly two turns of a tight superhelix. Using a combination of methods, most notably x-ray crystallography and fluorescence resonance energy transfer, we investigate the structural determinants and the structural changes that are inflicted upon the nucleosome and the interacting protein upon binding to nucleosomal DNA. Effects on higher-order structure are also studied using analytical ultracentrifugation and atomic force microscopy. Several of the factors under investigation are of clinical importance, either as targets for anti-cancer drugs, or because mutations in the corresponding gene are correlated with certain diseased states.

For example, by studying how Kaposi's sarcoma herpesvirus protein LANA (latency-associated nuclear antigen) enables the viral genome to tether onto chromosomes so that virus is not lost from cells, we found that LANA engages histones H2A and H2B to dock onto chromosomes by binding to the nucleosomal surface via a tight hairpin motif. This study (which is the result of an ongoing collaboration with Kenneth Kaye [Harvard Medical School]) unequivocally demonstrates how a highly structured nucleosomal surface acts as an interaction platform for molecular recognition.

Nucleosome Assembly and Histone Exchange
Eukaryotic chromatin is highly dynamic and turns over rapidly in the absence of DNA replication and transcription. Acidic histone chaperones such as Nucleosome Assembly Protein 1 (NAP1) are implicated in this process. Although initially identified as histone chaperones and chromatin assembly factors, additional functions include roles in tissue-specific transcription regulation, apoptosis, histone shuttling, cell cycle regulation etc., and thus extend beyond those of a simple chaperone and assembly factor. Some family members are essential in mammals due to an as yet uncharacterized role in neuronal development. Several have been characterized as oncoproteins, and many have been found in complex with enzymes that post-translationally modify histones, or are implicated in ATP-dependent chromatin remodeling.

In vitro, NAP1 reversibly removes and replaces H2A-H2B or histone variant dimers from assembled nucleosomes, resulting in active histone exchange and nucleosome sliding. The significance of these functions is being investigated in vivo. The crystal structure of yeast NAP1 is the first for a NAP family member and reveals a novel fold with implications for histone transport and exchange. The structure suggested several hypotheses regarding the function of the NAP1 protein family that are now being tested by a variety of methods, for example, small angle x-ray scattering, FRET, and in vivo studies (These studies are also supported by a grant from the National Institutes of Health.)

Histone Variants
The replacement of canonical histones with histone variants has emerged as an important pathway to alter the biochemical makeup of chromatin locally, with the potential to exert considerable influence on the structure and function of chromatin. Histone variants are distinct nonallelic forms of conventional, major-type histones that form the bulk of nucleosomes during replication and whose synthesis is tightly coupled to S phase. They are found in most eukaryotic organisms and are expressed in all tissue types. We investigate the structures of variant nucleosomes and the effect of histone variant incorporation on higher order structure formation, and also test the hypothesis that specific histone chaperones are involved in their dynamic exchange.

Selected Publications


Luger, K., Mäder, A., Richmond, R.K., Sargent, D. F. and Richmond, T.J. (1997). Structure of the nucleosome core particle at 2.8Å resolution. Nature, 389, 251-260.

Luger, K., Rechsteiner, T., Flaus, A., Waye, M. M. Y. and Richmond, T.J. (1997). Characterization of nucleosome core particles containing bacterial expressed histone proteins. J. Mol. Biol., 272, 301-311.

Suto, R.K., Clarkson, M.J., Tremethick, D.J. and Luger, K. (2000). Crystal Structure of a Nucleosome Core Particle Containing the Variant Histone H2A.Z. Nature Structural Biology, 7, 1121-1124.

Gottesfeld, J.M., Melander, C., Suto, R.K., Raviol, H., Luger, K. and Dervan, P.B. (2001). Sequence-specific Recognition of DNA in the Nucleosome by Pyrrole-Imidazole Polyamides. J. Mol. Biol., 309, 615-629.

Gottesfeld, J.M. and Luger, K. (2001). Energetics and Affinity of the Histone Octamer for Defined DNA Sequences. Biochemistry, 40, 10927-10933.

White, C.L., Suto R.K. and Luger, K. (2001). Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions. Embo J., 20, 5207-5218.

Fan, J.Y., Gordon, F., Luger, K., Hansen, J.C. and Tremethick, D.J. (2002). The essential histone variant H2A.Z regulates the equilibrium between different chromatin conformational states. Nature Structural Biology, 9, 172-176.

Georges, S.A., Kraus, W.L., Luger, K., Nyborg, J.K. and Laybourn, P.J. (2002). p300-Mediated Tax Transactivation from Recombinant Chromatin: Histone Tail Deletion Mimics Coactivator Function. Mol. Cell. Biol., 22, 127-137.

Davey, C.A., Sargent, D.F., Luger, K., Maeder, A.W. and Richmond, T.J. (2002). Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. J. Mol. Biol., 319, 1097-113.

Gottesfeld, J. M., Belitsky, J. M., Melander, C., Dervan, P. B. and Luger, K. (2002). Blocking transcription through a nucleosome with synthetic DNA ligands. J. Mol. Biol., 321, 249-263.

Suto, R. K., Edayathumangalam, R. S., White, C. L., Melander, C., Gottesfeld, J. M., Dervan, P. B. and Luger, K. (2002). Ligand binding alters the structure and dynamics of nucleosomal DNA. J. Mol. Biol. 326, 371-380.

Georges, S.A., Giebler, H.A., Cole, P.A., Luger, K., Laybourn, P.J. and Nyborg, J.K. (2003). Tax recruitment of CBP/p300, via the KIX domain, reveals a potent requirement for acetyltransferase activity that is chromatin dependent and histone tail independent. Mol. Cell. Biol., 23, 3392-404.

McBryant, S.J., Park, Y.J., Abernathy, S.M., Laybourn, P.J., Nyborg, J.K. and Luger, K. (2003). Preferential binding of the histone (H3-H4)2 tetramer by NAP1 is mediated by the amino-terminal histone tails. J. Biol. Chem., 278, 44574-83.

Muthurajan, U.M., Bao, Y., Forsberg, L.J., Edayathumangalam, R.S., Dyer, P.N., White, C.L. and Luger, K. (2004). Crystal Structures of Histone Sin Mutant Nucleosomes reveal altered Protein-DNA Interactions. Embo. J., 23, 260-271.

Edayathumangalam, R. S., Weyermann, P., Gottesfeld, J. M., Dervan, P. B. and Luger, K. (2004). Molecular recognition of the nucleosomal "supergroove". Proc. Natl. Acad. Sci. USA, 101, 6864-9 (cover illustration).

Park, Y. J., Dyer, P. N., Tremethick, D. J. and Luger, K. (2004). A New Fluorescence Resonance Energy Transfer Approach Demonstrates That the Histone Variant H2AZ Stabilizes the Histone Octamer within the nucleosome. J. Biol. Chem., 279, 24274-24282.

Black, Ben E., Foltz, Daniel R., Chakravarthy, Srinivas, Luger, K., Woods Jr., Virgil L. and Cleveland, Don W. (2004). Structural determinants for generating centromeric chromatin, Nature., 430, 578-82.

Bao, Y., Konesky, K., Park, Y. J., Rosu, S., Dyer, P. N., Rangasamy, D., Tremethick, D. J., Laybourn, P. J., and Luger, K. (2004). Nucleosomes containing the histone variant H2A.Bbd organize only 118 base pairs of DNA. Embo J., 23, 3314-24.

Edayathumangalam, R.S., Weyermann, P., Gottesfeld, J.M., Dervan, P.B. and Luger, K. (2004). Molecular recognition of the nucleosomal "supergroove". Proc. Natl. Acad. Sci. USA, 101, 6864-9.

Fan, J.Y., Rangasamy, D., Luger, K. and Tremethick, D.J. (2004). H2A.Z alters the nucleosome surface to promote HP1alpha-mediated chromatin fiber folding. Mol. Cell, 16, 655-61.

Park, Y.J., Chodaparambil, J.V., Bao, Y., McBryant, S.J. and Luger, K. (2004). Nucleosome assembly protein 1 exchanges histone H2A-H2B dimers and assists nucleosome sliding. J. Biol. Chem., 280:1817-1825.

White, C.L. and Luger, K. (2004). Defined structural changes occur in a nucleosome upon Amt1 transcription factor binding. J. Mol. Biol., 342, 1391-402.

Gordon, F., Luger, K. and Hansen, J. C. (2005). The core histone N-terminal tail domains function independently and additively during salt-dependent oligomerization of nucleosomal arrays. J. Biol. Chem. 280, 33701-33706.

Edayathumangalam, R.S., Weyermann, P., Dervan, P.B., Gottesfeld, J.M. and Luger, K. (2005). Nucleosomes in solution exist as a mixture of twist-defect states. J. Mol. Biol., 345, 103-14.

Chakravarthy, S., Gundimella, S. K., Caron, C., Perche, P. Y., Pehrson, J. R., Khochbin, S. and Luger, K. (2005). Structural characterization of the histone variant macroH2A. Mol. Cell. Biol., 25, 7616-7624.

Edayathumangalam, R. S. and Luger, K. (2005). The temperature of flash-cooling has dramatic effects on the diffraction quality of nucleosome crystals. Acta Crystallogr D Biol Crystallogr, 61, 891-898.

Barbera, A. J., Chodaparambil, J. V., Kelley-Clarke, B., Joukov, V., Walter, J. C., Luger, K. and Kaye, K. M. (2006). The nucleosomal surface as a docking station for Kaposi's sarcoma herpesvirus LANA. Science, 5762, 856-861.

Park, Y. J. and Luger, K. (2006). The structure of nucleosome assembly protein 1. Proc. Natl. Acad. Sci. USA, 103, 1248-1253.

Bao, Y., White, C. and Luger, K. (2006). Nucleosome core particles containing a Poly(dAdT) sequence element exhibit a locally distorted DNA structure. J. Mol. Biol., 361, 617-624.

Chakravarthy, S., and Luger, K. (2006). The histone variant macroh2a preferentially forms 'hybrid nucleosomes'. J. Biol. Chem., 281, 25522-31.

Subramanian, V., Ducept, P., Williams, R. M., and Luger, K. (2007). Effects of Photochemically Activated Alkylating Agents of the FR900482 Family on Chromatin. Chem Biol 14, 553-563.

Chodaparambil, J., Barbera, A. J., Lu, X., Kaye, K. M., Hansen, J. C., and Luger, K. (2007). A charged and contoured surface on the nucleosome regulates chromatin compaction. Nat Struct Mol Biol, 14, 1105-1107.

Clapier, C.R., Chakravarthy, S., Petosa, C., Fernandez-Tornero, C., Luger, K. and Muller, C.W. (2007). Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A-H2B histone dimer. Proteins, 71, 1-7.

Park, Y.J., McBryant, S.J. and Luger, K. (2008). A beta-hairpin comprising the nuclear localization sequence sustains the self-associated states of Nucleosome Assembly Protein 1. JMB, 375, 1076-1085.

Lu, X., Simon, M. D., Chodaparambil, J., Hansen, J. C., Shokat, K. M., and Luger, K. (2008). The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin structure. Nat Struct Mol Biol, 15, 1122-1124.

Park, Y. J., Sudhoff, K. B., Andrews, A. J., Stargell, L. A., and Luger, K. (2008). Histone chaperone specificity in Rtt109 activation. Nat Struct Mol Biol, 15, 957-964.

Andrews, A.J., Downing, G., Brown, K., Park, Y.J., and Luger, K. (2008). A Thermodynamic Model for Nap1-Histone Interactions. J. Biol. Chem., 283, 32412-32418.

Sekiya, T., Muthurajan, U., Luger, K., Tulin, A. and Zaret, K. (2009). Nucleosome-binding affinity as a primary determinant of the nuclear mobility of the pioneer transcription factor FoxA. Genes & Dev, 23: 804-809.

Lilyestrom, W., van der Woerd, M., Clark, N., Luger, K. (2009). Structural and Biophysical Studies of Human PARP-1 in Complex with Damaged DNA. J. Mol. Biol. (in press).

Andrews, A.J., Chen, X., Zevin, A., Stargell, L.A., Luger, K. (2010). The histone chaperone Nap1 promotes nucleosome assembly by eliminating non-nucleosomal histone DNA interactions. Mol Cell 37, 834-842 .

Watanabe, S., Resch, M., Lilyestrom, W., Clark, N., Hansen, J., Peterson; C., and Luger, K. (2010). Structural characterization of H3K56Q nucleosomes and nucleosomal arrays. Biochem Biophys Acta 1799, 480-486.

Andrews, A.J., Chen, X., Zevin, A., Stargell, L.A., and Luger, K. (2010). The Histone Chaperone Nap1 Promotes Nucleosome Assembly by Eliminating Nonnucleosomal Histone DNA Interactions. Mol Cell 37, 834-842.

Pujari, V. et al. (2010).The Transcription Factor Spn1 Regulates Gene Expression via a Highly Conserved Novel Structural Motif. J Mol Biol 404, 1-15.

Lilyestrom, W., van der Woerd, M.J., Clark, N. & Luger, K. (2010). Structural and biophysical studies of human PARP-1 in complex with damaged DNA. J Mol Biol 395, 983-94.

Panchenko, T. et al. (2011). Replacement of histone H3 with CENP-A directs global nucleosome array condensation and loosening of nucleosome superhelical termini. Proc Natl Acad Sci U S A 108, 16588-93.

Kappes, F. et al. (2011).  The DEK oncoprotein is a Su(var) that is essential to heterochromatin integrity. Genes Dev 25, 673-8.

Dechassa, M.L. et al. (2011). Structure and Scm3-mediated assembly of budding yeast centromeric nucleosomes. Nat Commun 2, 313.

Andrews, A.J., and Luger, K. (2011). Nucleosome structure(s) and stability: Variations on a theme. Annual Reviews of Biophysics 40, 99-117.

Winkler, D.D., and Luger, K. (2011). The histone chaperone FACT: structural insights and mechanisms for nucleosome reorganization. J Biol Chem 286, 18369-74.

Muthurajan, U.M., McBryant, S.J., Lu, X., Hansen, J.C. & Luger, K. (2011). The linker region of macroH2A promotes self-association of nucleosomal arrays. J Biol Chem 286, 23852-64.

Winkler, D.D., Muthurajan, U.M., Hieb, A.R. & Luger, K. (2011). Histone Chaperone FACT Coordinates Nucleosome Interaction through Multiple Synergistic Binding Events. J Biol Chem 286, 41883-92.

Yang, C., van der Woerd, M.J., Muthurajan, U.M., Hansen, J.C. & Luger, K. (2011). Biophysical analysis and small-angle X-ray scattering-derived structures of MeCP2-nucleosome complexes. Nucleic Acids Res 39, 4122-35.

Boehm, V., Hieb, A.R., Andrews, A.J., Gansen, A., Rocker, A., Toth, K., Luger, K., and Langowski, J. (2011). Nucleosomal DNA accessibility governed by the dimer/tetramer interface. Nucleic Acids Res., 39, 3093-102.

Winkler, D.D., Zhou, H., Dar, M.A., Zhang, Z. & Luger, K. (2012). Yeast CAF-1 assembles histone (H3-H4)2 tetramers prior to DNA deposition. Nucleic Acids Res 40, 10139-49.

Hieb, A.R., D'Arcy, S., Kramer, M.A., White, A.E. & Luger, K. (2012). Fluorescence strategies for high-throughput quantification of protein interactions. Nucleic Acids Res 40, e33.

Gerhold, C.B. et al. (2012). Structure of Actin-related protein 8 and its contribution to nucleosome binding. Nucleic Acids Res 40.21:11036-11046.       

Fierz, B., Kilic, S., Hieb, A.R., Luger, K. & Muir, T.W. Stability of Nucleosomes Containing Homogenously Ubiquitylated H2A and H2B Prepared Using Semisynthesis. J Am Chem Soc 134.48: 19548-19551.

Clark, N.J., Kramer, M., Muthurajan, U.M. & Luger, K. (2012). Alternative Modes of Binding of Poly(ADP-ribose) Polymerase 1 to Free DNA and Nucleosomes. J Biol Chem 287, 32430-9.

Sheinin, M. Y., Li, M., Soltani, M., Luger, K. & Wang, M. D. (2013). Torque modulates nucleosome stability and facilitates H2A/H2B dimer loss. Nat Commun 4, 2579.

Rogge, R. A., Kalashnikova, A. A., Muthurajan, U. M., Porter-Goff, M. E., Luger, K. & Hansen, J. C. (2013). Assembly of nucleosomal arrays from recombinant core histones and nucleosome positioning DNA. J Vis Exp.

Hsieh, F. K., Kulaeva, O. I., Patel, S. S., Dyer, P. N., Luger, K., Reinberg, D. & Studitsky, V. M. (2013). Histone chaperone FACT action during transcription through chromatin by RNA polymerase II. Proc Natl Acad Sci U S A 110, 7654-9.

D'Arcy, S. et al. (2013). The histone chaperone Nap1 shields histone surfaces required for nucleosome formation and can place H2A-H2B in an unconventional tetrameric form. Mol Cell 51, 662-677.

Kalashnikova, A.A. et al. (2013). Linker histone H1.0 interacts with an extensive network of proteins found in the nucleolus. Nucleic Acids Res.

Kapoor, P., Chen, M., Winkler, D.D., Luger, K. & Shen, X. (2013). Evidence for monomeric actin function in INO80 chromatin remodeling. Nat Struct Mol Biol.

Chen, C. C., Dechassa, M. L., Bettini, E., Ledoux, M. B., Belisario, C., Heun, P., Luger, K. & Mellone, B. G. (2014). CAL1 is the Drosophila CENP-A assembly factor. J Cell Biol.

Chodaparambil, J.V., Pate, K.T., Hepler, M.R., Tsai, B.P., Muthurajan, U.M., Luger, K., Waterman, M.L., Weis, W.I. (2014). Molecular functions of the TLE tetramerization domain in Wnt target gene repression.  EMBO J.  Mar 3. [Epub ahead of print].

Reviews, book chapters, methods articles

Luger, K. and Richmond, T.J. (1998). The histone tails of the nucleosome. Current Opinion in Gen. Development. 8,140-146.

Luger, K. and Richmond, T.J. (1998). DNA binding within the nucleosome core. Current Opinion in Structural Biology, 8, 33-40.

Luger, K., Rechsteiner, T. and Richmond, T.J. (1999). Expression and purification of recombinant histones, and nucleosome reconstitution. Methods Enzymology, 304, 3-19.

Luger, K. (2000). Nucleosomes: Structure and Function. Encyclopedia of Life Sciences.

Dyer, P. N., Edayathumangalam, R. S., White, C. L., Bao, Y., Chakravarthy, S., Muthurajan, U. M. and Luger, K. (2004). Reconstitution of nucleosome core particles from recombinant histones and DNA. Methods Enzymol. 375, 23-44.

Muthurajan, U.M., Park, Y.J., Edayathumangalam, R.S., Suto, R.K., Chakravarthy, S., Dyer, P.N. and Luger, K. (2003). Structure and dynamics of nucleosomal DNA. Biopolymers, 68, 547-56.

Luger, K. (2003). Structure and dynamic behavior of nucleosomes. Curr Opin Genet Dev, 13, 127-35.

Chakravarthy, S., Park, Y.J., Chodaparambil, J.V., Edayathumangalam, R.S. and Luger, K. (2004). Structure and dynamic properties of nucleosome core particles. FEBS Letters (Nobel edition), 579, 595-598.

Luger, K. and Hansen, J. C. (2005). Nucleosome and chromatin fiber dynamics. Curr. Opin. Struct. Biol. 15, 188-96.

Luger, K. (2006). Dynamic Nucleosomes. Chromosome Res. 14, 5-16.

Park, Y. J. and Luger, K. (2006). Structure and function of Nucleosome assembly proteins. Biochemistry and Cell Biology 84, 549-558.

Barbera, A. J., Chodaparambil, J. V., Kelley-Clarke, B., Luger, K. and Kaye, K. M. (2006). Kaposi's sarcoma-associated herpesvirus LANA hitches a ride on the chromosome. Cell Cycle 5, 1048-1052.

Chodaparambil, J.V., Edayathumangalam, R.S., Bao, Y., Park,Y.J. and Luger, K. (2006). Nucleosome structure and function. Ernst Schering Res Found Workshop. (57):29-46.

Park, Y.J. & Luger, K. (2008). Histone chaperones in nucleosome eviction and histone exchange. Curr Opin Struct Biol 18, 282-9.

Andrews, A.J. & Luger, K. (2009). Histone Modifications: Chemistry and Structural Consequences. Wiley Encyclopedia of Chemical Biology 1, 275-284 .

Dechassa, M.L., D'Arcy, S., and Luger, K. (2009). A Positive Spin on the Centromere. Cell, 138, 22-24.           

Hansen, J.C., Nyborg, J.K., Luger, K., and Stargell, L.A. (2010). Histone chaperones, histone acetylation, and the fluidity of the chromogenome. J Cell Physiol 224, 289-299.

Luger, K. & Phillips, S.E. (2010). Rise of the molecular machines. Curr Opin Struct Biol 20, 70-2.

Subramanian, V., Williams, R.M., Boger, D.L. & Luger, K. (2010). Methods to characterize the effect of DNA-modifying compounds on nucleosomal DNA. Methods Mol Biol 613, 173-92.

Andrews, A.J., and Luger, K. (2011). Nucleosome structure(s) and stability: Variations on a theme. Annual Reviews of Biophysics 40, 99-117

D'Arcy, S. & Luger, K. (2011). Understanding histone acetyltransferase Rtt109 structure and function: how many chaperones does it take? Curr Opin Struct Biol.

Andrews, A.J., and Luger, K. (2011). A coupled equilibrium approach to study nucleosome thermodynamics. Methods in Enzymology.

Dechassa, M.L. & Luger, K. (2011). Nucleosomes as control elements for accessing the genome. in In Genome organization and function in the cell nucleus. (ed. Rippe, K.). Wiley-VCH, Weinheim.

Luger, K., Dechassa, M.L. & Tremethick, D.J. (2012). New insights into nucleosome and chromatin structure: an ordered state or a disordered affair? Nat Rev Mol Cell Biol 13, 436-47.

Winkler, D.D., Luger, K. & Hieb, A.R. (2012). Quantifying Chromatin-Associated Interactions: The HI-FI System. Methods Enzymol 512, 243-74.

Phillips, S.E. & Luger, K. (2012). Proteins for packaging, partitioning, processing, and proofing of nucleic acids . Curr Opin Struct Biol.

Earnshaw, W.C. et al. (2013). Esperanto for histones: CENP-A, not CenH3, is the centromeric histone H3 variant. Chromosome Res.

Kalashnikova, A.A., Porter-Goff, M.E., Muthurajan, U.M., Luger, K. & Hansen, J.C. (2013). The role of the nucleosome acidic patch in modulating higher order chromatin structure. J R Soc Interface 10, 20121022.

NIH PubMed Publications List