Faculty & Research

Molecular Biology Faculty

Ileana M. Cristea

ASSOCIATE Professor of Molecular Biology

Ileana Cristea

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Phone (609) 258-9417
locationLewis Thomas Lab, 210
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Faculty Assistant
william mercado
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dial_pad (609) 258-1694


Research Focus

Proteomic-Genomic approaches to chromatin and its modulation by viruses

The research in my laboratory is aimed at understanding mechanisms that control the fate of cells under invasion by pathogens, with particular emphasis on the viral modulation of chromatin remodeling machineries. The wide range of diseases caused by viruses, from the common cold to arthritis to AIDS, is a reflection of the diverse ways in which viruses interact with host cells and manipulate their basic functions. How do viruses accomplish these tasks, and how do cells respond and adapt to infection? In approaching this question, we use the full power of differential genomics and proteomics to study the modulation of chromatin remodeling complexes in both normal and virally infected cells. The state-of-the-art mass spectrometry in my laboratory focuses on the use of novel instrument configurations, which are ideally suited for the fast and sensitive characterization of macromolecular complexes.

Exploring the temporal and spatial dynamics of protein interactions

Protein interactions, of a stable or transient nature, underlie the majority of cellular processes. Knowledge of the localization, composition, and organization of protein complexes at a particular point in space and time provides key insights into their functions. We have developed a strategy that uses a single fluorescent tag to both visualize proteins in live cells and capture their interacting macromolecular partners via high-affinity immunopurifications. My previous work showed that rapid isolations are essential to preserving protein complexes close to their original state in the cell. Accordingly, we use cryogenic cell lysis in combination with 5-60 minutes immunoisolations on magnetic beads coated with in-house developed antibodies. We found that this methodology opens new doors for almost every protein complex that we have approached, leading to both insights into cellular processes and new questions. However, gaining access to low-stoichiometry and short-lived interactions is still challenging, and further methodological improvements are a necessity. The work in my laboratory will seek to push the boundaries of current proteomic techniques, and continue to devise new tools for exploring protein interactions. Effort will be placed into further decreasing the time necessary to go from a live cell to an isolated protein complex.

Walking in the proteomic footprints of viral infection

By making use of finely tuned protein interactions, viruses succeed in sabotaging intricate host processes and turning cellular systems to their own use. Although virus-host interactions have been extensively studied, our knowledge of the detailed interactions between viral and host proteins during the course of infection remains quite limited. I was interested in approaching the dynamic viral infection by tracking the localization and interactions of viral proteins in host systems as a function of infection time. We have successfully implemented our new methodologies to uncover the viral-host protein interactomes of the mosquito-borne Alphavirus Sindbis, HIV-1, and, most recently, the human cytomegalovirus. While our findings led to new hypotheses as to how viruses manipulate host cellular processes, the richness of the novel identified interactions reminded us that we are still in virtually uncharted territory in understanding the complexity of the viral-host protein relationship.

Understanding the role of chromatin remodeling complexes during viral infection

In all eukaryotes, gene expression is regulated by chromatin remodeling complexes, which use an intricate system of specialized enzymes to coordinate a series of posttranslational modifications on the N-terminal tails of histones. Our preliminary studies indicated that viruses may modulate gene expression through interactions with chromatin remodeling complexes. Indeed, histone deacetylases are targeted during infection by numerous viruses, and are reported to mediate the latency stages of cells infected with HSV-1 and HIV. Our approach provides a close look at this relationship, showing that HIV, HCMV, and Sindbis viral proteins recruit members of the chromatin remodeling complexes, including histone deacetylases, acetyltransferases, demethylases, and methyltransferases, as well as histone chaperones. While such interactions are in part virus-specific, some may reveal common pathways utilized by viruses to determine the outcome of the infection or by the cell in response to injury.

Characterizing chromatin remodeling complexes in normal and virally infected cells

Now that we have robust and efficient methodologies for the study of macromolecular interactions, we have initiated a comprehensive mapping of the chromatin remodeling interactome in normal cells. The novel interacting partners of HDAC1 so far uncovered are indicative of the multi-faceted roles of HDAC complexes in the precise orchestration of histone modifications, and we are currently exploring the roles of these specific interactions. Additionally, these analyses of unperturbed cells provide a baseline for further studies of the way cells respond to changing conditions. In particular, we will examine the effects of viral infection on chromatin remodeling complexes using approaches such as 1) tracking the localization of members of the chromatin remodeling complexes, 2) revealing the proteins that assemble these complexes, 3) identifying changes in protein-DNA interactions, 4) mapping posttranslational modifications on chromatin remodeling complexes and their targets, 5) determining protein turnover using mass spectrometry, and 6) elucidating the structures of chromatin remodeling assemblies using proteomics-based methodologies.

The proteomic approaches employed in our laboratory add a powerful new dimension to the already considerable reach of molecular biology in querying nature. Employing new ways to look at long-standing questions is one of the strongest leitmotifs in science, giving us new opportunities to appreciate, as Darwin saw it, the "grandeur in this view of life."

Selected Publications

Koyuncu OO, Song R, Greco TM1, Cristea IM1, Enquist LW2. (2015) The number of alphaherpesvirus particles infecting axons and the axonal protein repertoire determines the outcome of neuronal infection. MBio. 6. pii: e00276-15. Pubmed

Rowles DL, Tsai YC, Greco TM, Lin AE, Li M, Yeh J, Cristea IM. (2015) The DNA methyltransferase DNMT3A associates with viral proteins and impacts HSV-1 infection. Proteomics. [Epub ahead of print]

Crow MS, Javitt A, Cristea IM. (2015) A proteomics perspective on viral DNA sensors in host defense and viral immune evasion mechanisms. J Mol Biol.  [Epub ahead of print]

Diner BA, Lum KK, Javitt A, Cristea IM. (2015) Interactions of the antiviral factor IFI16 mediate immune signaling and herpes simplex virus-1 immunosuppression. Mol Cell Proteomics. [Epub ahead of print]

Diner BA, Li T, Greco TM, Crow MS, Fuesler JA, Wang J, Cristea IM. (2015) The functional interactome of PYHIN immune regulators reveals IFIX is a sensor of viral DNA. Mol Syst Biol. 11:787. Pubmed

Mathias RA, Guise AJ, Cristea IM. (2015) Post-translational modifications regulate class IIa histone deacetylase function in health and disease. Mol Cell Proteomics. 14:456-470 Pubmed

Koyuncu E, Budayeva HG, Miteva YV,...Cristea IM. (2014) Sirtuins are evolutionarily conserved viral restriction factors. MBio. 5. pii: e02249-14. Pubmed

Mathias RA, Greco TM, Oberstein A,...Cristea IM. (2014) Sirtuin 4 is a lipoamidase regulating pyruvate dehydrogenase complex activity. Cell. 159: 1615-25. Pubmed

Castellana M, Wilson MZ, Xu Y, Joshi P, Cristea IM, Rabinowitz JD, Gitai Z, Wingreen NS. (2014) Enzyme clustering accelerates processing of intermediates through metabolic channeling. Nat Biotechnol. 32: 1011-8. Pubmed

Jean Beltran PM, Cristea IM. (2014) The life cycle and pathogenesis of human cytomegalovirus infection: lessons from proteomics. Expert Rev Proteomics. 11: 697-711. Pubmed

Budayeva HG, Cristea IM. (2014) A mass spectrometry view of stable and transient protein interactions. Adv Exp Med Biol. 806: 263-82. Pubmed

Guise AJ, Mathias RA, Rowland EA, Yu F, Cristea IM. (2014) Probing phosphorylation-dependent protein interactions within functional domains of histone deacetylase 5 (HDAC5). Proteomics. 14: 2156-66. Pubmed

Li T, Chen J, Cristea IM. (2013) Human cytomegalovirus tegument protein pUL83 inhibits IFI16-mediated DNA sensing for immune evasion. Cell Host Microbe. 14: 591-99. Pubmed

Miteva YV, Cristea IM. (2013) A proteomic perspective of SIRT6 phosphorylation and interactions, and their dependence on its catalytic activity. Mol Cell Proteomics. 13: 168-83.  Pubmed

Tsai YC, Greco TM, Cristea IM. (2013) SIRT7 plays a role in ribosome biogenesis and protein synthesis. Mol Cell Proteomics. 13: 73-83. Pubmed

Rowles DL, Terhune SS, Cristea IM. (2013) Discovery of host-viral protein complexes during infection. Methods Mol Biol. 1064: 43-70. Pubmed

Lin AE, Greco TM, Dohner K, Sodeik B, Cristea IM. (2013) A proteomic perspective of inbuilt viral protein regulation: pUL46 viral tegument protein is targeted for degradation by the viral ICP0 protein during HSV-1 infection. Mol Cell Proteomics. 12: 3237-52. Pubmed

Guise AJ, Budayeva HG, Diner BA, Cristea IM. (2013) Histone ceacetylases in Herpesvirus replication and virus-stimulated host defense. Viruses. 5: 1607-32. Pubmed

Kratchmarov R, Kramer T, Greco TM,...Cristea IM, Enquist LW. (2013) Glycoproteins gE and gI are required for efficient KIF1A-dependent anterograde axonal transport of alphaherpesvirus particles in neurons. J Virol. 87: 9431-40. Pubmed

Joshi P, Greco TM, Guise AJ,...Cristea IM. (2013) The functional interactome landscape of the human histone deacetylase family. Mol Syst Biol. 9: 672. Pubmed

Kramer T, Greco TM, Taylor MP, Ambrosini AE, Cristea IM, Enquist LW. (2012) Kinesin-3 mediates axonal sorting and directional transport of alphaherpesvirus particles in neurons. Cell Host Microbe. 12: 806-14. Pubmed

Miteva YV, Budayeva HG, Cristea IM. (2012) Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions. Anal Chem. 85: 749-68. Pubmed

Greco TM, Miteva Y, Conlon FL, Cristea IM. (2012) Complementary proteomic analysis of protein complexes. Methods Mol Biol. 917: 391-407. Pubmed

Guise AJ, Greco TM, Zhang IY, Yu F, Cristea IM. (2012) Aurora B-dependent regulation of class IIa histone deacetylases by mitotic nuclear localization signal phosphorylation. Mol Cell Proteomics. 11: 1220-29. Pubmed

Gudleski-O'Regan N, Greco TM, Cristea IM, Shenk T. (2012) Increased expression of LDL receptor-related protein 1 during human cytomegalovirus infection reduces virion cholesterol and infectivity. Cell Host Microbe. 12: 86-96. Pubmed

Li T, Diner BA, Chen J, Cristea IM. (2012) Acetylation modulates cellular distribution and DNA sensing ability of interferon-inducible protein IFI16. Proc Natl Acad Sci. 109: 10558-63. PubMed

Tsai YC, Greco TM, Boonmee A, Miteva Y, Cristea IM (2012) Functional proteomics establishes the interaction of SIRT7 with chromatin remodeling complexes and expands its role in regulation of RNA polymerase I transcription. Mol Cell Proteomics. 11: 60-76. PubMed

Sabouri N, McDonald KR, Webb CJ, Cristea IM, Zakian VA. (2012) DNA replication through hard-to-replicate sites, including both highly transcribed RNA Pol II and Pol III genes, requires the S. pombe Pfh1 helicase. Genes Dev. 26: 581-93. PubMed

Goodarzi H, Najafabadi HS, Oikonomou P,...Cristea IM, Tavazoie S (2012) Systematic discovery of structural elements governing stability of mammalian messenger RNAs.  Nature. 485: 264-68. PubMed

Cowles CE, Li Y, Semmelhack MF, Cristea IM, Silhavy TJ. (2011) The free and bound forms of Lpp occupy distinct subcellular locations in Escherichia coli. Mol Microbiol. 79: 1168-81. PubMed

Kramer T, Greco TM, Enquist LW, Cristea IM. J Virol. (2011) Proteomic characterization of Pseudorabies virus extracellular virions. J Virol. 85: 6427-41. PubMed

Blanco MA, Aleckovic M, Hua Y,...Cristea IM, Kang Y. (2011) Identification of Staphylococcal nuclease domain containing 1 (SND1) as a Metadherin-interacting protein with metastasis-promoting functions. J Biol Chem. 286: 19982-92. PubMed

Cowles CE, Li Y, Semmelhack MF, Cristea IM, Silhavy TJ. (2011) The free and bound forms of Lpp occupy distinct subcellular locations in Escherichia coli. Mol Microbiol. 79: 1168-81. PubMed

Greco TM, Yu F, Guise AJ, Cristea IM. (2010) Nuclear import of histone deacetylase 5 by requisite nuclear localization signal phosphorylation. Mol Cell Proteomics. 10: M110.004317. PubMed

Moorman NJ, Sharon-Friling R, Shenk T, Cristea IM. (2010) A targeted spatial-temporal proteomics approach implicates multiple cellular trafficking pathways in human cytomegalovirus virion maturation. Mol Cell Proteomics. 9: 851-60. PubMed

Terhune SS, Moorman NJ, Cristea IM,...Shenk T. (2010) Human cytomegalovirus UL29/28 protein interacts with components of the NuRD complex which promote accumulation of immediate-early RNA. PLoS Pathog. 6: e1000965. PubMed

Cristea IM, Moorman NJ, Terhune SS,...Shenk T. (2010) Human cytomegalovirus pUL83 stimulates activity of the viral immediate-early promoter through its interaction with the cellular IFI16 protein. J Virol. 84: 7803-14. PubMed

Carabetta VJ, Silhavy TJ, Cristea IM. (2010) The response regulator SprE (RssB) is required for maintaining PAP I-degradosome association during stationary phase. J Bacteriol. 192: 3713-21. PubMed

Cristea IM, Rozjabek H, Molloy KR,...Macdonald MR. (2010) Host factors associated with the Sindbis virus RNA-dependent RNA polymerase: a role for G3BP1 and G3BP2 in virus replication. J Virol. 84: 6720-32. PubMed

Carabetta VJ, Li T, Shakya A, Greco TM, Cristea IM. (2010) Integrating Lys-N proteolysis and N-terminal guanidination for improved fragmentation and relative quantification of singly-charged ions. J Am Soc Mass Spectrom. 21: 1050-60. PubMed

Goldberg AD, Banaszynski LA, Noh KM,...Cristea IM,...Allis CD. (2010) Distinct factors control histone variant H3.3 localization at specific genomic regions. Cell 140: 678-91. PubMed

Moorman NJ, Sharon-Friling R, Shenk T, Cristea IM. (2009) A targeted spatial-temporal proteomic approach implicates multiple cellular trafficking pathways in human cytomegalovirus virion maturation. Mol Cell Proteomics. 9: 851-60. PubMed

Luo Y, Li T, Yu F, Kramer T, Cristea IM. (2009) Resolving the composition of protein complexes using a MALDI LTQ orbitrap. J Am Soc Mass Spectrom. 21: 34-46. PubMed

Selimi F, Cristea IM, Heller E, Chait BT, Heintz N. (2009) Proteomic studies of a single CNS synapse type: the parallel fiber/purkinje cell synapse. PLoS Biol. 7: 948-57. PubMed

Moorman NJ, Cristea IM, Terhune SS, Rout MP, Chait BT, Shenk T. (2008) Human cytomegalovirus protein UL38 inhibits host cell stress responses by antagonizing the tuberous sclerosis protein complex. Cell Host Microbe. 3: 253-62. PubMed

Glavy JS, Krutchinsky A, Cristea IM,...Chait BT. (2007) Cell-cycle dependent phosphorylation of the nuclear pore Nup107-160 subcomplex. Proc Natl Acad Sci. 104: 3811-16. PubMed

Warwood S, Mohammed S, Cristea IM, Evans C, Whetton AD, Gaskell SJ. (2006) Guanidination chemistry for qualitative and quantitative proteomics. Rapid Commun Mass Spectrom. 20: 3245-56. PubMed

Cristea IM, Carroll JW, Rout MP, Rice CM, Chait BT, MacDonald MR. (2006) Tracking and elucidating alphavirus-host protein interactions. J Biol Chem. 281: 30269-78. PubMed

Wang QJ, Ding Y, Kohtz DS,...Cristea IM,...Yue Z. (2006) Induction of autophagy in axonal dystrophy and degeneration. J Neurosci. 26: 8057-68. PubMed

Cristea IM, Williams R, Chait BT, Rout MP. (2005) Fluorescent proteins as proteomic probes. Mol Cell Proteom. 4: 1933-41. PubMed

Cristea IM, Degli Esposti M. (2004) Membrane lipids and cell death: an overview. Chem Phys Lipids. 129: 133-60. PubMed

Sorice M, Circella A, Cristea IM,...Degli Esposti M. (2004) Cardiolipin and its metabolites move from mitochondria to other cellular membranes during death receptor-mediated apoptosis. Cell Death Differ. 11: 1133-45. PubMed

Meneses-lorente G, Guest P, Lawrence J,...Cristea I,...Watt A. (2004) A proteomic investigation of drug induced steatosis in rat liver. Chem Res Toxicol. 17: 205-12.

Cristea IM, Gaskell SJ, Whetton DW. (2004) Proteomics techniques and their application to hematology. Blood 103: 3624-34. PubMed

Degli Esposti M, Cristea IM, Gaskell SJ, Nakao Y, Dive C. (2003) Pro-apoptotic Bid binds to monolysocardiolipin, a new molecular connection between mitochondrial membranes and cell death. Cell Death Differ. 10: 1300-09. PubMed

Fairlamb IJS, Dickinson JM, Cristea IM. (2001) Influence of palladium(II) complexes on the cycloaddition of α-bromoalkyl ketenes to cyclopentadiene. Tetrahedron. 57: 2237.

Fairlamb IJS, Dickinson JM, Cristea IM. (2000) Palladium-catalysed [π2a + π2s] of α-bromoalkyl ketenes to cyclopentadiene. Tetrahedron Lett. 41: 3739.

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