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Craig L Peterson PhD

TitleProfessor
InstitutionUniversity of Massachusetts Medical School
DepartmentProgram in Molecular Medicine
AddressUniversity of Massachusetts Medical School
373 Plantation Street, Two Biotech, Suite 210
Worcester MA 01605
Phone508-856-5858
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    Other Positions
    InstitutionUMMS - School of Medicine
    DepartmentBiochemistry and Molecular Pharmacology

    InstitutionUMMS - School of Medicine
    DepartmentProgram in Molecular Medicine

    InstitutionUMMS - Graduate School of Biomedical Sciences
    DepartmentBiochemistry and Molecular Pharmacology

    InstitutionUMMS - Graduate School of Biomedical Sciences
    DepartmentInterdisciplinary Graduate Program

    InstitutionUMMS - Graduate School of Biomedical Sciences
    DepartmentMD/PhD Program

    InstitutionUMMS - Graduate School of Biomedical Sciences
    DepartmentTranslational Science


    Collapse Biography 
    Collapse education and training
    University of Washington, Seattle, WA, United StatesBSMolecular Biology
    University of California, Los Angeles, Los Angeles, CA, United StatesPH DMolecular Biology

    Collapse Overview 
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    Academic Background

    Peterson Lab Web Page

    Craig Peterson received his BS from the University of Washington in 1983 and his PhD from the University of California, Los Angeles in 1988. He was a Helen Hay Whitney Foundation postdoctoral fellow from 1988-1991, in the Department of Biochemistry and Biophysics at the University of California, San Francisco. In 1992, he joined the University of Massachusetts Medical School as a faculty member in the Program in Molecular Medicine.

    How chromosome structure influences nuclear processes

    craig peterson's picture The overall objective of our research is to determine how chromosome structure influences nuclear processes and to identify and characterize the cellular machines that contend with this structure.Over the years, our general strategy has been to employ yeast molecular genetics to develop detailed models that describe complex nuclear events that can then be directly tested and expanded by subsequent biophysical and biochemical approaches. Much of our efforts over the past few years have focused on ATP-dependent chromatin remodeling enzymes (e.g. SWI/SNF and INO80) that hydrolyze ~1,000 ATPs per minute to alter chromatin structure and thereby regulate transcription, DNA repair, or replication. Our studies are centered on both the regulation and mechanism of this chromatin "remodeling" reaction. Since most of these enzymes are enormous (>1 MDa), multi-subunit enzymes, we are also interested in understanding how these enzymes are assembled and what roles are played by individual subunits. To address these goals we use a broad spectrum of methodologies, including yeast molecular and classical genetics, modern analytical ultracentrifugation, molecular biology, and traditional biochemistry. Notably, these remodeling enzymes are conserved from yeast to mammals, play key roles in gene expression and the maintenance of genome integrity, and loss of their function leads to various disease states.

    In addition to our studies on chromatin remodeling enzymes, we also wish to understand the dynamics of chromatin fibers and how fiber condensation influences DNA repair, transcription, and DNA replication. These projects involve the biochemical reconstitution of defined nucleosomal arrays from recombinant histones and DNA templates that contain head-to-tail repeats of nucleosome positioning sequences. Typically, we perform sedimentation velocity experiments in the analytical ultracentrifuge to investigate how histone modifications (e.g. H4 K16 acetylation), histone variants, or heterochromatin proteins (e.g. HP1, Sir3) influence the folding dynamics of these reconstituted chromatin fibers. These biophysical studies are complemented by powerful biochemical assays where we assess how the structure of a chromatin fiber regulates various steps of DNA double strand break repair or DNA replication.

    As we learn more about the dynamics of chromatin fibers and the basic mechanics of DNA repair and DNA replication, we have initiated in vivo studies that probe how these processes are coordinated and regulated within cells. For instance, we have recently, found that a DNA double strand break can induce the re-localization of a chromosomal domain to the nuclear envelope and that this compartmentalization inhibits recombinational repair. Interestingly, localization to the nuclear periphery requires components of the telomerase complex and seems to be due to an attempt to heal the chromosome by formation of a new telomere. Similar types of chromosome healing events may also occur at stalled replication forks. We are currently using a variety of cell biological and molecular genetic approaches to dissect the complex decision-making processes that a cell employs in its attempts to maintain genome integrity.

    Figure

    Research Figure

    Figure Legend

    3 dimensional EM reconstruction of the 1.15 MDa yeast SWI/SNF chromatin remodeling complex (image courtesy of C. Woodcock and R. Horowitz). Top two panels show two views of yeast SWI/SNF -- dimensions are 27 nm by 8 nm. Bottom two panels show a theoretical docking of a mononucleosome core particle into the presumptive active site. Note the large cavity that provides a perfect fit for the nucleosome core when it is oriented with the entry/exit strands of DNA facing away from the SWI/SNF surface.

    Peterson Lab Web Page



    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Clapier CR, Iwasa J, Cairns BR, Peterson CL. Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes. Nat Rev Mol Cell Biol. 2017 May 17. PMID: 28512350.
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    2. Azmi IF, Watanabe S, Maloney MF, Kang S, Belsky JA, MacAlpine DM, Peterson CL, Bell SP. Nucleosomes influence multiple steps during replication initiation. Elife. 2017 Mar 21; 6. PMID: 28322723.
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    3. Adkins NL, Swygert SG, Kaur P, Niu H, Grigoryev SA, Sung P, Wang H, Peterson CL. Nucleosome-like, ssDNA-histone octamer complexes and the implication for DNA double-strand break repair. J Biol Chem. 2017 Feb 15. PMID: 28202543.
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    4. Echtenkamp FJ, Gvozdenov Z, Adkins NL, Zhang Y, Lynch-Day M, Watanabe S, Peterson CL, Freeman BC. Hsp90 and p23 Molecular Chaperones Control Chromatin Architecture by Maintaining the Functional Pool of the RSC Chromatin Remodeler. Mol Cell. 2016 Dec 01; 64(5):888-899. PMID: 27818141.
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    5. Krietenstein N, Wal M, Watanabe S, Park B, Peterson CL, Pugh BF, Korber P. Genomic Nucleosome Organization Reconstituted with Pure Proteins. Cell. 2016 Oct 20; 167(3):709-721.e12. PMID: 27768892.
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    6. Yu L, Rege M, Peterson CL, Volkert MR. RNA polymerase II depletion promotes transcription of alternative mRNA species. BMC Mol Biol. 2016 Aug 30; 17(1):20. PMID: 27578267.
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    7. Watanabe S, Peterson CL. Response to Comment on "A histone acetylation switch regulates H2A.Z deposition by the SWR-C remodeling enzyme". Science. 2016 Jul 22; 353(6297):358. PMID: 27463666.
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    8. Rege M, Subramanian V, Zhu C, Hsieh TH, Weiner A, Friedman N, Clauder-Münster S, Steinmetz LM, Rando OJ, Boyer LA, Peterson CL. Chromatin Dynamics and the RNA Exosome Function in Concert to Regulate Transcriptional Homeostasis. Cell Rep. 2015 Nov 24; 13(8):1610-22. PMID: 26586442.
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    9. Zhao H, Ghirlando R, Alfonso C, Arisaka F, Attali I, Bain DL, Bakhtina MM, Becker DF, Bedwell GJ, Bekdemir A, Besong TM, Birck C, Brautigam CA, Brennerman W, Byron O, Bzowska A, Chaires JB, Chaton CT, Cölfen H, Connaghan KD, Crowley KA, Curth U, Daviter T, Dean WL, Díez AI, Ebel C, Eckert DM, Eisele LE, Eisenstein E, England P, Escalante C, Fagan JA, Fairman R, Finn RM, Fischle W, de la Torre JG, Gor J, Gustafsson H, Hall D, Harding SE, Cifre JG, Herr AB, Howell EE, Isaac RS, Jao SC, Jose D, Kim SJ, Kokona B, Kornblatt JA, Kosek D, Krayukhina E, Krzizike D, Kusznir EA, Kwon H, Larson A, Laue TM, Le Roy A, Leech AP, Lilie H, Luger K, Luque-Ortega JR, Ma J, May CA, Maynard EL, Modrak-Wojcik A, Mok YF, Mücke N, Nagel-Steger L, Narlikar GJ, Noda M, Nourse A, Obsil T, Park CK, Park JK, Pawelek PD, Perdue EE, Perkins SJ, Perugini MA, Peterson CL, Peverelli MG, Piszczek G, Prag G, Prevelige PE, Raynal BD, Rezabkova L, Richter K, Ringel AE, Rosenberg R, Rowe AJ, Rufer AC, Scott DJ, Seravalli JG, Solovyova AS, Song R, Staunton D, Stoddard C, Stott K, Strauss HM, Streicher WW, Sumida JP, Swygert SG, Szczepanowski RH, Tessmer I, Toth RT, Tripathy A, Uchiyama S, Uebel SF, Unzai S, Gruber AV, von Hippel PH, Wandrey C, Wang SH, Weitzel SE, Wielgus-Kutrowska B, Wolberger C, Wolff M, Wright E, Wu YS, Wubben JM, Schuck P. A multilaboratory comparison of calibration accuracy and the performance of external references in analytical ultracentrifugation. PLoS One. 2015; 10(5):e0126420. PMID: 25997164.
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    10. Watanabe S, Tan D, Lakshminarasimhan M, Washburn MP, Hong EJ, Walz T, Peterson CL. Structural analyses of the chromatin remodelling enzymes INO80-C and SWR-C. Nat Commun. 2015 May 12; 6:7108. PMID: 25964121.
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    11. Jeronimo C, Watanabe S, Kaplan CD, Peterson CL, Robert F. The Histone Chaperones FACT and Spt6 Restrict H2A.Z from Intragenic Locations. Mol Cell. 2015 Jun 18; 58(6):1113-23. PMID: 25959393.
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    12. Bennett G, Peterson CL. SWI/SNF recruitment to a DNA double-strand break by the NuA4 and Gcn5 histone acetyltransferases. DNA Repair (Amst). 2015 Jun; 30:38-45. PMID: 25869823.
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    13. Xue Y, Van C, Pradhan SK, Su T, Gehrke J, Kuryan BG, Kitada T, Vashisht A, Tran N, Wohlschlegel J, Peterson CL, Kurdistani SK, Carey MF. The Ino80 complex prevents invasion of euchromatin into silent chromatin. Genes Dev. 2015 Feb 15; 29(4):350-5. PMID: 25691465.
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    14. Manning BJ, Peterson CL. Direct interactions promote eviction of the Sir3 heterochromatin protein by the SWI/SNF chromatin remodeling enzyme. Proc Natl Acad Sci U S A. 2014 Dec 16; 111(50):17827-32. PMID: 25453095.
      View in: PubMed
    15. Van C, Williams JS, Kunkel TA, Peterson CL. Deposition of histone H2A.Z by the SWR-C remodeling enzyme prevents genome instability. DNA Repair (Amst). 2015 Jan; 25:9-14. PMID: 25463393.
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    16. Swygert SG, Manning BJ, Senapati S, Kaur P, Lindsay S, Demeler B, Peterson CL. Solution-state conformation and stoichiometry of yeast Sir3 heterochromatin fibres. Nat Commun. 2014 Aug 28; 5:4751. PMID: 25163529.
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    17. Swygert SG, Peterson CL. Chromatin dynamics: interplay between remodeling enzymes and histone modifications. Biochim Biophys Acta. 2014 Aug; 1839(8):728-36. PMID: 24583555.
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    18. Peterson CL, Almouzni G. Nucleosome dynamics as modular systems that integrate DNA damage and repair. Cold Spring Harb Perspect Biol. 2013 Sep 01; 5(9). PMID: 24003210.
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    19. Carey MF, Peterson CL, Smale ST. PCR-mediated site-directed mutagenesis. Cold Spring Harb Protoc. 2013 Aug; 2013(8):738-42. PMID: 23906918.
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    20. Watanabe S, Peterson CL. Chromatin dynamics: flipping the switch on a chromatin remodeling machine. Cell Cycle. 2013 Aug 1; 12(15):2337-8. PMID: 23856580.
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    21. Carey MF, Peterson CL, Smale ST. Electrophoretic mobility-shift assays. Cold Spring Harb Protoc. 2013 Jul; 2013(7):636-9. PMID: 23818676.
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    22. Adkins NL, Niu H, Sung P, Peterson CL. Nucleosome dynamics regulates DNA processing. Nat Struct Mol Biol. 2013 Jul; 20(7):836-42. PMID: 23728291.
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    23. Carey MF, Peterson CL, Smale ST. DNase I footprinting. Cold Spring Harb Protoc. 2013 May; 2013(5):469-78. PMID: 23637368.
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    24. Carey MF, Peterson CL, Smale ST. Preparation of (32)P-end-labeled DNA fragments for performing DNA-binding experiments. Cold Spring Harb Protoc. 2013 May 01; 2013(5):464-8. PMID: 23637369.
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    25. Watanabe S, Radman-Livaja M, Rando OJ, Peterson CL. A histone acetylation switch regulates H2A.Z deposition by the SWR-C remodeling enzyme. Science. 2013 Apr 12; 340(6129):195-9. PMID: 23580526.
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    26. Carey MF, Peterson CL, Smale ST. The RNase protection assay. Cold Spring Harb Protoc. 2013 Mar; 2013(3). PMID: 23457339.
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    27. Carey MF, Peterson CL, Smale ST. The primer extension assay. Cold Spring Harb Protoc. 2013 Feb; 2013(2):164-73. PMID: 23378648.
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    28. Papamichos-Chronakis M, Peterson CL. Chromatin and the genome integrity network. Nat Rev Genet. 2013 Jan; 14(1):62-75. PMID: 23247436.
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    29. Manning BJ, Peterson CL. Releasing the brakes on a chromatin-remodeling enzyme. Nat Struct Mol Biol. 2013 Jan; 20(1):5-7. PMID: 23288358.
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    30. Bennett G, Papamichos-Chronakis M, Peterson CL. DNA repair choice defines a common pathway for recruitment of chromatin regulators. Nat Commun. 2013; 4:2084. PMID: 23811932.
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    31. Carey MF, Peterson CL, Smale ST. Confirming the functional importance of a protein-DNA interaction. Cold Spring Harb Protoc. 2012 Jul; 2012(7):733-57. PMID: 22753608.
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    32. Sanz AB, García R, Rodríguez-Peña JM, Díez-Muñiz S, Nombela C, Peterson CL, Arroyo J. Chromatin remodeling by the SWI/SNF complex is essential for transcription mediated by the yeast cell wall integrity MAPK pathway. Mol Biol Cell. 2012 Jul; 23(14):2805-17. PMID: 22621902.
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    33. Carey MF, Peterson CL, Smale ST. Identifying cis-acting DNA elements within a control region. Cold Spring Harb Protoc. 2012 Mar; 2012(3):279-96. PMID: 22383646.
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    34. Carey MF, Peterson CL, Smale ST. Experimental strategies for cloning or identifying genes encoding DNA-binding proteins. Cold Spring Harb Protoc. 2012 Feb; 2012(2):183-92. PMID: 22301659.
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    35. Carey MF, Peterson CL, Smale ST. Experimental strategies for the identification of DNA-binding proteins. Cold Spring Harb Protoc. 2012 Jan; 2012(1):18-33. PMID: 22194258.
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    36. Liu N, Peterson CL, Hayes JJ. SWI/SNF- and RSC-catalyzed nucleosome mobilization requires internal DNA loop translocation within nucleosomes. Mol Cell Biol. 2011 Oct; 31(20):4165-75. PMID: 21859889.
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    37. Watanabe S, Peterson CL. The INO80 family of chromatin-remodeling enzymes: regulators of histone variant dynamics. Cold Spring Harb Symp Quant Biol. 2010; 75:35-42. PMID: 21502417.
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    38. Peterson CL. The ins and outs of heterochromatic DNA repair. Dev Cell. 2011 Mar 15; 20(3):285-7. PMID: 21397838.
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    39. Wippo CJ, Israel L, Watanabe S, Hochheimer A, Peterson CL, Korber P. The RSC chromatin remodelling enzyme has a unique role in directing the accurate positioning of nucleosomes. EMBO J. 2011 Apr 6; 30(7):1277-88. PMID: 21343911.
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    40. Peterson CL. Chromatin: a ubiquitin crowbar opens chromatin. Nat Chem Biol. 2011 Feb; 7(2):68-9. PMID: 21245855.
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    41. Papamichos-Chronakis M, Watanabe S, Rando OJ, Peterson CL. Global regulation of H2A.Z localization by the INO80 chromatin-remodeling enzyme is essential for genome integrity. Cell. 2011 Jan 21; 144(2):200-13. PMID: 21241891.
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    42. Carey MF, Peterson CL, Smale ST. Magnesium-agarose electrophoretic mobility shift assay (EMSA) of transcription factor IID binding to DNA. Cold Spring Harb Protoc. 2010 Nov; 2010(11):pdb.prot5514. PMID: 21041387.
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    43. Carey MF, Peterson CL, Smale ST. Protein complex binding to promoter DNA: immobilized template assay. Cold Spring Harb Protoc. 2010 Aug; 2010(8):pdb.prot5465. PMID: 20679374.
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    44. Carey MF, Peterson CL, Smale ST. Potassium permanganate probing of Pol II open complexes. Cold Spring Harb Protoc. 2010 Aug; 2010(8):pdb.prot5479. PMID: 20679388.
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    45. Carey MF, Peterson CL, Smale ST. Purification of epitope-tagged transcription factor IID. Cold Spring Harb Protoc. 2010 Jul; 2010(7):pdb.prot5450. PMID: 20647354.
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    46. Carey MF, Peterson CL, Smale ST. Purification of mediator from HeLa cell lines expressing a flag-tagged mediator subunit. Cold Spring Harb Protoc. 2010 Jul; 2010(7):pdb.prot5451. PMID: 20647355.
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    47. Peterson CL. Transcriptional memory: mothers SET the table for daughters. Curr Biol. 2010 Mar 9; 20(5):R240-2. PMID: 20219175.
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    48. Kundu S, Peterson CL. Dominant role for signal transduction in the transcriptional memory of yeast GAL genes. Mol Cell Biol. 2010 May; 30(10):2330-40. PMID: 20212085.
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    49. Carey MF, Peterson CL, Smale ST. G-less cassette in vitro transcription using HeLa cell nuclear extracts. Cold Spring Harb Protoc. 2010 Mar; 2010(3):pdb.prot5387. PMID: 20194456.
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    50. Watanabe S, Resch M, Lilyestrom W, Clark N, Hansen JC, Peterson C, Luger K. Structural characterization of H3K56Q nucleosomes and nucleosomal arrays. Biochim Biophys Acta. 2010 May-Jun; 1799(5-6):480-6. PMID: 20100606.
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    51. Oza P, Peterson CL. Opening the DNA repair toolbox: localization of DNA double strand breaks to the nuclear periphery. Cell Cycle. 2010 Jan 1; 9(1):43-9. PMID: 20016273.
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    52. Carey MF, Peterson CL, Smale ST. In vitro transcription using HeLa cell extracts and primer extension. Cold Spring Harb Protoc. 2009 Dec; 2009(12):pdb.prot5331. PMID: 20150078.
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    53. Carey MF, Peterson CL, Smale ST. Dignam and Roeder nuclear extract preparation. Cold Spring Harb Protoc. 2009 Dec; 2009(12):pdb.prot5330. PMID: 20150077.
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    54. Sinha M, Peterson CL. Chromatin dynamics during repair of chromosomal DNA double-strand breaks. Epigenomics. 2009 Dec; 1(2):371-85. PMID: 20495614.
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    55. Sinha M, Watanabe S, Johnson A, Moazed D, Peterson CL. Recombinational repair within heterochromatin requires ATP-dependent chromatin remodeling. Cell. 2009 Sep 18; 138(6):1109-21. PMID: 19766565.
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    56. Carey MF, Peterson CL, Smale ST. Chromatin immunoprecipitation (ChIP). Cold Spring Harb Protoc. 2009 Sep; 2009(9):pdb.prot5279. PMID: 20147264.
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    57. Carey MF, Peterson CL, Smale ST. In vivo dimethyl sulfate (DMS) footprinting via ligation-mediated polymerase chain reaction (LM-PCR). Cold Spring Harb Protoc. 2009 Sep; 2009(9):pdb.prot5278. PMID: 20147263.
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    58. Carey MF, Peterson CL, Smale ST. In vivo DNase I, MNase, and restriction enzyme footprinting via ligation-mediated polymerase chain reaction (LM-PCR). Cold Spring Harb Protoc. 2009 Sep; 2009(9):pdb.prot5277. PMID: 20147262.
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    59. Oza P, Jaspersen SL, Miele A, Dekker J, Peterson CL. Mechanisms that regulate localization of a DNA double-strand break to the nuclear periphery. Genes Dev. 2009 Apr 15; 23(8):912-27. PMID: 19390086.
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    60. Peterson CL. Reconstitution of nucleosomal arrays using recombinant Drosophila ACF and NAP1. Cold Spring Harb Protoc. 2009 Apr; 2009(4):pdb.prot5114. PMID: 20147123.
      View in: PubMed
    61. Peterson CL. Purification of recombinant Drosophila NAP1. Cold Spring Harb Protoc. 2009 Apr; 2009(4):pdb.prot5116. PMID: 20147125.
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    62. Peterson CL. Purification of recombinant Drosophila ACF. Cold Spring Harb Protoc. 2009 Apr; 2009(4):pdb.prot5115. PMID: 20147124.
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    63. Kundu S, Peterson CL. Role of chromatin states in transcriptional memory. Biochim Biophys Acta. 2009 Jun; 1790(6):445-55. PMID: 19236904.
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    64. Peterson CL. Salt gradient dialysis reconstitution of nucleosomes. CSH Protoc. 2008; 2008:pdb.prot5113. PMID: 21356758.
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    65. Peterson CL, Hansen JC. Chicken erythrocyte histone octamer preparation. CSH Protoc. 2008; 2008:pdb.prot5112. PMID: 21356757.
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    66. Fu Y, Sinha M, Peterson CL, Weng Z. The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genet. 2008 Jul 25; 4(7):e1000138. PMID: 18654629.
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    67. Dechassa ML, Zhang B, Horowitz-Scherer R, Persinger J, Woodcock CL, Peterson CL, Bartholomew B. Architecture of the SWI/SNF-nucleosome complex. Mol Cell Biol. 2008 Oct; 28(19):6010-21. PMID: 18644858.
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    68. Sinha M, Peterson CL. A Rad51 presynaptic filament is sufficient to capture nucleosomal homology during recombinational repair of a DNA double-strand break. Mol Cell. 2008 Jun 20; 30(6):803-10. PMID: 18570881.
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    69. Papamichos-Chronakis M, Peterson CL. The Ino80 chromatin-remodeling enzyme regulates replisome function and stability. Nat Struct Mol Biol. 2008 Apr; 15(4):338-45. PMID: 18376411.
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    70. Triezenberg SJ, Peterson CL. Profound challenges do remain in our understanding of the mechanisms of gene regulation. Biochim Biophys Acta. 2008 Jan; 1779(1):1-2. PMID: 18082153.
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    71. Carruthers LM, Marton LJ, Peterson CL. Polyamine analogues: potent inducers of nucleosomal array oligomerization and inhibitors of yeast cell growth. Biochem J. 2007 Aug 1; 405(3):541-5. PMID: 17428198.
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    72. Yang X, Zaurin R, Beato M, Peterson CL. Swi3p controls SWI/SNF assembly and ATP-dependent H2A-H2B displacement. Nat Struct Mol Biol. 2007 Jun; 14(6):540-7. PMID: 17496903.
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    73. Peterson CL. Genome integrity: a HAT needs a chaperone. Curr Biol. 2007 May 1; 17(9):R324-6. PMID: 17470345.
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    74. Kundu S, Horn PJ, Peterson CL. SWI/SNF is required for transcriptional memory at the yeast GAL gene cluster. Genes Dev. 2007 Apr 15; 21(8):997-1004. PMID: 17438002.
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    75. Zhang Y, Smith CL, Saha A, Grill SW, Mihardja S, Smith SB, Cairns BR, Peterson CL, Bustamante C. DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC. Mol Cell. 2006 Nov 17; 24(4):559-68. PMID: 17188033.
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    76. Fry CJ, Norris A, Cosgrove M, Boeke JD, Peterson CL. The LRS and SIN domains: two structurally equivalent but functionally distinct nucleosomal surfaces required for transcriptional silencing. Mol Cell Biol. 2006 Dec; 26(23):9045-59. PMID: 17015465.
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    77. Papamichos-Chronakis M, Krebs JE, Peterson CL. Interplay between Ino80 and Swr1 chromatin remodeling enzymes regulates cell cycle checkpoint adaptation in response to DNA damage. Genes Dev. 2006 Sep 1; 20(17):2437-49. PMID: 16951256.
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    78. Shogren-Knaak M, Peterson CL. Switching on chromatin: mechanistic role of histone H4-K16 acetylation. Cell Cycle. 2006 Jul; 5(13):1361-5. PMID: 16855380.
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    79. Shundrovsky A, Smith CL, Lis JT, Peterson CL, Wang MD. Probing SWI/SNF remodeling of the nucleosome by unzipping single DNA molecules. Nat Struct Mol Biol. 2006 Jun; 13(6):549-54. PMID: 16732285.
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    80. Shogren-Knaak M, Ishii H, Sun JM, Pazin MJ, Davie JR, Peterson CL. Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science. 2006 Feb 10; 311(5762):844-7. PMID: 16469925.
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    81. Horn PJ, Peterson CL. Heterochromatin assembly: a new twist on an old model. Chromosome Res. 2006; 14(1):83-94. PMID: 16506098.
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    82. Chowdhury D, Keogh MC, Ishii H, Peterson CL, Buratowski S, Lieberman J. gamma-H2AX dephosphorylation by protein phosphatase 2A facilitates DNA double-strand break repair. Mol Cell. 2005 Dec 9; 20(5):801-9. PMID: 16310392.
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    83. Hill DA, Peterson CL, Imbalzano AN. Effects of HMGN1 on chromatin structure and SWI/SNF-mediated chromatin remodeling. J Biol Chem. 2005 Dec 16; 280(50):41777-83. PMID: 16253989.
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    84. Horn PJ, Bastie JN, Peterson CL. A Rik1-associated, cullin-dependent E3 ubiquitin ligase is essential for heterochromatin formation. Genes Dev. 2005 Jul 15; 19(14):1705-14. PMID: 16024659.
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    85. Smith CL, Peterson CL. A conserved Swi2/Snf2 ATPase motif couples ATP hydrolysis to chromatin remodeling. Mol Cell Biol. 2005 Jul; 25(14):5880-92. PMID: 15988005.
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    86. Cheung WL, Turner FB, Krishnamoorthy T, Wolner B, Ahn SH, Foley M, Dorsey JA, Peterson CL, Berger SL, Allis CD. Phosphorylation of histone H4 serine 1 during DNA damage requires casein kinase II in S. cerevisiae. Curr Biol. 2005 Apr 12; 15(7):656-60. PMID: 15823538.
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    87. Wolner B, Peterson CL. ATP-dependent and ATP-independent roles for the Rad54 chromatin remodeling enzyme during recombinational repair of a DNA double strand break. J Biol Chem. 2005 Mar 18; 280(11):10855-60. PMID: 15653683.
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    88. Smith CL, Peterson CL. ATP-dependent chromatin remodeling. Curr Top Dev Biol. 2005; 65:115-48. PMID: 15642381.
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    89. Vicent GP, Nacht AS, Smith CL, Peterson CL, Dimitrov S, Beato M. DNA instructed displacement of histones H2A and H2B at an inducible promoter. Mol Cell. 2004 Nov 5; 16(3):439-52. PMID: 15525516.
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    90. Peterson CL, Laniel MA. Histones and histone modifications. Curr Biol. 2004 Jul 27; 14(14):R546-51. PMID: 15268870.
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    91. Peterson CL, Côté J. Cellular machineries for chromosomal DNA repair. Genes Dev. 2004 Mar 15; 18(6):602-16. PMID: 15075289.
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    92. Boyer LA, Latek RR, Peterson CL. The SANT domain: a unique histone-tail-binding module? Nat Rev Mol Cell Biol. 2004 Feb; 5(2):158-63. PMID: 15040448.
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    93. Fry CJ, Shogren-Knaak MA, Peterson CL. Histone H3 amino-terminal tail phosphorylation and acetylation: synergistic or independent transcriptional regulatory marks? Cold Spring Harb Symp Quant Biol. 2004; 69:219-26. PMID: 16117652.
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    94. Shogren-Knaak MA, Peterson CL. Creating designer histones by native chemical ligation. Methods Enzymol. 2004; 375:62-76. PMID: 14870659.
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    95. Smith CL, Peterson CL. Coupling tandem affinity purification and quantitative tyrosine iodination to determine subunit stoichiometry of protein complexes. Methods. 2003 Sep; 31(1):104-9. PMID: 12893180.
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    96. Wolner B, van Komen S, Sung P, Peterson CL. Recruitment of the recombinational repair machinery to a DNA double-strand break in yeast. Mol Cell. 2003 Jul; 12(1):221-32. PMID: 12887907.
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    97. Jaskelioff M, Peterson CL. Chromatin and transcription: histones continue to make their marks. Nat Cell Biol. 2003 May; 5(5):395-9. PMID: 12724776.
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    98. Gaillard H, Fitzgerald DJ, Smith CL, Peterson CL, Richmond TJ, Thoma F. Chromatin remodeling activities act on UV-damaged nucleosomes and modulate DNA damage accessibility to photolyase. J Biol Chem. 2003 May 16; 278(20):17655-63. PMID: 12637512.
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    99. Peterson CL. Transcriptional activation: getting a grip on condensed chromatin. Curr Biol. 2003 Mar 4; 13(5):R195-7. PMID: 12620212.
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    100. Shogren-Knaak MA, Fry CJ, Peterson CL. A native peptide ligation strategy for deciphering nucleosomal histone modifications. J Biol Chem. 2003 May 2; 278(18):15744-8. PMID: 12595522.
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    101. Smith CL, Horowitz-Scherer R, Flanagan JF, Woodcock CL, Peterson CL. Structural analysis of the yeast SWI/SNF chromatin remodeling complex. Nat Struct Biol. 2003 Feb; 10(2):141-5. PMID: 12524530.
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    102. Jaskelioff M, Van Komen S, Krebs JE, Sung P, Peterson CL. Rad54p is a chromatin remodeling enzyme required for heteroduplex DNA joint formation with chromatin. J Biol Chem. 2003 Mar 14; 278(11):9212-8. PMID: 12514177.
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    103. Boyer LA, Langer MR, Crowley KA, Tan S, Denu JM, Peterson CL. Essential role for the SANT domain in the functioning of multiple chromatin remodeling enzymes. Mol Cell. 2002 Oct; 10(4):935-42. PMID: 12419236.
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    104. Horn PJ, Peterson CL. Molecular biology. Chromatin higher order folding--wrapping up transcription. Science. 2002 Sep 13; 297(5588):1824-7. PMID: 12228709.
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    105. Langer MR, Fry CJ, Peterson CL, Denu JM. Modulating acetyl-CoA binding in the GCN5 family of histone acetyltransferases. J Biol Chem. 2002 Jul 26; 277(30):27337-44. PMID: 11994311.
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    106. Peterson CL. HDAC's at work: everyone doing their part. Mol Cell. 2002 May; 9(5):921-2. PMID: 12049726.
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    107. Peterson CL. Chromatin remodeling: nucleosomes bulging at the seams. Curr Biol. 2002 Apr 2; 12(7):R245-7. PMID: 11937040.
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    108. Horn PJ, Carruthers LM, Logie C, Hill DA, Solomon MJ, Wade PA, Imbalzano AN, Hansen JC, Peterson CL. Phosphorylation of linker histones regulates ATP-dependent chromatin remodeling enzymes. Nat Struct Biol. 2002 Apr; 9(4):263-7. PMID: 11887184.
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    109. Peterson CL. Chromatin remodeling enzymes: taming the machines. Third in review series on chromatin dynamics. EMBO Rep. 2002 Apr; 3(4):319-22. PMID: 11943761.
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    110. Fry CJ, Peterson CL. Transcription. Unlocking the gates to gene expression. Science. 2002 Mar 8; 295(5561):1847-8. PMID: 11884741.
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    111. Horn PJ, Crowley KA, Carruthers LM, Hansen JC, Peterson CL. The SIN domain of the histone octamer is essential for intramolecular folding of nucleosomal arrays. Nat Struct Biol. 2002 Mar; 9(3):167-71. PMID: 11836537.
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    112. Brower-Toland BD, Smith CL, Yeh RC, Lis JT, Peterson CL, Wang MD. Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA. Proc Natl Acad Sci U S A. 2002 Feb 19; 99(4):1960-5. PMID: 11854495.
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    113. Horn PJ, Peterson CL. The bromodomain: a regulator of ATP-dependent chromatin remodeling? Front Biosci. 2001 Aug 1; 6:D1019-23. PMID: 11487477.
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    114. Fry CJ, Peterson CL. Chromatin remodeling enzymes: who's on first? Curr Biol. 2001 Mar 6; 11(5):R185-97. PMID: 11267889.
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    115. Peterson CL. Chromatin: mysteries solved? Biochem Cell Biol. 2001; 79(3):219-25. PMID: 11467736.
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    116. Gavin I, Horn PJ, Peterson CL. SWI/SNF chromatin remodeling requires changes in DNA topology. Mol Cell. 2001 Jan; 7(1):97-104. PMID: 11172715.
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    117. Krebs JE, Fry CJ, Samuels ML, Peterson CL. Global role for chromatin remodeling enzymes in mitotic gene expression. Cell. 2000 Sep 1; 102(5):587-98. PMID: 11007477.
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    118. Boyer LA, Peterson CL. Actin-related proteins (Arps): conformational switches for chromatin-remodeling machines? Bioessays. 2000 Jul; 22(7):666-72. PMID: 10878579.
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    119. Peterson CL. ATP-dependent chromatin remodeling: going mobile. FEBS Lett. 2000 Jun 30; 476(1-2):68-72. PMID: 10878253.
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    120. Boyer LA, Logie C, Bonte E, Becker PB, Wade PA, Wolffe AP, Wu C, Imbalzano AN, Peterson CL. Functional delineation of three groups of the ATP-dependent family of chromatin remodeling enzymes. J Biol Chem. 2000 Jun 23; 275(25):18864-70. PMID: 10779516.
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    121. Peterson CL, Logie C. Recruitment of chromatin remodeling machines. J Cell Biochem. 2000 May; 78(2):179-85. PMID: 10842313.
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    122. Jaskelioff M, Gavin IM, Peterson CL, Logie C. SWI-SNF-mediated nucleosome remodeling: role of histone octamer mobility in the persistence of the remodeled state. Mol Cell Biol. 2000 May; 20(9):3058-68. PMID: 10757790.
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    123. Boyer LA, Shao X, Ebright RH, Peterson CL. Roles of the histone H2A-H2B dimers and the (H3-H4)(2) tetramer in nucleosome remodeling by the SWI-SNF complex. J Biol Chem. 2000 Apr 21; 275(16):11545-52. PMID: 10766768.
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    124. Peterson CL, Workman JL. Promoter targeting and chromatin remodeling by the SWI/SNF complex. Curr Opin Genet Dev. 2000 Apr; 10(2):187-92. PMID: 10753786.
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    125. Krebs JE, Peterson CL. Understanding "active" chromatin: a historical perspective of chromatin remodeling. Crit Rev Eukaryot Gene Expr. 2000; 10(1):1-12. PMID: 10813389.
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    126. Pollard KJ, Samuels ML, Crowley KA, Hansen JC, Peterson CL. Functional interaction between GCN5 and polyamines: a new role for core histone acetylation. EMBO J. 1999 Oct 15; 18(20):5622-33. PMID: 10523306.
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    127. Krebs JE, Kuo MH, Allis CD, Peterson CL. Cell cycle-regulated histone acetylation required for expression of the yeast HO gene. Genes Dev. 1999 Jun 1; 13(11):1412-21. PMID: 10364158.
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    128. Flanagan JF, Peterson CL. A role for the yeast SWI/SNF complex in DNA replication. Nucleic Acids Res. 1999 May 1; 27(9):2022-8. PMID: 10198436.
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    129. Logie C, Tse C, Hansen JC, Peterson CL. The core histone N-terminal domains are required for multiple rounds of catalytic chromatin remodeling by the SWI/SNF and RSC complexes. Biochemistry. 1999 Feb 23; 38(8):2514-22. PMID: 10029546.
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    130. Logie C, Peterson CL. Purification and biochemical properties of yeast SWI/SNF complex. Methods Enzymol. 1999; 304:726-41. PMID: 10372393.
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    131. Peterson CL, Zhao Y, Chait BT. Subunits of the yeast SWI/SNF complex are members of the actin-related protein (ARP) family. J Biol Chem. 1998 Sep 11; 273(37):23641-4. PMID: 9726966.
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    132. Pollard KJ, Peterson CL. Chromatin remodeling: a marriage between two families? Bioessays. 1998 Sep; 20(9):771-80. PMID: 9819566.
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    133. Peterson CL. SWI/SNF complex: dissection of a chromatin remodeling cycle. Cold Spring Harb Symp Quant Biol. 1998; 63:545-52. PMID: 10384319.
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    134. Logie C, Peterson CL. Catalytic activity of the yeast SWI/SNF complex on reconstituted nucleosome arrays. EMBO J. 1997 Nov 17; 16(22):6772-82. PMID: 9362491.
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    135. Pollard KJ, Peterson CL. Role for ADA/GCN5 products in antagonizing chromatin-mediated transcriptional repression. Mol Cell Biol. 1997 Nov; 17(11):6212-22. PMID: 9343382.
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    136. Burns LG, Peterson CL. The yeast SWI-SNF complex facilitates binding of a transcriptional activator to nucleosomal sites in vivo. Mol Cell Biol. 1997 Aug; 17(8):4811-9. PMID: 9234737.
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    137. Wechser MA, Kladde MP, Alfieri JA, Peterson CL. Effects of Sin- versions of histone H4 on yeast chromatin structure and function. EMBO J. 1997 Apr 15; 16(8):2086-95. PMID: 9155034.
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    138. Burns LG, Peterson CL. Protein complexes for remodeling chromatin. Biochim Biophys Acta. 1997 Feb 7; 1350(2):159-68. PMID: 9048886.
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    139. Richmond E, Peterson CL. Functional analysis of the DNA-stimulated ATPase domain of yeast SWI2/SNF2. Nucleic Acids Res. 1996 Oct 1; 24(19):3685-92. PMID: 8871545.
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    140. Peterson CL. Multiple SWItches to turn on chromatin? Curr Opin Genet Dev. 1996 Apr; 6(2):171-5. PMID: 8722173.
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    141. Quinn J, Fyrberg AM, Ganster RW, Schmidt MC, Peterson CL. DNA-binding properties of the yeast SWI/SNF complex. Nature. 1996 Feb 29; 379(6568):844-7. PMID: 8587611.
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    142. Peterson CL, Tamkun JW. The SWI-SNF complex: a chromatin remodeling machine? Trends Biochem Sci. 1995 Apr; 20(4):143-6. PMID: 7770913.
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    143. Peterson CL. The SMC family: novel motor proteins for chromosome condensation? Cell. 1994 Nov 4; 79(3):389-92. PMID: 7954805.
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    144. Peterson CL, Dingwall A, Scott MP. Five SWI/SNF gene products are components of a large multisubunit complex required for transcriptional enhancement. Proc Natl Acad Sci U S A. 1994 Apr 12; 91(8):2905-8. PMID: 8159677.
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