Biology Department Biology Department  



John J. Dunn


Brookhaven National Laboratory
From: 05/01/1973 - 07/13/2012


Past Research Interests

Genome Signature Tags:
     It is well established that interactions between transcription factors and their cognate DNA binding sites form fundamental combinatorial networks within cells that control critical steps in gene expression. Currently, our understanding of how cells encode the diversity of information about where and when genes will be expressed is very limited. Cracking this 'regulatory code' by computational analysis and functional assays is a major problem in biology. The Dunn lab has combined Genomic Signature Tags (GSTs) technology, a method for identifying and quantitatively analyzing genomic DNAs originally devised in our lab, with chromatin immunoprecipitation (ChIP) assays to develop several whole genome, high-throughput, sequence-based approaches for delimiting the positions of bound regulatory proteins in living cells. In one protocol, pairs of 20-21 bp long GST's, derived from both ends of ChIP precipitated DNA fragments, are sequenced en masse to identify the genomic segments originally present in these complexes. Prior to sequencing, short bar-coding oligonucleotides are inserted between the GST pairs from each ChIP sample. The bar-codes allow different samples to be mixed and then sequenced in a multiplex format. We are also developing methods that will use antibodies biotinylated in vitro for ChIP to permit more stringent washing of the pulled-down samples. This should result in a higher signal to noise ration which would be advantageous for direct Solexa-based sequencing of the recovered ChIP DNA fragments.

     Vertebrate DNA is heavily methylated at cytosine residues in CpG dinucleotide sequences to form 5mCpG except for short stretches of CpG-rich DNA, CpG islands, about 0.5 to 2 kb long which are normally free of cytosine methylation. Methylation within CpG islands is a common way to regulate nearby gene activity without altering the DNA code. Recent studies have suggested that aberrant methylation within CpG islands which is referred to as an epigenetic modification may play an important role in mediating stable changes in nervous system function including the behavioral changes seen in psychiatric disorders such as schizophrenia. Our hypothesis is that similar changes are probably associated with methamphetamine (MA) associated drug-induced dependence and psychosis. Our goal is to develop methods to detect methylated CpG dinucleotides near genes with clinical relevance following MA treatment of rodents using DNA samples isolated from different brain regions. The technology is relevant to developing systems to understand drug addiction, cancer and ageing as well as the cellular responses of human cells to low doses of ionizing radiation for DOEís Low Dose Radiation Program. The methodology also is applicable to understanding how cytosine methylation regulates gene expression in plants and is therefore potentially important for future research as part of BNLís initiative to develop sustainable biofuels.
     The major principle behind our work is that largely intact CpG islands with methylated residues can be isolated by exploiting the differential affinity of these DNA fragments for recombinant proteins containing methyl-CpG binding domains. The fragments can then be identified by hybridization or by cloning and sequencing using our GST-based methods. All these approaches are being used in our present studies. In particular we are investigating whether the E. coli McrA protein, a putative mC-specific nuclease, can be used to cleave DNA at mC residues. To this end we have cloned, expressed and purified the recombinant protein to homogeneity. Current efforts are aimed at determining whether McrA is a nuclease or if it exerts its biological effect by binding to mC containing DNA. We also plan to test whether the DNA glycosylase/lyase activity of the Arabidopsis ROSI protein can be used to cleave vertebrate and plant DNA which contains mCpG and mCpNpG sequences at the mCs.

Lyme Disease:
     In an ongoing collaborative effort, we are conducting genomic and proteomic analyses of the Lyme disease spirochete, Borrelia burgdorferi to understand how specific gene products participate in immune evasion and pathogenicity. Our laboratory is part of a large group effort to determine the whole genome sequences of several pathogenic and non-pathogenic Borrelia strains. One aspect of our work involves developing multiple displacement amplification or MDA-based approaches to amplify specific plasmids for further analysis from the very complicated mixture of plasmids present in early Borrelia isolates. These same amplification techniques are being exploited as part of a collaborative project with Eli Hatchwell (Stony Brook University) to amplify human DNA and still retain its epigenetic profile. One problem with standard PCR-based DNA amplification methodology is that all methylated CpG dinucleotides in a DNA template are converted to unmodified CpGs.


Selected Publications

Note: The PDB files below can be viewed with
  • Gnatenko, D. V., Dunn J.J., Schwedes, J., and Bahou, W. F.
    Transcript profiling of human platelets using microarray and serial analysis of gene expression (SAGE).
    DNA and RNA Profiling in Human Blood, P. Bugert, Editor, Chapter 16, Vol. 496, pp. 245-272, Humana Press Inc., Totowa, NJ (January, 2009).
  • Gnatenko, D. V., Dunn J.J., Schwedes, J., and Bahou, W. F.
    Transcript profiling of human platelets using microarray and serial analysis of gene expression (SAGE).
    Methods in Molecular Biology, 496:245-272 (January, 2009).  PubMed
  • Mulligan E.A. and Dunn J.J.
    Cloning, purification and initial characterization of E. coli McrA, a putative 5-methylcytosine-specific nuclease.
    Protein Expression and Purification, 62(1):98-103 (2008). PubMed
  • Schutzer S.S., Schlater L.R.K., Nierman W.C., Luft B.J., DeShazer D., Dunn J.J., Fraser C.M. and Ronning C.M.
    Characterization of clinically-attenuated Burkholderia mallei by whole genome sequencing: Candidate for exclusion from Select Agent lists.
    PLoS ONE, 30;3(4):e2058 (2008). PubMed
  • Xu Y., Gao S., Bruno J. F., Luft B.J. and Dunn J.J.
    Rapid detection and identification of a pathogenís DNA using phi29 DNA polymerase.
    Biochemical and Biophysical Research Communications, 375(4):522-525 (2008). PubMed
  • Dunn J.J., McCorkle S.R., Everett L. and Anderson C.W..
    Paired-end Genomic Signature Tags: A Method for the Functional Analysis of Genomes and Epigenomes.
    Genet Eng(NY), 28:159-173 (2007).   PubMed
  • Otto S.J., McCorkle S.R., Hover J., Conaco C., Han J.-J., Impey S., Yochum G.S., Dunn J.J., Goodman R.H. and Mandel G.
    A new binding motif for the transcriptional repressor REST uncovers large gene networks devoted to neuronal functions.
    J. Neurosci., 27(25):6729-6739 (2007).  PubMed
  • Graziano V., McGrath W.J., DeGruccio A.M., Dunn J.J., and Mangel W.F.
    Enzymatic activity of the SARS coronavirus main proteinase dimer.
    FEBS Lett., 580(11):2577-2583 (2006).  PubMed
  • van der Lelie D., Lesaulnier C., McCorkle S., Geets J., Taghavi S. and Dunn J.J.
    Use of single-point genome signature tags as a universal tagging method for microbial genome surveys.
    Appl. Environ. Microbiol., 72(3):2092-2101 (2006).
  • Yang X.-H., Li Y., Dunn J.J. and Luft B.J.
    Characterization of a unique Borreliacidal epitope on the outer surface protein C of Borrelia burgdorferi.
    FEMS Immunol. Med. Microbiol., 48:64-74 (2006).  PubMed
  • Budowle B., Schutzer S.E., Asher M.S., Atlas R.M., Burans J. P., Chakraborty R., Dunn J.J., Fraser C.M., Franz D.R., Leighton T.J., Morse S.A., Murch R.S., Ravel J., Rock D.L., Slezak T.R., Velsko S.P., Walsh A.C. and Walters R.A.
    Toward a system of microbial forensics: From sample collection to interpretation of evidence.
    Meeting Review. Appl. Environ. Microbiol., 71(5):2209-2213 (2005).  PubMed
  • Colvis C.M., Pollock J.D., Goodman R.H., Impey S., Dunn J., Mandel G., Champagne F.A., Mayford M., Korzus E., Kumar A., Renthal W., Theobald D. E., and Nestler E. J.
    Epigenetic mechanisms and gene networks in the nervous system.
    J. Neurosci., 25(45):10379-10389 (2005).
  • Jacobs J.M., Yang X., Luft B.J., Dunn J.J., Camp D.J. 2nd and Smith R.D.
    Proteomic analysis of Lyme disease: global protein comparison of three strains of Borrelia burgdorferi.
    Proteomics, 5(5):1446-1453 (2005). PubMed
  • Koide S., Yang X., Huang X., Dunn J.J. and Luft B.J.
    Structure-based design of a second-generation Lyme disease vaccine based on a C-terminal fragment of Borrelia burgdorferi OspA.
    JJ Mol Biol., 350(2):290-299 (2005). PubMed
  • Becker M., Bunikis J., Lade B.D., Dunn J.J., Barbour A.G. and Lawson C.L.
    Structural investigation of orrelia burgdorferi OspB, a bactericidal
    Fab target.

    JJ Biol Chem., 280(17):17363-17370 (2005). PubMed
    PDB files: 1P4P, 1RJL; Jmol viewer
  • Agarwal R., Eswaramoorthy S., Kumaran D., Dunn J.J. and Swaminathan S.
    CCloning, high level expression, purification, and crystallization of the full length Clostridium botulinum neurotoxin type E light chain.
    Protein Expr Purif., 34:95-102 (2004). PubMed
  • Impey S., McCorkle S.R., Cha-Molstad H., Dwyer J.M., Yochum G.S., Boss J.M., McWeeney S., Dunn J.J., Mandel G. and Goodman> Defining the CREB regulon: a genome-wide analysis of transcription factor regulatory regions.
    Cell, 119(7):1041-1054 (2004). PubMed
  • Qiu W.G., Schultzer S.E., Bruno J.F., Attie O., Xu Y., Dunn J.J., Fraser C.M., Casjens S.R. and Luft B.J.
    Genetic exchange and plasmid transfers in Borrelia burgdorferi sensu stricto revealed by three-way genome comparisons and multilocus sequence typing.
    Proc Natl Acad Sci USA, 101(39):14150-14155 (2004). PubMed  Full Text (pdf)
  • Gnatenko D.V., Dunn J.J., McCorkle S.R., Weissmann D., Perrotta P. and Bahou W.F.
    Transcript profiling of human platelets using microarray and serial analysis of gene expression.
    Blood, 101:2285-2293 (2003). PubMed  Full Text (pdf)
  • Rithidech K. and Dunn J.J.
    Combining Multiplex and Touchdown PCR for Microsatellite Analysis.
    In: Methods in Molecular Biology, Vol. 226, pp299-303. PCR Protocols, Second Edition Edited by: J.M.S. Bartlett and D. Stirling, Humana Press Inc., Totowa, NJ (2003).
  • Dunn J.J., McCorkle S.R., Praissman L.A., Hind G., van der Lelie D., Bahou W.F., Gnatenko D.V. and Krause M.
    Genomic signature tags (GSTs): A new system for profiling genomic DNA.
    Genome Res., 12:1756-1765 (2002). PubMed  Full Text (pdf)
  • Luft B.J., Dunn J.J. and Lawson C.L.
    Approaches toward the directed design of a vaccine against Borrelia burgdorferi.
    J Infect Dis. 185 Suppl 1:S46-51 (2002). PubMed
  • Rithidech K., Dunn J.J., Roe B.A., Gordon C.R. and Cronkite E.P.
    Evidence for two commonly deleted regions on mouse chromosome 2 in gamma-ray-induced acute myeloid leukemic cells.
    Exp Hematol., 30:564-570 (2002). PubMed
  • Anderson C.W., Dunn J.J., Freimuth P.I., Galloway A.M. and Allalunis-Turner M.J.
    Frameshift mutation in PRKDC, the gene for DNA-PKcs, in the DNA repair-defective, human, Glioma-derived cell line M059J
    Radiat Res., 156:2-9 (2001). PubMed
  • Kumaran D., Eswaramoorthy S., Dunn J.J. and Swaminathan S.
    Crystallization and preliminary X-ray analysis of Borrelia burgdorferi outer surface protein C (OspC).
    Acta Cryst., D57:298-300 (2001). PubMed
  • Kumaran D., Eswaramoorthy S., Luft B., Koide S., Dunn J.J., Lawson C.L. and Swaminathan S.
    Crystal structure of outer surface protein C (OspC) from the Lyme disease spirochete, Borrelia burgdorferi.
    EMBO J., 20:971-978 (2001). PubMed PDB files: 1F1M, 1GGQ; Jmol viewer
  • Ding W., Huang X., Yang X., Dunn J.J., Luft B.J., Koide S. and Lawson C.L.
    Structural identification of a key protective B-cell epitope in Lyme disease antigen OspA.
    J Mol Biol., 302:1153-1164 (2000). PubMed PDB file 1FJ1; Jmol viewer
  • Gomes-Solecki M.J.C., Dunn J.J., Luft B.J., Castillo J., Dykhuizen D.E., Yang X., Glass J.D. and Dattwyler R.J.
    Recombinant Chimeric Borrelia Proteins for Diagnosis of Lyme Disease.
    J Clinical Microbiol., 38:2530-2535 (2000). PubMed Full Text (pdf)
  • Huang X., Link K., Koide A., Dunn J.J., Luft B.J. and Koide S.
    1H, 13C, and 15N NMR backbone assignments of 37 kDa surface antigen OspC from Borrelia burgdorferi.
    J Biomol NMR, 14:283-284 (1999). PubMed
  • McNulty J.J. and Dunn J.J.
    High throughput transformation and plating using petristrips.
    BioTechniques, 26:390-392 (1999). PubMed
  • Seinost G., Dykhuizen D.E., Dattwyler R.J., Golde W.T., Dunn J.J., Wang I.N., Wormser G.O., Schriefer M.E. and Luft B.J.
    Four clones of Borrelia burgdorferi sensu stricto cause invasive infection in humans.
    Infect Immun., 67:3518-3524 (1999).  PubMed  Full Text (pdf)
  • Seinost G., Golde W.T., Berger B.W., Dunn J.J., Qiu D., Dunkin D.S., Dykhuizen D.E., Luft B.J. and Dattwyler R.J.
    Infection with multiple strains of Borrelia burgdorferi sensu stricto in patients with Lyme disease.
    Arch Dermatol., 135:1329-1333 (1999). PubMed
  • Wang I.N., Dykhuizen D.E., Dunn J.J. and Luft B.J.
    Genetic diversity of ospC in a local population of Borrelia burgdorferi sensu stricto.
    Genetics, 151:15-30 (1999). PubMed  Full Text (pdf)
  • Dunn J.J., Buchstein S.R., Butler L.L., Fisenne S., Polin D.S., Lade B.N. and Luft B.J.
    Complete nucleotide sequence of a circular plasmid from Borrelia burgdorferi.
    J Bacteriol., 176:2706-2717 (1994). PubMed  Full Text (pdf)
  • Macdonald L.E., Durbin R.K., Dunn J.J. and McAllister W.T.
    Characterization of two types of termination signal for bacteriophage T7 RNA polymerase.
    J Mol Biol., 238:145-158 (1994). PubMed
  • Kieleczawa J., Dunn J.J. and Studier F.W.
    DNA sequencing by primer walking with strings of contiguous hexamers.
    Science, 258:1787-1791 (1992). PubMed


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Last Modified: July 17, 2012
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